Merge branch 'master' into core-updates

doc/guix.texi

@@ -5854,8 +5854,11 @@ should be added to the package definition via the
 
 In its @code{configure} phase, this build system will make any source inputs
 specified in the @code{#:cargo-inputs} and @code{#:cargo-development-inputs}
-parameters available to cargo.  The @code{install} phase installs any crate
+parameters available to cargo.  The @code{update-cargo-lock} phase will,
-the binaries if they are defined by the crate.
+when there is a @code{Cargo.lock} file, update the @code{Cargo.lock} file
+with the inputs and their versions available at build time.  The
+@code{install} phase installs any crate the binaries if they are defined by
+the crate.
 @end defvr
 
 @cindex Clojure (programming language)
@@ -25507,7 +25510,7 @@ evaluates to.  As an example, @var{file} might contain a definition like this:
             %base-services))))
 
 (list (machine
-       (system %system)
+       (operating-system %system)
        (environment managed-host-environment-type)
        (configuration (machine-ssh-configuration
                        (host-name "localhost")
@@ -25527,12 +25530,28 @@ complex deployment may involve, for example, starting virtual machines through
 a Virtual Private Server (VPS) provider.  In such a case, a different
 @var{environment} type would be used.
 
+Do note that you first need to generate a key pair on the coordinator machine
+to allow the daemon to export signed archives of files from the store
+(@pxref{Invoking guix archive}).
+
+@example
+# guix archive --generate-key
+@end example
+
+@noindent
+Each target machine must authorize the key of the master machine so that it
+accepts store items it receives from the coordinator:
+
+@example
+# guix archive --authorize < coordinator-public-key.txt
+@end example
+
 @deftp {Data Type} machine
 This is the data type representing a single machine in a heterogeneous Guix
 deployment.
 
 @table @asis
-@item @code{system}
+@item @code{operating-system}
 The object of the operating system configuration to deploy.
 
 @item @code{environment}

gnu/local.mk

@@ -238,6 +238,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/haskell-check.scm		\
   %D%/packages/haskell-crypto.scm		\
   %D%/packages/haskell-web.scm			\
+  %D%/packages/haskell-xyz.scm			\
   %D%/packages/ham-radio.scm			\
   %D%/packages/hexedit.scm			\
   %D%/packages/hugs.scm				\
@@ -771,6 +772,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/elfutils-tests-ptrace.patch		\
   %D%/packages/patches/elixir-path-length.patch			\
   %D%/packages/patches/einstein-build.patch			\
+  %D%/packages/patches/emacs-dired-toggle-sudo-emacs-26.patch   \
   %D%/packages/patches/emacs-exec-path.patch			\
   %D%/packages/patches/emacs-fix-scheme-indent-function.patch	\
   %D%/packages/patches/emacs-json-reformat-fix-tests.patch	\
@@ -806,7 +808,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/findutils-localstatedir.patch		\
   %D%/packages/patches/findutils-makedev.patch			\
   %D%/packages/patches/findutils-test-xargs.patch		\
-  %D%/packages/patches/flac-CVE-2017-6888.patch		\
   %D%/packages/patches/flann-cmake-3.11.patch			\
   %D%/packages/patches/flint-ldconfig.patch			\
   %D%/packages/patches/foomatic-filters-CVE-2015-8327.patch	\
@@ -961,6 +962,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/inkscape-poppler-0.76.patch		\
   %D%/packages/patches/intltool-perl-compatibility.patch	\
   %D%/packages/patches/irrlicht-use-system-libs.patch		\
+  %D%/packages/patches/isc-dhcp-4.4.1-fixes-for-newer-bind.patch	\
   %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\
   %D%/packages/patches/jacal-fix-texinfo.patch			\
   %D%/packages/patches/jamvm-arm.patch				\
@@ -1026,7 +1028,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/libotr-test-auth-fix.patch		\
   %D%/packages/patches/libmad-armv7-thumb-pt1.patch		\
   %D%/packages/patches/libmad-armv7-thumb-pt2.patch		\
-  %D%/packages/patches/libmad-frame-length.patch		\
+  %D%/packages/patches/libmad-length-check.patch		\
+  %D%/packages/patches/libmad-md_size.patch			\
   %D%/packages/patches/libmad-mips-newgcc.patch			\
   %D%/packages/patches/libmp4v2-c++11.patch			\
   %D%/packages/patches/libmygpo-qt-fix-qt-5.11.patch		\
@@ -1047,7 +1050,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/libutils-add-includes.patch		\
   %D%/packages/patches/libutils-remove-damaging-includes.patch	\
   %D%/packages/patches/libvdpau-va-gl-unbundle.patch		\
-  %D%/packages/patches/libvirt-remove-ATTRIBUTE_UNUSED.patch	\
   %D%/packages/patches/libvpx-CVE-2016-2818.patch		\
   %D%/packages/patches/libvpx-use-after-free-in-postproc.patch	\
   %D%/packages/patches/libxslt-generated-ids.patch		\
@@ -1078,6 +1080,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/lxsession-use-gapplication.patch         \
   %D%/packages/patches/make-glibc-compat.patch			\
   %D%/packages/patches/make-impure-dirs.patch			\
+  %D%/packages/patches/mame-rapidjson-fix.patch			\
   %D%/packages/patches/mariadb-client-test-32bit.patch		\
   %D%/packages/patches/mars-install.patch			\
   %D%/packages/patches/mars-sfml-2.3.patch			\
@@ -1124,6 +1127,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/nfs-utils-missing-headers.patch		\
   %D%/packages/patches/ngircd-handle-zombies.patch		\
   %D%/packages/patches/nm-plugin-path.patch			\
+  %D%/packages/patches/nss-freebl-stubs.patch			\
   %D%/packages/patches/nss-increase-test-timeout.patch		\
   %D%/packages/patches/nss-pkgconfig.patch			\
   %D%/packages/patches/ntfs-3g-CVE-2019-9755.patch		\
@@ -1169,6 +1173,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/patchelf-rework-for-arm.patch		\
   %D%/packages/patches/patchutils-test-perms.patch		\
   %D%/packages/patches/patch-hurd-path-max.patch		\
+  %D%/packages/patches/pcre2-fix-jit_match-crash.patch		\
   %D%/packages/patches/perl-autosplit-default-time.patch	\
   %D%/packages/patches/perl-deterministic-ordering.patch	\
   %D%/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch \
@@ -1291,8 +1296,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/scheme48-tests.patch			\
   %D%/packages/patches/scotch-build-parallelism.patch		\
   %D%/packages/patches/scotch-integer-declarations.patch	\
-  %D%/packages/patches/scribus-poppler.patch			\
-  %D%/packages/patches/scribus-poppler-0.73.patch		\
   %D%/packages/patches/sdl-libx11-1.6.patch			\
   %D%/packages/patches/seq24-rename-mutex.patch			\
   %D%/packages/patches/sharutils-CVE-2018-1000097.patch		\
@@ -1308,6 +1311,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/soundconverter-remove-gconf-dependency.patch	\
   %D%/packages/patches/sssd-curl-compat.patch			\
   %D%/packages/patches/steghide-fixes.patch			\
+  %D%/packages/patches/strace-ipc-tests.patch			\
   %D%/packages/patches/streamlink-update-test.patch		\
   %D%/packages/patches/stumpwm-fix-broken-read-one-line.patch	\
   %D%/packages/patches/superlu-dist-awpm-grid.patch		\

gnu/machine.scm

@@ -34,7 +34,7 @@
             machine?
             this-machine
 
-            machine-system
+            machine-operating-system
             machine-environment
             machine-configuration
             machine-display-name
@@ -85,14 +85,14 @@
   make-machine
   machine?
   this-machine
-  (system        machine-system)       ; <operating-system>
+  (operating-system machine-operating-system) ; <operating-system>
-  (environment   machine-environment)  ; symbol
+  (environment      machine-environment)      ; symbol
-  (configuration machine-configuration ; configuration object
+  (configuration    machine-configuration     ; configuration object
-                 (default #f)))        ; specific to environment
+                    (default #f)))            ; specific to environment
 
 (define (machine-display-name machine)
   "Return the host-name identifying MACHINE."
-  (operating-system-host-name (machine-system machine)))
+  (operating-system-host-name (machine-operating-system machine)))
 
 (define (machine-remote-eval machine exp)
   "Evaluate EXP, a gexp, on MACHINE. Ensure that all the elements EXP refers to

gnu/machine/ssh.scm

@@ -20,6 +20,9 @@
   #:use-module (gnu machine)
   #:autoload   (gnu packages gnupg) (guile-gcrypt)
   #:use-module (gnu system)
+  #:use-module (gnu system file-systems)
+  #:use-module (gnu system uuid)
+  #:use-module (guix diagnostics)
   #:use-module (guix gexp)
   #:use-module (guix i18n)
   #:use-module (guix modules)
@@ -29,6 +32,7 @@
   #:use-module (guix scripts system reconfigure)
   #:use-module (guix ssh)
   #:use-module (guix store)
+  #:use-module (guix utils)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-19)
   #:use-module (srfi srfi-26)
@@ -40,6 +44,7 @@
             machine-ssh-configuration
 
             machine-ssh-configuration-host-name
+            machine-ssh-configuration-build-locally?
             machine-ssh-configuration-port
             machine-ssh-configuration-user
             machine-ssh-configuration-session))
@@ -62,15 +67,17 @@
   make-machine-ssh-configuration
   machine-ssh-configuration?
   this-machine-ssh-configuration
-  (host-name machine-ssh-configuration-host-name) ; string
+  (host-name      machine-ssh-configuration-host-name) ; string
-  (port      machine-ssh-configuration-port       ; integer
+  (build-locally? machine-ssh-configuration-build-locally?
-             (default 22))
+                  (default #t))
-  (user      machine-ssh-configuration-user       ; string
+  (port           machine-ssh-configuration-port       ; integer
-             (default "root"))
+                  (default 22))
-  (identity  machine-ssh-configuration-identity   ; path to a private key
+  (user           machine-ssh-configuration-user       ; string
-             (default #f))
+                  (default "root"))
-  (session   machine-ssh-configuration-session    ; session
+  (identity       machine-ssh-configuration-identity   ; path to a private key
-             (default #f)))
+                  (default #f))
+  (session        machine-ssh-configuration-session    ; session
+                  (default #f)))
 
 (define (machine-ssh-session machine)
   "Return the SSH session that was given in MACHINE's configuration, or create
@@ -96,7 +103,149 @@ one from the configuration's parameters if one was not provided."
   "Internal implementation of 'machine-remote-eval' for MACHINE instances with
 an environment type of 'managed-host."
   (maybe-raise-unsupported-configuration-error machine)
-  (remote-eval exp (machine-ssh-session machine)))
+  (remote-eval exp (machine-ssh-session machine)
+               #:build-locally?
+               (machine-ssh-configuration-build-locally?
+                (machine-configuration machine))))
+
+
+;;;
+;;; Safety checks.
+;;;
+
+(define (machine-check-file-system-availability machine)
+  "Raise a '&message' error condition if any of the file-systems specified in
+MACHINE's 'system' declaration do not exist on the machine."
+  (define file-systems
+    (filter (lambda (fs)
+              (and (file-system-mount? fs)
+                   (not (member (file-system-type fs)
+                                %pseudo-file-system-types))
+                   (not (memq 'bind-mount (file-system-flags fs)))))
+            (operating-system-file-systems (machine-operating-system machine))))
+
+  (define (check-literal-file-system fs)
+    (define remote-exp
+      #~(catch 'system-error
+          (lambda ()
+            (stat #$(file-system-device fs))
+            #t)
+          (lambda args
+            (system-error-errno args))))
+
+    (mlet %store-monad ((errno (machine-remote-eval machine remote-exp)))
+      (when (number? errno)
+        (raise (condition
+                (&message
+                 (message (format #f (G_ "device '~a' not found: ~a")
+                                  (file-system-device fs)
+                                  (strerror errno)))))))
+      (return #t)))
+
+  (define (check-labeled-file-system fs)
+    (define remote-exp
+      (with-imported-modules '((gnu build file-systems))
+        #~(begin
+            (use-modules (gnu build file-systems))
+            (find-partition-by-label #$(file-system-label->string
+                                        (file-system-device fs))))))
+
+    (mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
+      (unless result
+        (raise (condition
+                (&message
+                 (message (format #f (G_ "no file system with label '~a'")
+                                  (file-system-label->string
+                                   (file-system-device fs))))))))
+      (return #t)))
+
+  (define (check-uuid-file-system fs)
+    (define remote-exp
+      (with-imported-modules (source-module-closure
+                              '((gnu build file-systems)
+                                (gnu system uuid)))
+        #~(begin
+            (use-modules (gnu build file-systems)
+                         (gnu system uuid))
+
+            (define uuid
+              (string->uuid #$(uuid->string (file-system-device fs))))
+
+            (find-partition-by-uuid uuid))))
+
+    (mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
+      (unless result
+        (raise (condition
+                (&message
+                 (message (format #f (G_ "no file system with UUID '~a'")
+                                  (uuid->string (file-system-device fs))))))))
+      (return #t)))
+
+  (mbegin %store-monad
+    (mapm %store-monad check-literal-file-system
+          (filter (lambda (fs)
+                    (string? (file-system-device fs)))
+                  file-systems))
+    (mapm %store-monad check-labeled-file-system
+          (filter (lambda (fs)
+                    (file-system-label? (file-system-device fs)))
+                  file-systems))
+    (mapm %store-monad check-uuid-file-system
+          (filter (lambda (fs)
+              (uuid? (file-system-device fs)))
+                  file-systems))))
+
+(define (machine-check-initrd-modules machine)
+  "Raise a '&message' error condition if any of the modules needed by
+'needed-for-boot' file systems in MACHINE are not available in the initrd."
+  (define file-systems
+    (filter file-system-needed-for-boot?
+            (operating-system-file-systems (machine-operating-system machine))))
+
+  (define (missing-modules fs)
+    (define remote-exp
+      (let ((device (file-system-device fs)))
+        (with-imported-modules (source-module-closure
+                                '((gnu build file-systems)
+                                  (gnu build linux-modules)
+                                  (gnu system uuid)))
+          #~(begin
+              (use-modules (gnu build file-systems)
+                           (gnu build linux-modules)
+                           (gnu system uuid))
+
+              (define dev
+                #$(cond ((string? device) device)
+                        ((uuid? device) #~(find-partition-by-uuid
+                                           (string->uuid
+                                            #$(uuid->string device))))
+                        ((file-system-label? device)
+                         #~(find-partition-by-label
+                            (file-system-label->string #$device)))))
+
+              (missing-modules dev '#$(operating-system-initrd-modules
+                                       (machine-operating-system machine)))))))
+    (mlet %store-monad ((missing (machine-remote-eval machine remote-exp)))
+      (return (list fs missing))))
+
+  (mlet %store-monad ((device (mapm %store-monad missing-modules file-systems)))
+    (for-each (match-lambda
+                ((fs missing)
+                 (unless (null? missing)
+                   (raise (condition
+                           (&message
+                            (message (format #f (G_ "~a missing modules ~{ ~a~}~%")
+                                             (file-system-device fs)
+                                             missing))))))))
+              device)
+    (return #t)))
+
+(define (check-deployment-sanity machine)
+  "Raise a '&message' error condition if it is clear that deploying MACHINE's
+'system' declaration would fail."
+  (mbegin %store-monad
+    (machine-check-file-system-availability machine)
+    (machine-check-initrd-modules machine)))
 
 
 ;;;
@@ -165,8 +314,9 @@ of MACHINE's system profile, ordered from most recent to oldest."
   "Internal implementation of 'deploy-machine' for MACHINE instances with an
 environment type of 'managed-host."
   (maybe-raise-unsupported-configuration-error machine)
-  (mlet %store-monad ((boot-parameters (machine-boot-parameters machine)))
+  (mlet %store-monad ((_ (check-deployment-sanity machine))
-    (let* ((os (machine-system machine))
+                      (boot-parameters (machine-boot-parameters machine)))
+    (let* ((os (machine-operating-system machine))
            (eval (cut machine-remote-eval machine <>))
            (menu-entries (map boot-parameters->menu-entry boot-parameters))
            (bootloader-configuration (operating-system-bootloader os))

gnu/packages/admin.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
-;;; Copyright © 2014, 2015, 2016, 2018 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2014, 2015, 2016, 2018, 2019 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015, 2016 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com>
@@ -684,9 +684,9 @@ connection alive.")
 (define-public isc-dhcp
   (let* ((bind-major-version "9")
          (bind-minor-version "11")
-         (bind-patch-version "4")
+         (bind-patch-version "9")
-         (bind-release-type "-P")         ; for patch release, use "-P"
+         (bind-release-type "")         ; for patch release, use "-P"
-         (bind-release-version "2")      ; for patch release, e.g. "6"
+         (bind-release-version "")      ; for patch release, e.g. "6"
          (bind-version (string-append bind-major-version
                                       "."
                                       bind-minor-version
@@ -710,7 +710,18 @@ connection alive.")
          #:phases
          (modify-phases %standard-phases
            (add-after 'unpack 'replace-bundled-bind
-             (lambda* (#:key inputs #:allow-other-keys)
+             (lambda* (#:key inputs native-inputs #:allow-other-keys)
+               ;; XXX TODO: Remove the following invocation of 'patch' when
+               ;; isc-dhcp is updated.  It should be needed only for 4.4.1.
+               (let ((patch (string-append (assoc-ref (or native-inputs inputs)
+                                                      "patch")
+                                           "/bin/patch"))
+                     (the-patch (assoc-ref (or native-inputs inputs)
+                                           "fixes-for-newer-bind.patch")))
+                 (format #t "applying '~a'...~%" the-patch)
+                 (invoke patch "--force" "--no-backup-if-mismatch"
+                         "-p1" "--input" the-patch))
+
                (delete-file "bind/bind.tar.gz")
                (copy-file (assoc-ref inputs "bind-source-tarball")
                           "bind/bind.tar.gz")
@@ -743,15 +754,18 @@ connection alive.")
                ;; shell is used.
                (with-directory-excursion "bind"
                  (substitute* "Makefile"
-                   (("\\./configure")
+                   (("\\./configure ")
                     (let ((sh (which "sh")))
                       (string-append "./configure CONFIG_SHELL="
-                                     sh " SHELL=" sh))))
+                                     sh " SHELL=" sh " "))))
 
                  (let ((bind-directory (string-append "bind-" ,bind-version)))
                    (invoke "tar" "xf" "bind.tar.gz")
                    (for-each patch-shebang
                              (find-files bind-directory ".*"))
+                   (substitute* (string-append bind-directory "/configure")
+                     (("/usr/bin/file")
+                      (which "file")))
                    (invoke "tar" "cf" "bind.tar.gz"
                            bind-directory
                            ;; avoid non-determinism in the archive
@@ -787,7 +801,15 @@ connection alive.")
                            (list inetutils net-tools coreutils sed))))
                  #t))))))
 
-      (native-inputs `(("perl" ,perl)))
+      (native-inputs
+       `(("perl" ,perl)
+         ("file" ,file)
+
+         ;; XXX TODO: Remove the following patch, and also the 'patch'
+         ;; program, when isc-dhcp is updated.
+         ("fixes-for-newer-bind.patch"
+          ,(search-patch "isc-dhcp-4.4.1-fixes-for-newer-bind.patch"))
+         ("patch" ,patch)))
 
       (inputs `(("inetutils" ,inetutils)
                 ("net-tools" ,net-tools)
@@ -803,7 +825,7 @@ connection alive.")
                                         "/bind-" bind-version ".tar.gz"))
                     (sha256
                      (base32
-                      "04fq17zksd2b3w6w6padps5n7b6s2lasxpksbhl4378h56vgfnm8"))))
+                      "03n57as73ygw6g3lqsmq2idkykajpbskzgixixdvi5a76m4g0fwn"))))
 
                 ;; When cross-compiling, we need the cross Coreutils and sed.
                 ;; Otherwise just use those from %FINAL-INPUTS.
@@ -1181,7 +1203,7 @@ commands and their arguments.")
 (define-public wpa-supplicant-minimal
   (package
     (name "wpa-supplicant-minimal")
-    (version "2.8")
+    (version "2.9")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1189,7 +1211,7 @@ commands and their arguments.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "15ixzm347n8w6gdvi3j3yks3i15qmp6by9ayvswm34d929m372d6"))
+                "05qzak1mssnxcgdrafifxh9w86a4ha69qabkg4bsigk499xyxggw"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -2606,7 +2628,7 @@ buffers.")
      `(#:tests? #f              ; many of the tests try to load kernel modules
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
+         (replace 'bootstrap
            (lambda _
              ;; Don't run configure in this phase.
              (setenv "NOCONFIGURE" "1")

gnu/packages/algebra.scm

@@ -236,8 +236,7 @@ the real span of the lattice.")
     (build-system gnu-build-system)
     (native-inputs
      `(("texlive" ,(texlive-union
-                    (list texlive-fonts-amsfonts
+                    (list texlive-amsfonts)))))
-                          texlive-latex-amsfonts)))))
     (inputs `(("gmp" ,gmp)
               ("libx11" ,libx11)
               ("perl" ,perl)
@@ -345,7 +344,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "1.5.0-61")
+    (version "1.5.0-63")
     (source (origin
               (method url-fetch)
               ;; "~parisse/giac" is not used because the maintainer regularly
@@ -357,7 +356,7 @@ precision.")
                                   "source/giac_" version ".tar.gz"))
               (sha256
                (base32
-                "050vzpqq77fhky32sbisc0ysimgp60xjv39q7y45jkaabdkmclwh"))))
+                "1jp7awyp8j8w6fhn802z8ddbq1fxhkyk9xdf0mq0mm0chpkylwqk"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)

gnu/packages/audio.scm

@@ -3692,7 +3692,7 @@ library.")
 (define-public faudio
   (package
     (name "faudio")
-    (version "19.07")
+    (version "19.08")
     (source
      (origin
        (method git-fetch)
@@ -3701,7 +3701,7 @@ library.")
              (commit version)))
        (file-name (string-append name "-" version "-checkout"))
        (sha256
-        (base32 "1wf6skc5agaikc9qgwk8bx56sad31fafs53lqqn4jmx8i76pl0lw"))))
+        (base32 "1v13kfhyr46241vb6a4dcb4gw5f149525sprwa9cj4rv6wlcqgm5"))))
     (arguments
      '(#:tests? #f                      ; No tests.
        #:configure-flags '("-DFFMPEG=ON")))

gnu/packages/bioconductor.scm

@@ -38,7 +38,8 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages statistics)
-  #:use-module (gnu packages web))
+  #:use-module (gnu packages web)
+  #:use-module (srfi srfi-1))
 
 
 ;;; Annotations
@@ -1211,14 +1212,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.18.1")
+    (version "3.18.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji"))))
+         "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1520,14 +1521,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
+         "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -3528,14 +3529,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.8.1")
+    (version "1.8.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69"))))
+         "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3620,14 +3621,14 @@ annotations and ontologies.")
 (define-public r-abaenrichment
   (package
     (name "r-abaenrichment")
-    (version "1.14.0")
+    (version "1.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ABAEnrichment" version))
        (sha256
         (base32
-         "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
+         "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
     (properties `((upstream-name . "ABAEnrichment")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4840,14 +4841,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "1.34.4")
+    (version "1.34.6")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "1230p8nsakifmpsqfiaj8rpm7npa8ab903mfjmayfa71n6yzvcbs"))))
+         "0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -5128,3 +5129,25 @@ data, to only emphasize the data that actually matters.")
 accessibility data.  It also extends the monocle package for use in chromatin
 accessibility data.")
     (license license:expat)))
+
+;; This is the latest commit on the "monocle3" branch.
+(define-public r-cicero-monocle3
+  (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
+        (revision "1"))
+    (package (inherit r-cicero)
+      (name "r-cicero-monocle3")
+      (version (git-version "1.3.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/cole-trapnell-lab/cicero-release.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
+      (propagated-inputs
+       `(("r-monocle3" ,r-monocle3)
+         ,@(alist-delete "r-monocle"
+                         (package-propagated-inputs r-cicero)))))))

gnu/packages/bioinformatics.scm

@@ -13,6 +13,7 @@
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -4195,8 +4196,15 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
        (modify-phases %standard-phases
          (add-after 'unpack 'set-cc
            (lambda _ (setenv "CC" "gcc") #t))
-         ;; FIXME: This fails with "permission denied".
+
-         (delete 'reset-gzip-timestamps))))
+         (add-before 'reset-gzip-timestamps 'make-files-writable
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Make sure .gz files are writable so that the
+             ;; 'reset-gzip-timestamps' phase can do its work.
+             (let ((out (assoc-ref outputs "out")))
+               (for-each make-file-writable
+                         (find-files out "\\.gz$"))
+               #t))))))
     (native-inputs
      `(("python-cython" ,python-cython)
        ("python-pytest" ,python-pytest)
@@ -7439,13 +7447,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.26.5")
+    (version "3.26.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "0iba4krz30dx5b0s89n5cfkwn64867s7vmvvfqms9lbcr4kj439m"))))
+                "17vadhamjv4x0l4qqq2p2fi6j2bkllz5zd8dq761vgd5ic23zizm"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7506,13 +7514,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.40.2")
+    (version "3.40.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1d4ig2b7fa9mwja52isxrwmprfdjdk1mlcf2skhdp51l24z6wbk7"))))
+                "166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7639,13 +7647,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.40.1")
+    (version "2.40.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "1abl0c4qbhfqf9ixdp74183phm7s8rszrr5ldczm59b8vyng8rhx"))))
+                "022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -7672,13 +7680,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.18.0")
+    (version "1.18.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "0v8rhf3hbgb3v32h2pmsv1y6q2x4airmpp50fk7z6ardcn4aza7x"))))
+                "1j6wbls4qgvi5gj99c51r00jhxrzxk3x3258wg7dcjzbfqypvyw3"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -7800,13 +7808,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.14.0")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci"))))
+                "0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -7864,13 +7872,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.44.0")
+    (version "1.44.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "161gcks9b12993g9k27gf7wfh8lgd8m8rr7x2slgfqqssk0yrmpd"))))
+                "03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -7911,13 +7919,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.36.3")
+    (version "1.36.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0zkd57i5qjxsravv0gbyckc0wrnqzgxd61ibh3jmhmrccrr9ihn3"))))
+                "0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -8335,13 +8343,13 @@ paired-end data.")
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.10.0")
+    (version "1.10.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "1h4vf5gzilqbdrd8m9l3zc2m4sca8cir8366a7njgd558k7ld5kl"))))
+                "06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz"))))
     (properties `((upstream-name . "RCAS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9399,14 +9407,14 @@ of mass spectrometry based proteomics data.")
 (define-public r-msnid
   (package
     (name "r-msnid")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnID" version))
        (sha256
         (base32
-         "18mp8zacawhfapfwpq8czbswxix2ykvqhwjga54v0a99zg3k87h3"))))
+         "1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb"))))
     (properties `((upstream-name . "MSnID")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10406,14 +10414,14 @@ provided.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.12.1")
+    (version "1.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "0n8zc1x582vwb0zfhrjmnqbnpqky9zbhjc2j836i0a4yisklwdcp"))))
+         "0afradisrr5gn0lf2kxjw55vdm3lm9mlgx53qlr9r40c1hrydpf5"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (inputs
@@ -14804,3 +14812,406 @@ trees by inserting random mutations.  The tbsp package implements an
 alternative method to detect significant, cell type specific sequence
 mutations from scRNA-Seq data.")
       (license license:expat))))
+
+(define-public tabixpp
+  (package
+   (name "tabixpp")
+   (version "1.0.0")
+   (source (origin
+     (method git-fetch)
+     (uri (git-reference
+           (url "https://github.com/ekg/tabixpp")
+           (commit (string-append "v" version))))
+     (file-name (git-file-name name version))
+     (sha256
+      (base32 "08vx6nsipk971cyr8z53rnzwkvlld63kcn1fw0pwddynz91xfny8"))))
+   (build-system gnu-build-system)
+   (inputs
+    `(("htslib" ,htslib)
+      ("zlib" ,zlib)))
+   (arguments
+    `(#:tests? #f ; There are no tests to run.
+      #:phases
+      (modify-phases %standard-phases
+        (delete 'configure) ; There is no configure phase.
+        ;; The build phase needs overriding the location of htslib.
+        (replace 'build
+          (lambda* (#:key inputs #:allow-other-keys)
+            (let ((htslib-ref (assoc-ref inputs "htslib")))
+              (invoke "make"
+                      (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
+                      "HTS_HEADERS="    ; No need to check for headers here.
+                      (string-append "LIBPATH=-L. -L" htslib-ref "/include")))))
+        (replace 'install
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+              (install-file "tabix++" bin))
+            #t)))))
+   (home-page "https://github.com/ekg/tabixpp")
+   (synopsis "C++ wrapper around tabix project")
+   (description "This is a C++ wrapper around the Tabix project which abstracts
+some of the details of opening and jumping in tabix-indexed files.")
+   (license license:expat)))
+
+(define tabixpp-freebayes
+  ;; This version works with FreeBayes while the released
+  ;; version doesn't. The released creates a variable with the name \"vcf\"
+  ;; somewhere, which is also the name of a namespace in vcflib.
+  (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7"))
+    (package
+      (inherit tabixpp)
+      (name "tabixpp-freebayes")
+      (version (git-version "0.0.0" "1" commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ekg/tabixpp/")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g")))))))
+
+(define-public smithwaterman
+  ;; TODO: Upgrading smithwaterman breaks FreeBayes.
+  (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
+    (package
+      (name "smithwaterman")
+      (version (string-append "0-1." (string-take commit 7)))
+      (source (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/ekg/smithwaterman/")
+              (commit commit)))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f ; There are no tests to run.
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure) ; There is no configure phase.
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+                 (install-file "smithwaterman" bin))
+               #t)))))
+      (home-page "https://github.com/ekg/smithwaterman")
+      (synopsis "Implementation of the Smith-Waterman algorithm")
+      (description "Implementation of the Smith-Waterman algorithm.")
+      ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9.
+      (license (list license:gpl2 license:expat)))))
+
+(define-public multichoose
+  (package
+    (name "multichoose")
+    (version "1.0.3")
+    (source (origin
+      (method git-fetch)
+      (uri (git-reference
+            (url "https://github.com/ekg/multichoose/")
+            (commit (string-append "v" version))))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32 "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; Tests require node.
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; There is no configure phase.
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+               ;; TODO: There are Python modules for these programs too.
+               (install-file "multichoose" bin)
+               (install-file "multipermute" bin))
+             #t)))))
+    (home-page "https://github.com/ekg/multichoose")
+    (synopsis "Efficient loopless multiset combination generation algorithm")
+    (description "This library implements an efficient loopless multiset
+combination generation algorithm which is (approximately) described in
+\"Loopless algorithms for generating permutations, combinations, and other
+combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM),
+1973. (Algorithm 7.)")
+    (license license:expat)))
+
+(define-public fsom
+  (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3"))
+    (package
+      (name "fsom")
+      (version (git-version "0.0.0" "1" commit))
+      (source (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/ekg/fsom/")
+              (commit commit)))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f ; There are no tests to run.
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure) ; There is no configure phase.
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+                 (install-file "fsom" bin))
+               #t)))))
+      (home-page "https://github.com/ekg/fsom")
+      (synopsis "Manage SOM (Self-Organizing Maps) neural networks")
+      (description "A tiny C library for managing SOM (Self-Organizing Maps)
+neural networks.")
+      (license license:gpl3))))
+
+(define-public fastahack
+  (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd"))
+    (package
+      (name "fastahack")
+      (version (git-version "0.0.0" "1" commit))
+      (source (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/ekg/fastahack/")
+              (commit commit)))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0hfdv67l9g611i2ck4l92pd6ygmsp9g1ph4zx1ni7qkpsikf0l19"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure) ; There is no configure phase.
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+                 (install-file "fastahack" bin))
+               #t)))))
+      (home-page "https://github.com/ekg/fastahack")
+      (synopsis "Indexing and sequence extraction from FASTA files")
+      (description "Fastahack is a small application for indexing and
+extracting sequences and subsequences from FASTA files.  The included library
+provides a FASTA reader and indexer that can be embedded into applications
+which would benefit from directly reading subsequences from FASTA files.  The
+library automatically handles index file generation and use.")
+      (license (list license:expat license:gpl2)))))
+
+(define-public vcflib
+  (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92")
+        (revision "1"))
+    (package
+      (name "vcflib")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/vcflib/vcflib/")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq"))))
+      (build-system gnu-build-system)
+      (inputs
+       `(("zlib" ,zlib)))
+      (native-inputs
+       `(("perl" ,perl)
+         ("python" ,python-2)
+         ;; Submodules.
+         ;; This package builds against the .o files so we need to extract the source.
+         ("tabixpp-src" ,(package-source tabixpp-freebayes))
+         ("smithwaterman-src" ,(package-source smithwaterman))
+         ("multichoose-src" ,(package-source multichoose))
+         ("fsom-src" ,(package-source fsom))
+         ("filevercmp-src" ,(package-source filevercmp))
+         ("fastahack-src" ,(package-source fastahack))
+         ("intervaltree-src"
+          ,(origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/ekg/intervaltree/")
+                   (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
+             (file-name "intervaltree-src-checkout")
+             (sha256
+              (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))))
+      (arguments
+       `(#:tests? #f ; no tests
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (delete 'check)
+           (add-after 'unpack 'unpack-submodule-sources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((unpack (lambda (source target)
+                               (with-directory-excursion target
+                                 (if (file-is-directory? (assoc-ref inputs source))
+                                     (copy-recursively (assoc-ref inputs source) ".")
+                                     (invoke "tar" "xvf"
+                                             (assoc-ref inputs source)
+                                             "--strip-components=1"))))))
+                 (and
+                  (unpack "intervaltree-src" "intervaltree")
+                  (unpack "fastahack-src" "fastahack")
+                  (unpack "filevercmp-src" "filevercmp")
+                  (unpack "fsom-src" "fsom")
+                  (unpack "multichoose-src" "multichoose")
+                  (unpack "smithwaterman-src" "smithwaterman")
+                  (unpack "tabixpp-src" "tabixpp")))))
+           (replace 'build
+             (lambda* (#:key inputs make-flags #:allow-other-keys)
+               (with-directory-excursion "tabixpp"
+                 (invoke "make"))
+               (invoke "make" "CC=gcc"
+                       (string-append "CFLAGS=\"" "-Itabixpp " "\"")
+                       "all")))
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+                     (lib (string-append (assoc-ref outputs "out") "/lib")))
+                 (for-each (lambda (file)
+                             (install-file file bin))
+                           (find-files "bin" ".*"))
+                 ;; The header files in src/ do not interface libvcflib,
+                 ;; therefore they are left out.
+                 (install-file "libvcflib.a" lib))
+               #t)))))
+      (home-page "https://github.com/vcflib/vcflib/")
+      (synopsis "Library for parsing and manipulating VCF files")
+      (description "Vcflib provides methods to manipulate and interpret
+sequence variation as it can be described by VCF.  It is both an API for parsing
+and operating on records of genomic variation as it can be described by the VCF
+format, and a collection of command-line utilities for executing complex
+manipulations on VCF files.")
+      (license license:expat))))
+
+(define-public freebayes
+  (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
+        (revision "1")
+        (version "1.0.2"))
+    (package
+      (name "freebayes")
+      (version (git-version version revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ekg/freebayes.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
+      (build-system gnu-build-system)
+      (inputs
+       `(("bamtools" ,bamtools)
+         ("htslib" ,htslib)
+         ("zlib" ,zlib)))
+      (native-inputs
+       `(("bc" ,bc)                     ; Needed for running tests.
+         ("samtools" ,samtools)         ; Needed for running tests.
+         ("parallel" ,parallel)         ; Needed for running tests.
+         ("perl" ,perl)                 ; Needed for running tests.
+         ("procps" ,procps)             ; Needed for running tests.
+         ("python" ,python-2)           ; Needed for running tests.
+         ("vcflib-src" ,(package-source vcflib))
+         ;; These are submodules for the vcflib version used in freebayes.
+         ;; This package builds against the .o files so we need to extract the source.
+         ("tabixpp-src" ,(package-source tabixpp-freebayes))
+         ("smithwaterman-src" ,(package-source smithwaterman))
+         ("multichoose-src" ,(package-source multichoose))
+         ("fsom-src" ,(package-source fsom))
+         ("filevercmp-src" ,(package-source filevercmp))
+         ("fastahack-src" ,(package-source fastahack))
+         ("intervaltree-src"
+          ,(origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/ekg/intervaltree/")
+                   (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
+             (file-name "intervaltree-src-checkout")
+             (sha256
+              (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))
+         ;; These submodules are needed to run the tests.
+         ("bash-tap-src" ,(package-source bash-tap))
+         ("test-simple-bash-src"
+          ,(origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/ingydotnet/test-simple-bash/")
+                   (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
+             (file-name "test-simple-bash-src-checkout")
+             (sha256
+              (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
+      (arguments
+       `(#:make-flags
+         (list "CC=gcc"
+               (string-append "BAMTOOLS_ROOT="
+                              (assoc-ref %build-inputs "bamtools")))
+         #:test-target "test"
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (add-after 'unpack 'fix-tests
+             (lambda _
+               (substitute* "test/t/01_call_variants.t"
+                 (("grep -P \"\\(\\\\t500\\$\\|\\\\t11000\\$\\|\\\\t1000\\$\\)\"")
+                  "grep -E '	(500|11000|1000)$'"))
+               #t))
+           (add-after 'unpack 'unpack-submodule-sources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((unpack (lambda (source target)
+                               (with-directory-excursion target
+                                 (if (file-is-directory? (assoc-ref inputs source))
+                                     (copy-recursively (assoc-ref inputs source) ".")
+                                     (invoke "tar" "xvf"
+                                             (assoc-ref inputs source)
+                                             "--strip-components=1"))))))
+                 (and
+                  (unpack "vcflib-src" "vcflib")
+                  (unpack "fastahack-src" "vcflib/fastahack")
+                  (unpack "filevercmp-src" "vcflib/filevercmp")
+                  (unpack "fsom-src" "vcflib/fsom")
+                  (unpack "intervaltree-src" "vcflib/intervaltree")
+                  (unpack "multichoose-src" "vcflib/multichoose")
+                  (unpack "smithwaterman-src" "vcflib/smithwaterman")
+                  (unpack "tabixpp-src" "vcflib/tabixpp")
+                  (unpack "test-simple-bash-src" "test/test-simple-bash")
+                  (unpack "bash-tap-src" "test/bash-tap")))))
+           (add-after 'unpack-submodule-sources 'fix-makefiles
+             (lambda _
+               ;; We don't have the .git folder to get the version tag from.
+               (substitute* "vcflib/Makefile"
+                 (("^GIT_VERSION.*")
+                  (string-append "GIT_VERSION = v" ,version)))
+               (substitute* "src/Makefile"
+                 (("-I\\$\\(BAMTOOLS_ROOT\\)/src")
+                  "-I$(BAMTOOLS_ROOT)/include/bamtools"))
+               #t))
+           (add-before 'build 'build-tabixpp-and-vcflib
+             (lambda* (#:key inputs make-flags #:allow-other-keys)
+               (with-directory-excursion "vcflib"
+                 (with-directory-excursion "tabixpp"
+                   (apply invoke "make"
+                          (string-append "HTS_LIB="
+                                         (assoc-ref inputs "htslib")
+                                         "/lib/libhts.a")
+                          make-flags))
+                 (apply invoke "make"
+                        (string-append "CFLAGS=-Itabixpp")
+                        "all"
+                        make-flags))))
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+                 (install-file "bin/freebayes" bin)
+                 (install-file "bin/bamleftalign" bin))
+               #t)))))
+      (home-page "https://github.com/ekg/freebayes")
+      (synopsis "Haplotype-based variant detector")
+      (description "FreeBayes is a Bayesian genetic variant detector designed to
+find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
+indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
+complex events (composite insertion and substitution events) smaller than the
+length of a short-read sequencing alignment.")
+      (license license:expat))))

gnu/packages/bittorrent.scm

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

gnu/packages/certs.scm

@@ -76,7 +76,7 @@
 (define-public nss-certs
   (package
     (name "nss-certs")
-    (version "3.44.1")
+    (version "3.45")
     (source (origin
               (method url-fetch)
               (uri (let ((version-with-underscores
@@ -87,7 +87,7 @@
                       "nss-" version ".tar.gz")))
               (sha256
                (base32
-                "1y0jvva4s3j7cjz22kqw2lsml0an1295bgpc2raf7kc9r60cpr7w"))))
+                "12sfq9xvpwpc22qnjsg1if1lmchiy33byrh92wn91phz7li0abqi"))))
     (build-system gnu-build-system)
     (outputs '("out"))
     (native-inputs

gnu/packages/chromium.scm

@@ -73,7 +73,8 @@
   #:use-module (srfi srfi-1))
 
 (define %preserved-third-party-files
-  '("base/third_party/dmg_fp" ;X11-style
+  '("base/third_party/cityhash" ;Expat
+    "base/third_party/dmg_fp" ;X11-style
     "base/third_party/dynamic_annotations" ;BSD-2
     "base/third_party/icu" ;Unicode, X11-style
     "base/third_party/superfasthash" ;BSD-3
@@ -85,7 +86,7 @@
     "courgette/third_party/divsufsort" ;Expat
     "net/third_party/mozilla_security_manager" ;MPL-1.1/GPL2+/LGPL2.1+
     "net/third_party/nss" ;MPL-2.0
-    "net/third_party/quic" ;BSD-3
+    "net/third_party/quiche" ;BSD-3
     "net/third_party/uri_template" ;ASL2.0
     "third_party/abseil-cpp" ;ASL2.0
     "third_party/adobe/flash/flapper_version.h" ;no license, trivial
@@ -105,6 +106,10 @@
     "third_party/blink" ;BSD-3, LGPL2+
     "third_party/boringssl" ;OpenSSL/ISC (Google additions are ISC)
     "third_party/boringssl/src/third_party/fiat" ;Expat
+    "third_party/boringssl/src/third_party/sike" ;Expat
+    ;; XXX: these files are generated by fp-$arch.pl in the above directory.
+    "third_party/boringssl/linux-aarch64/crypto/third_party/sike/asm/fp-armv8.S"
+    "third_party/boringssl/linux-x86_64/crypto/third_party/sike/asm/fp-x86_64.S"
     "third_party/breakpad" ;BSD-3
     "third_party/brotli" ;Expat
     "third_party/cacheinvalidation" ;ASL2.0
@@ -164,6 +169,7 @@
     "third_party/nasm" ;BSD-2
     "third_party/node" ;Expat
     "third_party/node/node_modules/polymer-bundler/lib/third_party/UglifyJS2" ;BSD-2
+    "third_party/openscreen" ;BSD-3
     "third_party/ots" ;BSD-3
     "third_party/pdfium" ;BSD-3
     "third_party/pdfium/third_party/agg23" ;Expat
@@ -182,9 +188,10 @@
     "third_party/s2cellid" ;ASL2.0
     "third_party/sfntly" ;ASL2.0
     "third_party/skia" ;BSD-3
+    "third_party/skia/include/third_party/skcms" ;BSD-3
     "third_party/skia/third_party/gif" ;MPL1.1/GPL2+/LGPL2.1+
     "third_party/skia/third_party/skcms" ;BSD-3
-    "third_party/skia/third_party/vulkan" ;BSD-3
+    "third_party/skia/third_party/vulkanmemoryallocator" ;BSD-3, Expat
     "third_party/smhasher" ;Expat, public domain
     "third_party/speech-dispatcher" ;GPL2+
     "third_party/spirv-headers" ;ASL2.0
@@ -231,9 +238,9 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %chromium-version "75.0.3770.142")
+(define %chromium-version "76.0.3809.100")
-(define %ungoogled-revision "5d8abc38b43a62f379615a0dc972b29d9aebb4b4")
+(define %ungoogled-revision "8eba5c0df1a318012e3deab39a9add252a0d56a3")
-(define %debian-revision "debian/75.0.3770.90-1")
+(define %debian-revision "debian/76.0.3809.87-2")
 (define package-revision "0")
 (define %package-version (string-append %chromium-version "-"
                                         package-revision "."
@@ -247,7 +254,7 @@ from forcing GEXP-PROMISE."
                         %chromium-version ".tar.xz"))
     (sha256
      (base32
-      "1b550hc9sav0qdnh4hiin2bb3jmfyrb3dhbmnc0v8662rjknq3ji"))))
+      "0vfjfxsqf8jrmd7y08ln1lpbilwi150875zn2bawwdq87vd3mncc"))))
 
 (define %ungoogled-origin
   (origin
@@ -258,7 +265,7 @@ from forcing GEXP-PROMISE."
                               (string-take %ungoogled-revision 7)))
     (sha256
      (base32
-      "1vk8jzzsn20ysn4nlz84mwwhfa9nnywzd1lrahlhcky9pf6xzpwa"))))
+      "08fd9whfc1qky44xqxbypr7jz1rg6cma017wj4b5c5b14grxz6k6"))))
 
 (define %debian-origin
   (origin
@@ -272,7 +279,29 @@ from forcing GEXP-PROMISE."
                                   (string-take %debian-revision 7))))
     (sha256
      (base32
-      "0sh6z2lx44zb31qrpa29vm0sw09dxi7i9h6fsq3ivfxjs7v98bbx"))))
+      "1fjhpzrxmgjr7i31li1vsfmp0qkbi0cpyc7p1zjwvf2x4da0v907"))))
+
+(define (gentoo-patch name hash revision)
+  (origin
+    (method url-fetch)
+    (uri (string-append "https://gitweb.gentoo.org/repo/gentoo.git/plain"
+                        "/www-client/chromium/files/" name "?id=" revision))
+    (file-name name)
+    (sha256 (base32 hash))))
+
+(define-syntax-rule (gentoo-patches (name hash) ...)
+  (list (gentoo-patch name hash "9fd80e7d75aa63843ec33c9d44fee32596ae8f25")
+        ...))
+
+(define %auxiliary-patches
+  ;; XXX: Debians "gcc/wrong-namespace.patch" and "fixes/inspector.patch" does
+  ;; not work for us, so we take these upstream fixes via Gentoo instead.
+  (gentoo-patches
+   ("chromium-76-quiche.patch" "1cs0y16jn7r1nxh0j36vqcsdvigl902kdcqfmyivnxgblrx66l2i")
+   ("chromium-76-gcc-blink-namespace1.patch"
+    "0k7nrn0dhvqxj4sg2gndzxih0l1f77h6pv7jhcdz7h69sm4xci2z")
+   ("chromium-76-gcc-blink-namespace2.patch"
+    "014y2d8ii9sr340sjbv1fhsjd5s3dl0vbmq5wzlkdjsp91dcn9ch")))
 
 ;; This is a "computed" origin that does the following:
 ;; *) Runs the Ungoogled scripts on a pristine Chromium tarball.
@@ -314,6 +343,12 @@ from forcing GEXP-PROMISE."
                    (force-output)
                    (invoke "tar" "xf" #+chromium-source)
 
+                   ;; Ungoogled-Chromium contains a forked subset of the Debian
+                   ;; patches.  Disable those, as we apply newer versions later.
+                   (substitute* "patches/series"
+                     ((".*/debian_buster/.*")
+                      ""))
+
                    (format #t "Ungooglifying...~%")
                    (force-output)
                    (invoke "python3" "utils/prune_binaries.py" chromium-dir
@@ -330,16 +365,7 @@ from forcing GEXP-PROMISE."
                      (force-output)
                      (let* ((debian  #+debian-source)
                             (patches (string-append debian "/debian/patches"))
-                            (series  (string-append patches "/series"))
+                            (series  (string-append patches "/series")))
-                            (grep-q (lambda (query file)
-                                      (with-input-from-file file
-                                        (lambda ()
-                                          (let loop ((line (read-line))
-                                                     (match #f))
-                                            (if (or match (eof-object? line))
-                                                (if match #t #f)
-                                                (loop (read-line)
-                                                      (string-contains line query)))))))))
                        (with-input-from-file series
                          (lambda ()
                            (let loop ((line (read-line)))
@@ -347,19 +373,35 @@ from forcing GEXP-PROMISE."
                                (when (and (> (string-length line) 1)
                                           ;; Skip the Debian-specific ones.
                                           (not (string-prefix? "debianization/" line))
+                                          (not (string-prefix? "buster/" line))
                                           ;; And those that conflict with Ungoogled.
                                           (not (any (cute string-suffix? <> line)
                                                     '("widevine-buildflag.patch"
                                                       "signin.patch"
-                                                      "third-party-cookies.patch")))
+                                                      "third-party-cookies.patch"
-                                          ;; Ungoogled includes a subset of the Debian
+
-                                          ;; patches.  Exclude those already present.
+                                                      ;; XXX: 'fixes/inspector.patch'
-                                          (not (grep-q line "../patches/series")))
+                                                      ;; makes v8 reuse the top-level
+                                                      ;; third_party/inspector_protocol
+                                                      ;; instead of its own bundled copy,
+                                                      ;; but that does not work here for
+                                                      ;; some reason.  Ignore that patch
+                                                      ;; and those that depend on it.
+                                                      "wrong-namespace.patch"
+                                                      "explicit-specialization.patch"
+                                                      "inspector.patch"))))
                                  (invoke "patch" "--force" "-p1" "--input"
                                          (string-append patches "/" line)
                                          "--no-backup-if-mismatch"))
                                (loop (read-line)))))))
 
+                     (format #t "Applying Guix-specific patches...~%")
+                     (force-output)
+                     (for-each (lambda (patch)
+                                 (invoke "patch" "--force" "-p1" "--input"
+                                         patch "--no-backup-if-mismatch"))
+                               '#+%auxiliary-patches)
+
                      (format #t "Pruning third party files...~%")
                      (force-output)
                      (apply invoke "python"
@@ -458,7 +500,6 @@ from forcing GEXP-PROMISE."
              "is_clang=false"
              ;; Disable debugging features to save space.  These are normally
              ;; pulled in by "is_official_build", but that requires "is_clang".
-             "blink_symbol_level=0"
              "enable_iterator_debugging=false"
              "exclude_unwind_tables=true"
              ;; Optimize for building everything at once, as opposed to
@@ -488,7 +529,7 @@ from forcing GEXP-PROMISE."
                    '("use_vaapi=true")
                    '())
 
-             ;; Don't arbitrarily restrict formats supported by system ffmpeg.
+             ;; Do not artifically restrict formats supported by system ffmpeg.
              "proprietary_codecs=true"
              "ffmpeg_branding=\"Chrome\""
 
@@ -561,12 +602,12 @@ from forcing GEXP-PROMISE."
              (substitute* "third_party/webrtc/rtc_base/strings/json.h"
                (("#include \"third_party/jsoncpp/") "#include \"json/"))
 
-             (substitute* '("ui/gfx/skia_util.h"
+             (substitute* '("components/viz/common/gpu/vulkan_context_provider.h"
                             "components/viz/common/resources/resource_format_utils.h")
                (("third_party/vulkan/include/") ""))
 
              (substitute* "third_party/skia/include/gpu/vk/GrVkVulkan.h"
-               (("\\.\\./\\.\\./include/third_party/vulkan/") ""))
+               (("include/third_party/vulkan/") ""))
 
              ;; Building chromedriver embeds some files using the ZIP
              ;; format which doesn't support timestamps before
@@ -587,6 +628,9 @@ from forcing GEXP-PROMISE."
              (setenv "AR" "ar") (setenv "NM" "nm")
              (setenv "CC" "gcc") (setenv "CXX" "g++")
 
+             ;; Prevent GCC from optimizing away null pointer safety checks.
+             (setenv "CXXFLAGS" "-fno-delete-null-pointer-checks")
+
              ;; Work around <https://bugs.gnu.org/30756>.
              (unsetenv "C_INCLUDE_PATH")
              (unsetenv "CPLUS_INCLUDE_PATH")

gnu/packages/crates-io.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2019 Ivan Petkov <ivanppetkov@gmail.com>
+;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -22,27 +23,473 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages))
 
-(define-public rust-unicode-xid
+;;;
+;;; Please: Try to add new module packages in alphabetic order.
+;;;
+
+(define-public rust-autocfg
   (package
-    (name "rust-unicode-xid")
+    (name "rust-autocfg")
-    (version "0.1.0")
+    (version "0.1.5")
     (source
       (origin
         (method url-fetch)
-        (uri (crate-uri "unicode-xid" version))
+        (uri (crate-uri "autocfg" version))
-        (file-name
+        (file-name (string-append name "-" version ".tar.gz"))
-          (string-append name "-" version ".tar.gz"))
         (sha256
-          (base32
+         (base32
-            "1z57lqh4s18rr4x0j4fw4fmp9hf9346h0kmdgqsqx0fhjr3k0wpw"))))
+          "0asl6fnc35yk5l2rxwhp25v128jgm45dp754h9z8x51b6n90w4r2"))))
     (build-system cargo-build-system)
-    (home-page
+    (home-page "https://github.com/cuviper/autocfg")
-      "https://github.com/unicode-rs/unicode-xid")
+    (synopsis "Automatic cfg for Rust compiler features")
-    (synopsis "Determine Unicode XID related properties")
+    (description "Rust library for build scripts to automatically configure
-    (description "Determine whether characters have the XID_Start
+code based on compiler support.  Code snippets are dynamically tested to see
-or XID_Continue properties according to Unicode Standard Annex #31.")
+if the @code{rustc} will accept them, rather than hard-coding specific version
-    ;; Dual licensed.
+support.")
-    (license (list license:asl2.0 license:expat))))
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-bencher
+  (package
+    (name "rust-bencher")
+    (version "0.1.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bencher" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1x8p2xblgqssay8cdykp5pkfc0np0jk5bs5cx4f5av097aav9zbx"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/bluss/bencher/")
+    (synopsis "Port of the libtest benchmark runner to Rust stable")
+    (description "This package provides a port of the libtest (unstable Rust)
+benchmark runner to Rust stable releases.  Supports running benchmarks and
+filtering based on the name.  Benchmark execution works exactly the same way
+and no more (caveat: black_box is still missing!).")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-bitflags
+  (package
+    (name "rust-bitflags")
+    (version "1.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bitflags" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1zc1qb1hwsnl2d8rhzicsv9kqd5b2hwbrscrcfw5as4sfr35659x"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/bitflags/bitflags")
+    (synopsis "Macro to generate structures which behave like bitflags")
+    (description "This package provides a macro to generate structures which
+behave like a set of bitflags.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-cfg-if
+  (package
+    (name "rust-cfg-if")
+    (version "0.1.9")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cfg-if" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0csygklgz3ybpr0670rkip49zh76m43ar3k7xgypkzbzrwycx1ml"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/alexcrichton/cfg-if")
+    (synopsis "Define an item depending on parameters")
+    (description "This package provides a macro to ergonomically define an item
+depending on a large number of #[cfg] parameters.  Structured like an
+@code{if-else} chain, the first matching branch is the item that gets emitted.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-discard
+  (package
+    (name "rust-discard")
+    (version "1.0.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "discard" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1h67ni5bxvg95s91wgicily4ix7lcw7cq0a5gy9njrybaibhyb91"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/Pauan/rust-discard")
+    (synopsis "Allow for intentionally leaking memory")
+    (description "There are situations where you need to intentionally leak some
+memory but not other memory.  This package provides a discard trait which allows
+for intentionally leaking memory")
+    (license license:expat)))
+
+(define-public rust-doc-comment
+  (package
+    (name "rust-doc-comment")
+    (version "0.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "doc-comment" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "15rsqxgarfpb1yim9sbp9yfgj7p2dq6v51c6bq1a62paii9ylgcj"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/GuillaumeGomez/doc-comment")
+    (synopsis "Macro to generate doc comments")
+    (description "This package provides a way to generate doc comments
+from macros.")
+    (license license:expat)))
+
+(define-public rust-dtoa
+  (package
+    (name "rust-dtoa")
+    (version "0.4.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "dtoa" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0phbm7i0dpn44gzi07683zxaicjap5064w62pidci4fhhciv8mza"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/dtolnay/dtoa")
+    (synopsis "Fast functions for printing floating-point primitives")
+    (description "This crate provides fast functions for printing
+floating-point primitives to an @code{io::Write}.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-fallible-iterator
+  (package
+    (name "rust-fallible-iterator")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "fallible-iterator" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1xq759lsr8gqss7hva42azn3whgrbrs2sd9xpn92c5ickxm1fhs4"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/sfackler/rust-fallible-iterator")
+    (synopsis "Fallible iterator traits")
+    (description "If the @code{std} or @code{alloc} features are enabled, this
+crate provides implementations for @code{Box}, @code{Vec}, @code{BTreeMap}, and
+@code{BTreeSet}.  If the @code{std} feature is enabled, this crate additionally
+provides implementations for @code{HashMap} and @code{HashSet}.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-fnv
+  (package
+    (name "rust-fnv")
+    (version "1.0.6")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "fnv" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ww56bi1r5b8id3ns9j3qxbi7w5h005rzhiryy0zi9h97raqbb9g"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/servo/rust-fnv")
+    (synopsis "implementation of the Fowler-Noll-Vo hash function")
+    (description "The @code{fnv} hash function is a custom @code{Hasher}
+implementation that is more efficient for smaller hash keys.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-fs-extra
+  (package
+    (name "rust-fs-extra")
+    (version "1.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "fs_extra" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0x6675wdhsx277k1k1235jwcv38naf20d8kwrk948ds26hh4lajz"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/webdesus/fs_extra")
+    (synopsis "Extra filesystem methods")
+    (description "Expanding opportunities standard library @code{std::fs} and
+@code{std::io}.  Recursively copy folders with recept information about
+process and much more.")
+    (license license:expat)))
+
+(define-public rust-futures
+  (package
+    (name "rust-futures")
+    (version "0.1.28")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "futures" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0saq8ffjw1pwf1pzhw3kq1z7dfq6wpd8x93dnni6vbkc799kkp25"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/rust-lang-nursery/futures-rs")
+    (synopsis "Implementation of zero-cost futures in Rust")
+    (description "An implementation of @code{futures} and @code{streams}
+featuring zero allocations, composability, and iterator-like interfaces.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-hex
+  (package
+    (name "rust-hex")
+    (version "0.3.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "hex" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0xsdcjiik5j750j67zk42qdnmm4ahirk3gmkmcqgq7qls2jjcl40"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/KokaKiwi/rust-hex")
+    (synopsis "Encode and decode data to/from hexadecimals")
+    (description "This crate allows for encoding and decoding data into/from
+hexadecimal representation.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-itoa
+  (package
+    (name "rust-itoa")
+    (version "0.4.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "itoa" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0zvg2d9qv3avhf3d8ggglh6fdyw8kkwqg3r4622ly5yhxnvnc4jh"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/dtolnay/itoa")
+    (synopsis "Fast functions for printing integer primitives")
+    (description "This crate provides fast functions for printing integer
+primitives to an @code{io::Write}.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-json
+  (package
+    (name "rust-json")
+    (version "0.11.14")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "json" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1hj8c6xj5c2aqqszi8naaflmcdbya1i9byyjrq4iybxjb4q91mq1"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/maciejhirsz/json-rust")
+    (synopsis "JSON implementation in Rust")
+    (description "This crate provides a JSON implementation in Rust, reducing
+friction with idiomatic Rust structs to ease interopability.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-maplit
+  (package
+    (name "rust-maplit")
+    (version "1.0.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "maplit" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0hsczmvd6zkqgzqdjp5hfyg7f339n68w83n4pxvnsszrzssbdjq8"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/bluss/maplit")
+    (synopsis "Collection of Map macros")
+    (description "This crate provides a collection of @code{literal} macros for
+@code{HashMap}, @code{HashSet}, @code{BTreeMap}, and @code{BTreeSet.}")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-matches
+  (package
+    (name "rust-matches")
+    (version "0.1.8")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "matches" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "020axl4q7rk9vz90phs7f8jas4imxal9y9kxl4z4v7a6719mrz3z"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/SimonSapin/rust-std-candidates")
+    (synopsis "Macro to evaluate whether an expression matches a pattern.")
+    (description "This package provides a macro to evaluate, as a boolean,
+whether an expression matches a pattern.")
+    (license license:expat)))
+
+(define-public rust-md5
+  (package
+    (name "rust-md5")
+    (version "0.6.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "md5" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "17b2xm4h4cvxsdjsf3kdrzqv2za60kak961xzi5kmw6g6djcssvy"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/stainless-steel/md5")
+    (synopsis "MD5 hash function in Rust")
+    (description "The package provides the MD5 hash function.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-peeking-take-while
+  (package
+    (name "rust-peeking-take-while")
+    (version "0.1.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "peeking_take_while" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "16bhqr6rdyrp12zv381cxaaqqd0pwysvm1q8h2ygihvypvfprc8r"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/fitzgen/peeking_take_while")
+    (synopsis "Provides the peeking_take_while iterator adaptor method")
+    (description
+      "Like @code{Iterator::take_while}, but calls the predicate on a peeked
+value.  This allows you to use @code{Iterator::by_ref} and
+@code{Iterator::take_while} together, and still get the first value for which
+the @code{take_while} predicate returned false after dropping the @code{by_ref}.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-percent-encoding
+  (package
+    (name "rust-percent-encoding")
+    (version "2.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "percent-encoding" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0m6rkp3iy11la04p6z3492rns6n693pvmx585dvfmzzlzak2hkxs"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/servo/rust-url/")
+    (synopsis "Percent encoding and decoding")
+    (description "This crate provides percent encoding and decoding.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-pin-utils
+  (package
+    (name "rust-pin-utils")
+    (version "0.1.0-alpha.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pin-utils" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "11xmyx00n4m37d546by2rxb8ryxs12v55cc172i3yak1rqccd52q"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/rust-lang-nursery/pin-utils")
+    (synopsis "Utilities for pinning")
+    (description "This crate provides utilities for pinning values on the stack.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-plain
+  (package
+    (name "rust-plain")
+    (version "0.2.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "plain" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "19n1xbxb4wa7w891268bzf6cbwq4qvdb86bik1z129qb0xnnnndl"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/randomites/plain")
+    (synopsis "Rust library that allows reinterpreting data safely")
+    (description "This package provides a small Rust library that allows users
+ to reinterpret data of certain types safely.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-pocket-resources
+  (package
+    (name "rust-pocket-resources")
+    (version "0.3.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pocket-resources" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1n2i5vmi8fdbw89wm5nz1ws1z9f1qax911p6ksg4scmdg23z6df1"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/tomaka/pocket-resources")
+    (synopsis "Include resources in your applications")
+    (description "This crate allows you to include resources in your
+applications.")
+    (license license:expat)))
+
+(define-public rust-ppv-lite86
+  (package
+    (name "rust-ppv-lite86")
+    (version "0.2.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "ppv-lite86" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "06snnv338w341nicfqba2jgln5dsla72ndkgrw7h1dfdb3vgkjz3"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/cryptocorrosion/cryptocorrosion")
+    (synopsis "Implementation of the crypto-simd API for x86")
+    (description "This crate provides an implementation of the crypto-simd API
+for x86.")
+    (license (list license:asl2.0
+                   license:expat))))
 
 (define-public rust-proc-macro2
   (package
@@ -69,6 +516,26 @@ in terms of the upstream unstable API.")
     ;; Dual licensed.
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-quick-error
+  (package
+    (name "rust-quick-error")
+    (version "1.2.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "quick-error" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1w6kgwwv7p7zr0yyg5rb315lkk24bimywklwx7fsvsbwi10bjx4j"))))
+    (build-system cargo-build-system)
+    (home-page "http://github.com/tailhook/quick-error")
+    (synopsis "Macro which makes error types pleasant to write")
+    (description "This crate provides a macro which makes error types pleasant
+to write.")
+    (license (list license:asl2.0
+                   license:expat))))
+
 (define-public rust-quote
   (package
     (name "rust-quote")
@@ -90,3 +557,396 @@ in terms of the upstream unstable API.")
     (description "Quasi-quoting macro quote!(...)")
     ;; Dual licensed.
     (license (list license:asl2.0 license:expat))))
+
+(define-public rust-rustc-std-workspace-core
+  (package
+    (name "rust-rustc-std-workspace-core")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rustc-std-workspace-core" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1309xhwyai9xpz128xrfjqkmnkvgjwddznmj7brbd8i8f58zamhr"))))
+    (build-system cargo-build-system)
+    (home-page "https://crates.io/crates/rustc-std-workspace-core")
+    (synopsis "Explicitly empty crate for rust-lang/rust integration")
+    (description "This crate provides an explicitly empty crate for
+rust-lang/rust integration.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-scoped-tls
+  (package
+    (name "rust-scoped-tls")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "scoped-tls" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1hj8lifzvivdb1z02lfnzkshpvk85nkgzxsy2hc0zky9wf894spa"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/alexcrichton/scoped-tls")
+    (synopsis "Rust library providing the old standard library's scoped_thread_local")
+    (description "This crate provides a library implementation of the standard
+library's old @code{scoped_thread_local!} macro for providing scoped access to
+@dfn{thread local storage} (TLS) so any type can be stored into TLS.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-scopeguard
+  (package
+    (name "rust-scopeguard")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "scopeguard" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "03aay84r1f6w87ckbpj6cc4rnsxkxcfs13n5ynxjia0qkgjiabml"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/bluss/scopeguard")
+    (synopsis "Scope guard which will run a closure even out of scope")
+    (description "This package provides a RAII scope guard that will run a
+given closure when it goes out of scope, even if the code between panics
+(assuming unwinding panic).  Defines the macros @code{defer!},
+@code{defer_on_unwind!}, @code{defer_on_success!} as shorthands for guards
+with one of the implemented strategies.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-semver-parser
+  (package
+    (name "rust-semver-parser")
+    (version "0.9.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "semver-parser" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ahqhvgpzhcsd28id7xnrjv4419i9yyalhm7d7zi430qx0hi2vml"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/steveklabnik/semver-parser")
+    (synopsis "Parsing of the semver spec")
+    (description "This package provides for parsing of the semver spec.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-shlex
+  (package
+    (name "rust-shlex")
+    (version "0.1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "shlex" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1lmv6san7g8dv6jdfp14m7bdczq9ss7j7bgsfqyqjc3jnjfippvz"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/comex/rust-shlex")
+    (synopsis "Split a string into shell words, like Python's shlex")
+    (description "This crate provides a method to split a string into shell
+words, like Python's shlex.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-slab
+  (package
+    (name "rust-slab")
+    (version "0.4.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "slab" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1y59xsa27jk84sxzswjk60xcjf8b4fm5960jwpznrrcmasyva4f1"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/carllerche/slab")
+    (synopsis "Pre-allocated storage for a uniform data type")
+    (description "This create provides a pre-allocated storage for a uniform
+data type.")
+    (license license:expat)))
+
+(define-public rust-spin
+  (package
+    (name "rust-spin")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "spin" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0m9clchsj0rf13bggsgvbv9haiy0f6rhvnvkpvkk8720a5pkydj4"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/mvdnes/spin-rs.git")
+    (synopsis "Synchronization primitives based on spinning")
+    (description "This crate provides synchronization primitives based on
+spinning.  They may contain data, are usable without @code{std},and static
+initializers are available.")
+    (license license:expat)))
+
+(define-public rust-stdweb-internal-runtime
+  (package
+    (name "rust-stdweb-internal-runtime")
+    (version "0.1.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "stdweb-internal-runtime" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1nhpyra7glbwcpakhpj5a3d7h7kx1ynif473nzshmk226m91f8ym"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/koute/stdweb")
+    (synopsis "Internal runtime for the @code{stdweb} crate")
+    (description "This crate provides internal runtime for the @code{stdweb}
+crate.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-strsim
+  (package
+    (name "rust-strsim")
+    (version "0.9.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "strsim" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1xphwhf86yxxmcpvm4mikj8ls41f6nf7gqyjm98b74mfk81h6b03"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/dguo/strsim-rs")
+    (synopsis "Rust implementations of string similarity metrics")
+    (description "This crate includes implementations of string similarity
+metrics.  It includes Hamming, Levenshtein, OSA, Damerau-Levenshtein, Jaro,
+and Jaro-Winkler.")
+    (license license:expat)))
+
+(define-public rust-synstructure-test-traits
+  (package
+    (name "rust-synstructure-test-traits")
+    (version "0.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "synstructure_test_traits" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1b3fs2b9kc1gy9dilaxqjbdl4z0mlrbbxjzkprdx953rif1c3q66"))))
+    (build-system cargo-build-system)
+    (home-page "https://crates.io/crates/synstructure_test_traits")
+    (synopsis "Helper test traits for synstructure doctests")
+    (description
+     "This package provides helper test traits for synstructure doctests.")
+    (license license:expat)))
+
+(define-public rust-typenum
+  (package
+    (name "rust-typenum")
+    (version "1.10.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "typenum" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0sc1jirllfhdi52z1xv9yqzxzpk6v7vadd13n7wvs1wnjipn6bb1"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/paholg/typenum")
+    (synopsis "Rust library for type-level numbers evaluated at compile time")
+    (description "Typenum is a Rust library for type-level numbers evaluated at
+compile time.  It currently supports bits, unsigned integers, and signed
+integers.  It also provides a type-level array of type-level numbers, but its
+implementation is incomplete.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-ucd-util
+  (package
+    (name "rust-ucd-util")
+    (version "0.1.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "ucd-util" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0x088q5z0m09a2jqcfgsnq955y8syn1mgn35cl78qinkxm4kp6zs"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/BurntSushi/ucd-generate")
+    (synopsis "library for working with the Unicode character database")
+    (description "This package provides a small utility library for working
+with the Unicode character database.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-unicode-width
+  (package
+    (name "rust-unicode-width")
+    (version "0.1.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unicode-width" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "09k5lipygardwy0660jhls08fsgknrazzivmn804gps53hiqc8w8"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/unicode-rs/unicode-width")
+    (synopsis "Determine displayed width according to Unicode rules")
+    (description "This crate allows you to determine displayed width of
+@code{char} and @code{str} types according to Unicode Standard Annex #11 rules.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-unicode-xid
+  (package
+    (name "rust-unicode-xid")
+    (version "0.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unicode-xid" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1z57lqh4s18rr4x0j4fw4fmp9hf9346h0kmdgqsqx0fhjr3k0wpw"))))
+    (build-system cargo-build-system)
+    (home-page
+      "https://github.com/unicode-rs/unicode-xid")
+    (synopsis "Determine Unicode XID related properties")
+    (description "Determine whether characters have the XID_Start
+or XID_Continue properties according to Unicode Standard Annex #31.")
+    ;; Dual licensed.
+    (license (list license:asl2.0 license:expat))))
+
+(define-public rust-unindent
+  (package
+    (name "rust-unindent")
+    (version "0.1.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unindent" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1x21ilf78aqcq9xzb9b7i628wm10rhk0jp0chlv06rkc690l8jw3"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/dtolnay/indoc")
+    (synopsis "Remove a column of leading whitespace from a string")
+    (description "This crate allows you to remove a column of leading
+whitespace from a string.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-wasm-bindgen-shared
+  (package
+    (name "rust-wasm-bindgen-shared")
+    (version "0.2.48")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "wasm-bindgen-shared" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "08rnfhjyk0f6liv8n4rdsvhx7r02glkhcbj2lp9lcbkbfpad9hnr"))))
+    (build-system cargo-build-system)
+    (home-page "https://rustwasm.github.io/wasm-bindgen/")
+    (synopsis "Shared support between wasm-bindgen and wasm-bindgen cli")
+    (description "This package provides shared support between
+@code{wasm-bindgen} and @code{wasm-bindgen} cli, an internal dependency.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-winapi
+  (package
+    (name "rust-winapi")
+    (version "0.3.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "winapi" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0w7pbhcl087lkggxdflfp2i92rq89ahsfdkjkv44fgmiy9m3h3pi"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-winapi-i686-pc-windows-gnu"
+         ,rust-winapi-i686-pc-windows-gnu)
+        ("rust-winapi-x86-64-pc-windows-gnu"
+         ,rust-winapi-x86-64-pc-windows-gnu))))
+    (home-page "https://github.com/retep998/winapi-rs")
+    (synopsis "Raw FFI bindings for all of Windows API.")
+    (description
+     "Raw FFI bindings for all of Windows API.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-winapi-i686-pc-windows-gnu
+  (package
+    (name "rust-winapi-i686-pc-windows-gnu")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "winapi-i686-pc-windows-gnu" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1dmpa6mvcvzz16zg6d5vrfy4bxgg541wxrcip7cnshi06v38ffxc"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/retep998/winapi-rs")
+    (synopsis "Import libraries for the i686-pc-windows-gnu target")
+    (description "This crate provides import libraries for the
+i686-pc-windows-gnu target.  Please don't use this crate directly, depend on
+@code{winapi} instead.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-winapi-x86-64-pc-windows-gnu
+  (package
+    (name "rust-winapi-x86-64-pc-windows-gnu")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "winapi-x86_64-pc-windows-gnu" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0gqq64czqb64kskjryj8isp62m2sgvx25yyj3kpc2myh85w24bki"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/retep998/winapi-rs")
+    (synopsis "Import libraries for the x86_64-pc-windows-gnu target")
+    (description "This package provides import libraries for the
+x86_64-pc-windows-gnu target.  Please don't use this crate directly, depend on
+@code{winapi} instead.")
+    (license (list license:asl2.0
+                   license:expat))))

gnu/packages/cups.scm

@@ -57,7 +57,7 @@
 (define-public cups-filters
   (package
     (name "cups-filters")
-    (version "1.25.0")
+    (version "1.25.1")
     (source(origin
               (method url-fetch)
               (uri
@@ -65,7 +65,7 @@
                               "cups-filters-" version ".tar.xz"))
               (sha256
                (base32
-                "1laiscq8yvynw862calkgbz9irrdkmd5l821q6a6wik1ifd186c1"))
+                "0nlq44jnjcnrbdv0dv5myg5kaycmk6a4klynpvj65xvn3l9cq28s"))
               (modules '((guix build utils)))
               (snippet
                ;; install backends, banners and filters to cups-filters output

gnu/packages/databases.scm

@@ -132,12 +132,13 @@
     (name "4store")
     (version "1.1.6")
     (source (origin
-      (method url-fetch)
+      (method git-fetch)
-      (uri (string-append "https://github.com/4store/4store/archive/v"
+      (uri (git-reference
-                          version ".tar.gz"))
+             (url "https://github.com/4store/4store.git")
-      (file-name (string-append name "-" version ".tar.gz"))
+             (commit (string-append "v" version))))
+      (file-name (git-file-name name version))
       (sha256
-       (base32 "004fmcf1w75zhc1x3zc6kc97j4jqn2v5nhk6yb3z3cpfrhzi9j50"))
+       (base32 "1kzdfmwpzy64cgqlkcz5v4klwx99w0jk7afckyf7yqbqb4rydmpk"))
       (patches (search-patches "4store-unset-preprocessor-directive.patch"
                                "4store-fix-buildsystem.patch"))))
     (build-system gnu-build-system)
@@ -160,12 +161,6 @@
        ("cyrus-sasl" ,cyrus-sasl)
        ("openssl" ,openssl)
        ("util-linux" ,util-linux)))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'generate-configure
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     ;; http://www.4store.org has been down for a while now.
     (home-page "https://github.com/4store/4store")
     (synopsis "Clustered RDF storage and query engine")
@@ -616,15 +611,15 @@ Language.")
 (define-public mariadb
   (package
     (name "mariadb")
-    (version "10.1.40")
+    (version "10.1.41")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://downloads.mariadb.org/f/"
+              (uri (string-append "https://downloads.mariadb.com/MariaDB"
-                                  name "-" version "/source/"
+                                  "/mariadb-" version "/source/mariadb-"
-                                  name "-" version ".tar.gz"))
+                                  version ".tar.gz"))
               (sha256
                (base32
-                "19375bnq0yg52kqh6cy00s5rglcxdrs5bb2hy7dqv2xqa9z7lxci"))
+                "1wh0073lqw3d9xs150bf2q3qvjwa6886mfi9khmsn7p8vapw6irb"))
               (patches (search-patches "mariadb-client-test-32bit.patch"))
               (modules '((guix build utils)))
               (snippet
@@ -806,14 +801,14 @@ as a drop-in replacement of MySQL.")
 (define-public postgresql
   (package
     (name "postgresql")
-    (version "10.9")
+    (version "10.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "0m0gbf7nwgag6a1z5f9xszwzgf2xhx0ncakyxwxlzs87n1zk32wm"))
+                "0lzj46dwd9cw94gnqm36bxd7jlhfdyqjrfzr3c4xd3prfn2rnkxd"))
               (patches (search-patches "postgresql-disable-resolve_symlinks.patch"))))
     (build-system gnu-build-system)
     (arguments
@@ -853,27 +848,27 @@ pictures, sounds, or video.")
   (package
     (inherit postgresql)
     (name "postgresql")
-    (version "11.4")
+    (version "11.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "12ycjlqncijgmd5z078ybwda8ilas96lc7nxxmdq140mzpgjv002"))))))
+                "106ikalvrilihlvhq7xj7snq98hgbgq6qsgjrd252wgw1c327pvz"))))))
 
 (define-public postgresql-9.6
   (package
     (inherit postgresql)
     (name "postgresql")
-    (version "9.6.14")
+    (version "9.6.15")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "08hsqczy1ixkjyf2vr3s9x69agfz9yr8lh31fir4z0dfr5jw421z"))))))
+                "02hp69h2p02asfblkaahblzdz2zmawd2r11h6237y5j7yadgxn9w"))))))
 
 (define-public python-pymysql
   (package

gnu/packages/docbook.scm

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

gnu/packages/docker.scm

@@ -63,12 +63,13 @@
     (arguments '(#:tests? #f))
     (inputs
      `(("python-requests" ,python-requests-2.20)
-       ("python-docker-pycreds" ,python-docker-pycreds)
        ("python-ipaddress" ,python-ipaddress)
-       ("python-paramiko" ,python-paramiko)
        ("python-six" ,python-six)
        ("python-urllib3" ,python-urllib3-1.24)
        ("python-websocket-client" ,python-websocket-client)))
+    (propagated-inputs
+     `(("python-docker-pycreds" ,python-docker-pycreds)
+       ("python-paramiko" ,python-paramiko))) ; adds SSH support
     (home-page "https://github.com/docker/docker-py/")
     (synopsis "Python client for Docker")
     (description "Docker-Py is a Python client for the Docker container
@@ -113,17 +114,11 @@ client.")
     ;; TODO: Tests require running Docker daemon.
     (arguments '(#:tests? #f))
     (inputs
-     `(("python2-backport-ssl-match-hostname"
+     `(("python-cached-property"
-        ,python2-backport-ssl-match-hostname)
-       ("python-cached-property"
         ,python-cached-property)
-       ("python-colorama" ,python-colorama)
        ("python-docker-py" ,python-docker-py)
-       ("python-docker-pycreds" ,python-docker-pycreds)
        ("python-dockerpty" ,python-dockerpty)
        ("python-docopt" ,python-docopt)
-       ("python-ipaddress" ,python-ipaddress)
-       ("python-paramiko" ,python-paramiko)
        ("python-jsonschema" ,python-jsonschema-2.6)
        ("python-pyyaml" ,python-pyyaml)
        ("python-requests" ,python-requests-2.20)
@@ -586,6 +581,9 @@ provisioning etc.")
              ;; information, and the DWARF symbol table.
              (setenv "LDFLAGS" "-s -w")
 
+             ;; Make sure "docker -v" prints a usable version string.
+             (setenv "VERSION" ,%docker-version)
+
              ;; Make build reproducible.
              (setenv "BUILDTIME" "1970-01-01 00:00:01.000000000+00:00")
              (symlink "src/github.com/docker/cli/scripts" "./scripts")

gnu/packages/education.scm

@@ -251,7 +251,7 @@ easy.")
 (define-public snap
   (package
     (name "snap")
-    (version "5.0.4")
+    (version "5.0.8")
     (source
      (origin
        (method git-fetch)
@@ -261,7 +261,7 @@ easy.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1zdypxifvxjkzhi4n9mkck8l419wc0pg103339yzhsbb9kkd3jlr"))))
+         "0fwfssdgv3mfzyv8hw1a1z5ky1yn0p59kyl6l9fxsm4w2ckgyizd"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))

gnu/packages/emacs-xyz.scm

@@ -51,6 +51,7 @@
 ;;; Copyright © 2019 Baptiste Strazzulla <bstrazzull@hotmail.fr>
 ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autitici.org>
 ;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
+;;; Copyright © 2019 Amin Bandali <bandali@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -876,7 +877,7 @@ in certain cases.  It also enables recursion for anonymous functions.")
 (define-public emacs-xr
   (package
     (name "emacs-xr")
-    (version "1.12")
+    (version "1.13")
     (source
      (origin
        (method url-fetch)
@@ -884,7 +885,7 @@ in certain cases.  It also enables recursion for anonymous functions.")
              "https://elpa.gnu.org/packages/xr-" version ".tar"))
        (sha256
         (base32
-         "1vv87h0h8ldc1mbsn45w5z1m6jq8j2js4xz23a9ixdby06g60y3g"))))
+         "1km4x92pii8c4bcimks4xzhmwpypdf183z0zh7raj062jz4jb74r"))))
     (build-system emacs-build-system)
     (home-page "http://elpa.gnu.org/packages/xr.html")
     (synopsis "Convert string regexp to rx notation")
@@ -929,7 +930,7 @@ optional minor mode which can apply this command automatically on save.")
 (define-public emacs-relint
   (package
     (name "emacs-relint")
-    (version "1.8")
+    (version "1.10")
     (source
      (origin
        (method url-fetch)
@@ -937,7 +938,7 @@ optional minor mode which can apply this command automatically on save.")
              "https://elpa.gnu.org/packages/relint-" version ".el"))
        (sha256
         (base32
-         "1bl6m2h7131acbmr0kqfnjjpv2syiv2mxfnm61g874ynnvkmmkm3"))))
+         "1l0lh4pkksw7brmhhbaikwzs4zkgd2962ks1zy7m262dvkhxjfv8"))))
     (build-system emacs-build-system)
     (propagated-inputs `(("emacs-xr" ,emacs-xr)))
     (home-page "https://github.com/mattiase/relint")
@@ -2473,7 +2474,7 @@ column by drawing a thin line down the length of the editing window.")
 (define-public emacs-inf-ruby
   (package
     (name "emacs-inf-ruby")
-    (version "2.5.1")
+    (version "2.5.2")
     (source
      (origin
        (method git-fetch)
@@ -2482,7 +2483,7 @@ column by drawing a thin line down the length of the editing window.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1r452h6cyypqlc59q8dx5smkwhck4qjcg1pf9qdw539cpva5q77z"))))
+        (base32 "0a1hhvfbl6mq8rjsi77fg9fh5a91hi5scjrg9rjqc5ffbql67y0v"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/nonsequitur/inf-ruby")
     (synopsis "Provides a REPL buffer connected to a Ruby subprocess in Emacs")
@@ -3389,6 +3390,76 @@ for the current function or variable in the minibuffer.")
 completion candidate when using the Company text completion framework.")
     (license license:gpl3+)))
 
+(define-public emacs-math-symbol-lists
+  (let ((commit "dc7531cff0c845d5470a50c24d5d7309b2ced7eb")
+        (revision "1"))
+    (package
+      (name "emacs-math-symbol-lists")
+      (version (git-version "1.2.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/vspinu/math-symbol-lists.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "094m21i9rns6m59cmhxcivxxafbg52w8f8na4y3v47aq67zmhhqm"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/vspinu/math-symbol-lists")
+      (synopsis "Lists of Unicode math symbols and @code{LaTeX} commands")
+      (description "This is a storage package used by completion engines like
+@code{company-math}.")
+      (license license:gpl3+))))
+
+(define-public emacs-company-math
+  (let ((commit "600e49449644f6835f9dc3501bc58461999e8ab9")
+        (revision "1"))
+    (package
+      (name "emacs-company-math")
+      (version (git-version "1.3" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/vspinu/company-math.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1ps2lpkzn8mjbpcbvvy1qz3xbgrh6951x8y9bsd1fm32drdph9lh"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-math-symbol-lists" ,emacs-math-symbol-lists)
+         ("emacs-company" ,emacs-company)))
+      (home-page "https://github.com/vspinu/company-math")
+      (synopsis "Completion backends for Unicode math symbols and @code{LaTeX} tags")
+      (description "This package provides a backend for use with
+@code{company-mode} allowing for completion of common math symbols.")
+      (license license:gpl3+))))
+
+(define-public emacs-nswbuff
+  (let ((commit "362da7f3687e2eb5bb11667347de85f4a9d002bc")
+        (revision "1"))
+    (package
+      (name "emacs-nswbuff")
+      (version (git-version "1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/joostkremers/nswbuff.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0l2xfz8z5qd4hz3kv6zn7h6qq3narkilri8a071y1n8j31jps4ma"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/joostkremers/nswbuff")
+      (synopsis "Quickly switch between buffers")
+      (description "This package allows for navigating between buffers within
+a customizable list.")
+      (license license:gpl3+))))
+
 (define-public emacs-multiple-cursors
   (package
     (name "emacs-multiple-cursors")
@@ -3410,6 +3481,32 @@ completion candidate when using the Company text completion framework.")
 simultaneous cursors.")
     (license license:gpl3+)))
 
+(define-public emacs-mc-extras
+  (let ((commit "053abc52181b8718559d7361a587bbb795faf164")
+        (revision "1"))
+    (package
+      (name "emacs-mc-extras")
+      (version (git-version "1.2.4" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/knu/mc-extras.el.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "16y48qrd20m20vypvys5jp4v4gc1qrqlkm75s1pk1r68i9zrw481"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-multiple-cursors" ,emacs-multiple-cursors)))
+      (home-page "https://github.com/knu/mc-extras.el")
+      (synopsis "Extra functions for manipulating multiple cursors")
+      (description
+       "This package provides additional functions for
+@code{multiple-cursors}, including functions for marking s-expressions,
+comparing characters, removing cursors, and more.")
+      (license license:bsd-2))))
+
 (define-public emacs-typo
   (package
     (name "emacs-typo")
@@ -4011,6 +4108,38 @@ minutes is started automatically.  Every 4 breaks a long break is
 started with 20 minutes.  All values are customizable.")
     (license license:gpl3+)))
 
+(define-public emacs-org-sidebar
+  (let ((commit "74ca98b9920f3de3f13d49866581435e1ec63ec5")
+        (revision "1"))
+    (package
+      (name "emacs-org-sidebar")
+      (version (git-version "0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/alphapapa/org-sidebar.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "03p1ndyw2qp2skib5hszc4xyh84w7p2mhkd4a9dy6qv8q47xpsqn"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-dash" ,emacs-dash)
+         ("emacs-org-super-agenda" ,emacs-org-super-agenda)
+         ("emacs-org" ,emacs-org)
+         ("emacs-org-ql" ,emacs-org-ql)
+         ("emacs-s" ,emacs-s)))
+      (home-page "https://github.com/alphapapa/org-sidebar")
+      (synopsis "Helpful sidebar for Org buffers")
+      (description "This package provides a sidebar for Org buffers.  At the
+top is a chronological list of scheduled and deadlined tasks in the current
+buffer (similar to the Org agenda ,but without all its features), and below
+that is a list of all other non-done to-do items.  If the buffer is narrowed,
+the sidebar only shows items in the narrowed portion; this allows seeing an
+overview of tasks in a subtree.")
+      (license license:gpl3+))))
+
 (define-public emacs-org-trello
   (package
     (name "emacs-org-trello")
@@ -4604,45 +4733,50 @@ automatically.")
     (license license:gpl3+)))
 
 (define-public emacs-ivy
-  (package
+  ;; The latest release version introduced a new feature, swiper-isearch, that
-    (name "emacs-ivy")
+  ;; generally works well but had some noticeable bugs; this later commit
-    (version "0.12.0")
+  ;; includes fixes for several of them.
-    (source
+  (let ((commit "d3e4514fd72f217c704ae18afdf711bb9036a04d")
-     (origin
+        (revision "1"))
-       (method git-fetch)
+    (package
-       (uri (git-reference
+      (name "emacs-ivy")
-             (url "https://github.com/abo-abo/swiper.git")
+      (version (git-version "0.12.0" revision commit))
-             (commit version)))
+      (source
-       (file-name (git-file-name name version))
+       (origin
-       (sha256
+         (method git-fetch)
-        (base32
+         (uri (git-reference
-         "0xgngn3jhmyn6mlkk9kmgfgh0w5i50b27syr4cgfgarg6p77j05w"))))
+               (url "https://github.com/abo-abo/swiper.git")
-    (build-system emacs-build-system)
+               (commit commit)))
-    (arguments
+         (file-name (git-file-name name version))
-     `(#:phases
+         (sha256
-       (modify-phases %standard-phases
+          (base32
-         (add-after 'install 'install-doc
+           "142axxc6vsl14cfyvzj9csiykxdn7vhw88fy955hzx7av4qfqg4x"))))
-           (lambda* (#:key outputs #:allow-other-keys)
+      (build-system emacs-build-system)
-             (let* ((out (assoc-ref outputs "out"))
+      (arguments
-                    (info (string-append out "/share/info")))
+       `(#:phases
-               (with-directory-excursion "doc"
+         (modify-phases %standard-phases
-                 (invoke "makeinfo" "ivy.texi")
+           (add-after 'install 'install-doc
-                 (install-file "ivy.info" info)
+             (lambda* (#:key outputs #:allow-other-keys)
-                 #t)))))))
+               (let* ((out (assoc-ref outputs "out"))
-    (propagated-inputs
+                      (info (string-append out "/share/info")))
-     `(("emacs-hydra" ,emacs-hydra)))
+                 (with-directory-excursion "doc"
-    (native-inputs
+                   (invoke "makeinfo" "ivy.texi")
-     `(("texinfo" ,texinfo)))
+                   (install-file "ivy.info" info)
-    (home-page "http://oremacs.com/swiper/")
+                   #t)))))))
-    (synopsis "Incremental vertical completion for Emacs")
+      (propagated-inputs
-    (description
+       `(("emacs-hydra" ,emacs-hydra)))
-     "This package provides @code{ivy-read} as an alternative to
+      (native-inputs
+       `(("texinfo" ,texinfo)))
+      (home-page "http://oremacs.com/swiper/")
+      (synopsis "Incremental vertical completion for Emacs")
+      (description
+       "This package provides @code{ivy-read} as an alternative to
 @code{completing-read} and similar functions.  No attempt is made to determine
 the best candidate.  Instead, the user can navigate candidates with
 @code{ivy-next-line} and @code{ivy-previous-line}.  The matching is done by
 splitting the input text by spaces and re-building it into a regular
 expression.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-ivy-pass
   (let ((commit "5b523de1151f2109fdd6a8114d0af12eef83d3c5")
@@ -5228,7 +5362,7 @@ strings, and code folding.")
 (define-public emacs-nodejs-repl
   (package
     (name "emacs-nodejs-repl")
-    (version "0.2.1")
+    (version "0.2.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5237,7 +5371,7 @@ strings, and code folding.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "05ccv87rnw7fss3lib8m9sywjrj6n92fnd7mmhmjh27g2klqc83z"))))
+                "1kkj888k9x5n0i7xkia177gzsa84my3g8n0n7v65281cc4f1yhk5"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/abicky/nodejs-repl.el")
     (synopsis "Node.js REPL inside Emacs")
@@ -5580,28 +5714,35 @@ environments (virtualenv) inside Emacs.")
     (license license:gpl3+)))
 
 (define-public emacs-highlight-indentation
-  (package
+  ;; Last release version is from 2015.
-    (name "emacs-highlight-indentation")
+  (let ((commit "d03803f2c06749c430443a3d24e039cbafc9c58f")
-    (version "0.7.0")
+        (revision "1"))
-    (source (origin
+    (package
-              (method git-fetch)
+      (name "emacs-highlight-indentation")
-              (uri (git-reference
+      (version (git-version "0.7.0" revision commit))
-                    (url "https://github.com/antonj/Highlight-Indentation-for-Emacs.git")
+      (source
-                    (commit (string-append "v" version))))
+       (origin
-              (file-name (git-file-name name version))
+         (method git-fetch)
-              (sha256
+         (uri (git-reference
-               (base32
+               (url "https://github.com/antonj/Highlight-Indentation-for-Emacs.git")
-                "00l54k75qk24a0znzl4ij3s3nrnr2wy9ha3za8apphzlm98m907k"))))
+               (commit commit)))
-    (build-system emacs-build-system)
+         (file-name (git-file-name name version))
-    (home-page "https://github.com/antonj/Highlight-Indentation-for-Emacs/")
+         (sha256
-    (synopsis "Highlighting indentation for Emacs")
+          (base32
-    (description "Provides two minor modes to highlight indentation guides in Emacs:
+           "1jq0gf4kcx9hvrw40rnw5c2qynjpjw1vsjbi2i4lqjbsnfnxn4wz"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/antonj/Highlight-Indentation-for-Emacs/")
+      (synopsis "Highlighting indentation for Emacs")
+      (description "This package provides two minor modes to highlight
+indentation guides in Emacs:
+
 @enumerate
 @item @code{highlight-indentation-mode}, which displays guidelines
-indentation (space indentation only).
+  indentation (space indentation only).
-@item @code{highlight-indentation-current-column-mode}, which displays guidelines for the current-point indentation (space indentation only).
+@item @code{highlight-indentation-current-column-mode}, which displays
+  guidelines for the current-point indentation (space indentation only).
 @end enumerate")
-    (license license:gpl2+)))
+      (license license:gpl2+))))
 
 (define-public emacs-elpy
   (package
@@ -5931,7 +6072,7 @@ ack, ag, helm and pt.")
 (define-public emacs-helm
   (package
     (name "emacs-helm")
-    (version "3.2")
+    (version "3.3")
     (source
      (origin
        (method git-fetch)
@@ -5940,7 +6081,7 @@ ack, ag, helm and pt.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12yyprpgh2by2pd41i4z9gz55fxg0f90x03bfrsf791xwbhf6931"))))
+        (base32 "0fqhw7r9fcsja5d3pgbipw7pkw9nj534faav6hi45413hc3gyv92"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-async" ,emacs-async)
@@ -6119,21 +6260,21 @@ xref, etc...) are still available, but with better integration.")
       (license license:gpl3+))))
 
 (define-public emacs-lua-mode
-  (let ((commit "652e299cb967fccca827dda381d61a9c144d97de")
+  (let ((commit "95c64bb5634035630e8c59d10d4a1d1003265743")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "emacs-lua-mode")
-      (version (string-append "20151025." revision "-" (string-take commit 9)))
+      (version (git-version "20151025" revision commit))
       (home-page "https://github.com/immerrr/lua-mode/")
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
                       (url home-page)
                       (commit commit)))
-                (file-name (string-append name "-" version ".checkout"))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "053025k930wh0lak6rc1973ynfrmm8zsyzfqhhd39x7abkl41hc9"))))
+                  "1mra4db25ds64526dsj8m5yv0kfq3lgggjh1x6xmqypdaryddbcp"))))
       (build-system emacs-build-system)
       (synopsis "Major mode for lua")
       (description
@@ -6399,12 +6540,11 @@ aligning text objects based on separators.")
       (license license:gpl3+))))
 
 (define-public emacs-evil-expat
-  (let ((commit "4c344ea19b789002d759a202ffbf594730d2c59a")
+  (let ((commit "f4fcd0aa3edc359adb5c986b5dd9188d220d84e2")
-        (version "0.0.1")
         (revision "1"))
     (package
       (name "emacs-evil-expat")
-      (version (git-version version revision commit))
+      (version (git-version "0.0.1" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -6414,7 +6554,7 @@ aligning text objects based on separators.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "16v7fnldxag6l1lsnrnhdjkga9qi78lbdfbb82k6pmv04991mbkr"))))
+           "0872ix682hkdz0k8pn6sb54rqkx00rz5fxpd5j2snx406yagpaxz"))))
       (build-system emacs-build-system)
       (propagated-inputs `(("emacs-evil" ,emacs-evil)))
       (home-page "https://github.com/edkolev/evil-expat")
@@ -6587,14 +6727,14 @@ passive voice.")
     (name "emacs-org")
     ;; emacs-org-contrib inherits from this package.  Please update its sha256
     ;; checksum as well.
-    (version "9.2.3")
+    (version "9.2.5")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://elpa.gnu.org/packages/org-"
+              (uri (string-append "https://elpa.gnu.org/packages/org-"
                                   version ".tar"))
               (sha256
                (base32
-                "0hqy4lns9q5p0l1ylgmlckqprn9sbasszhznanmv0rsh0gzhsbyw"))))
+                "1pid1sykgz83i4ry5n8f270finag6sm7ckqxn5lkikyya43wlzx1"))))
     (build-system emacs-build-system)
     (home-page "https://orgmode.org/")
     (synopsis "Outline-based notes management and organizer")
@@ -6608,14 +6748,14 @@ programming and reproducible research.")
   (package
     (inherit emacs-org)
     (name "emacs-org-contrib")
-    (version "20190715")
+    (version "20190805")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://orgmode.org/elpa/org-plus-contrib-"
                                   version ".tar"))
               (sha256
                (base32
-                "0yxxkcaxhp5bmjsfdd9pz79rj9s7nb4gj5ci51sh4pf8mimk9542"))))
+                "1mw91hwbqyjq5pyz9hzdhvjlc2bphqpi23yqd3sdk1crpc87s40c"))))
     (arguments
      `(#:modules ((guix build emacs-build-system)
                   (guix build utils)
@@ -7159,6 +7299,56 @@ find files owned by packages...  And much more, including performing all the
 above over the network.")
       (license license:gpl3+))))
 
+(define-public emacs-helm-org-rifle
+  (package
+    (name "emacs-helm-org-rifle")
+    (version "1.6.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/alphapapa/helm-org-rifle")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1r38xhwvgbv6kn5x159phz3xgss7f1rc7icq27rnr4d8aj91wm6k"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-dash" ,emacs-dash)
+       ("emacs-f" ,emacs-f)
+       ("emacs-helm" ,emacs-helm)
+       ("emacs-s" ,emacs-s)))
+    (home-page "https://github.com/alphapapa/helm-org-rifle")
+    (synopsis "Rifle through Org files")
+    (description "This package searches both headings and contents of entries
+in Org buffers and displays matching entries.")
+    (license license:gpl3+)))
+
+(define-public emacs-dired-toggle-sudo
+  (package
+    (name "emacs-dired-toggle-sudo")
+    (version "1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/renard/dired-toggle-sudo")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0ajj8d6k5in2hclcrqckinfh80ylddplva0ryfbkzsjkfq167cv2"))
+       (patches
+        (search-patches
+         "emacs-dired-toggle-sudo-emacs-26.patch"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/renard/dired-toggle-sudo")
+    (synopsis "Browse directory with @code{sudo} privileges")
+    (description "This package allows for the use of @code{dired} with
+@code{sudo} privileges.")
+    (license license:wtfpl2)))
+
 (define-public emacs-memoize
   (package
     (name "emacs-memoize")
@@ -8528,12 +8718,11 @@ the actual transformations.")
       (license license:gpl2+))))
 
 (define-public emacs-dired-hacks
-  (let ((commit "2c1234592aee91dcd9401bcd67213e6a4a464fd9")
+  (let ((commit "886befe113fae397407c804f72c45613d1d43535")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "emacs-dired-hacks")
-      (version (string-append "0.0.1-" revision "."
+      (version (git-version "0.0.1" revision commit))
-                              (string-take commit 7)))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -8542,7 +8731,7 @@ the actual transformations.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1g7mky41cahpryzj6frdgzdymknpqq7pidzfjj9304887kijmhj3"))))
+                  "1cvibg90ggyrivpjmcfprpi2fx7dpa68f8kzg08s88gw5ib75djl"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-dash" ,emacs-dash)
@@ -8553,7 +8742,9 @@ the actual transformations.")
       (synopsis
        "Collection of useful dired additions")
       (description
-       "Collection of Emacs dired mode additions:
+       "This package provides the following collection of Emacs dired mode
+additions:
+
 @itemize
 @item dired-avfs
 @item dired-columns
@@ -8623,6 +8814,32 @@ available key bindings that follow C-x (or as many as space allows given your
 settings).")
     (license license:gpl3+)))
 
+(define-public emacs-hercules
+  (let ((commit "3345904a0dab4c7a4d4478f0766f1d9f5d1bb501")
+        (revision "1"))
+    (package
+      (name "emacs-hercules")
+      (version (git-version "0.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.com/jjzmajic/hercules.el.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0cpq8h6l47nqhzch6snax5yrhxl8p4wn35q13ci35lj3iq8kmlk8"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-which-key" ,emacs-which-key)))
+      (home-page "https://gitlab.com/jjzmajic/hercules.el")
+      (synopsis "Call a chain of related commands without repeated prefix keys")
+      (description
+       "This package provides sticky-key-like functionality to obviate the
+need for repeated prefix-key sequences, and can reuse existing keymaps. The
+list of commands is displayed in a handy popup.")
+      (license license:gpl3+))))
+
 (define-public emacs-ws-butler
   (package
     (name "emacs-ws-butler")
@@ -10433,29 +10650,32 @@ as well as functions for navigating between these headings.")
     (license license:gpl3+)))
 
 (define-public emacs-org-super-agenda
-  (package
+  ;; emacs-org-sidebar depends on a newer commit than the latest release version.
-   (name "emacs-org-super-agenda")
+  (let ((commit "375bde4ca72494ac88a2a9738754f047fe45cc4e")
-   (version "1.1")
+        (revision "1"))
-   (source (origin
+    (package
-            (method git-fetch)
+      (name "emacs-org-super-agenda")
-            (uri (git-reference
+      (version (git-version "1.1.1" revision commit))
-                  (url "https://github.com/alphapapa/org-super-agenda")
+      (source (origin
-                  (commit version)))
+                (method git-fetch)
-            (file-name (git-file-name name version))
+                (uri (git-reference
-            (sha256
+                      (url "https://github.com/alphapapa/org-super-agenda")
-             (base32
+                      (commit commit)))
-              "0vzf91lsxnhwf52kvm8ycpf0wb9c8l91689vyhwgv4wz8q6cvjwp"))))
+                (file-name (git-file-name name version))
-   (build-system emacs-build-system)
+                (sha256
-   (propagated-inputs
+                 (base32
-    `(("emacs-org" ,emacs-org)
+                  "0hrwf02fqjm0d9gj146ax67ib76093qpqh7066dcxj2gy20625yj"))))
-      ("emacs-dash" ,emacs-dash)
+      (build-system emacs-build-system)
-      ("emacs-ht" ,emacs-ht)
+      (propagated-inputs
-      ("emacs-s" ,emacs-s)))
+       `(("emacs-org" ,emacs-org)
-   (home-page "https://github.com/alphapapa/org-super-agenda")
+         ("emacs-dash" ,emacs-dash)
-   (synopsis "Supercharged Org agenda")
+         ("emacs-ht" ,emacs-ht)
-   (description "This package allows items in the Org agenda to be grouped
+         ("emacs-s" ,emacs-s)))
+      (home-page "https://github.com/alphapapa/org-super-agenda")
+      (synopsis "Supercharged Org agenda")
+      (description "This package allows items in the Org agenda to be grouped
 into sections while preserving the structure imposed by any timestamps.")
-   (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-org-make-toc
   (package
@@ -11752,7 +11972,7 @@ downloading manager for Emacs.")
 (define-public emacs-helpful
   (package
     (name "emacs-helpful")
-    (version "0.16")
+    (version "0.17")
     (source
      (origin
        (method git-fetch)
@@ -11761,7 +11981,7 @@ downloading manager for Emacs.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1pzlx3galyryd3hd84hnd7r5s6yl9sdrfhy1s6dgz40glw41wmpr"))))
+        (base32 "0v2y0x9pwi08y2mgjjiw5brfb5haa7pbmy4540glw904ffxxcblj"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-elisp-refs" ,emacs-elisp-refs)
@@ -12676,6 +12896,29 @@ When @code{gac-automatically-push-p} is non-nil, it also tries to push to
 the current upstream.")
     (license license:gpl3+)))
 
+(define-public emacs-scroll-on-drag
+  (let ((commit "888abd04c34753b1fc4b2fe541bc004ebec5c996")
+        (revision "1"))
+    (package
+      (name "emacs-scroll-on-drag")
+      (version (git-version "0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.com/ideasman42/emacs-scroll-on-drag.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1si4hdqa3jw1inbyh3wb3i5i9grbms1nwky3vyk9zg7iznwm8a9p"))))
+      (build-system emacs-build-system)
+      (home-page "https://gitlab.com/ideasman42/emacs-scroll-on-drag")
+      (synopsis "Interactive scrolling")
+      (description "This package permits scrolling at increasing speeds based
+on drag distance.")
+      (license license:gpl3+))))
+
 (define-public emacs-company-restclient
   (package
     (name "emacs-company-restclient")
@@ -13692,12 +13935,11 @@ server with @code{M-x pinentry-start}.")
       (license license:gpl3+))))
 
 (define-public emacs-so-long
-  (let ((commit "3ebe97decdb5cbbfba82ca686e0ad2c7d2722b4a")
+  (let ((commit "cfae473b1bf65f78ddb015159e667ec0103d881c")
-        (version "1.0")
+        (revision "2"))
-        (revision "1"))
     (package
       (name "emacs-so-long")
-      (version (git-version version revision commit))
+      (version (git-version "1.0" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -13707,7 +13949,7 @@ server with @code{M-x pinentry-start}.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0fi71g5rsdsi978jz8406k8hvzgnssm9wxar8yqfhs97178r9s5m"))))
+           "0g943n5cl9lz5s7hszg6yvp10xd1xvd8mfgxyg0yckmp8fqkswin"))))
       (build-system emacs-build-system)
       (home-page "https://www.emacswiki.org/emacs/SoLong")
       (synopsis "Improve performance in files with long lines")
@@ -13744,12 +13986,13 @@ accept and reject GitHub pull requests.")
       (license license:gpl3+))))
 
 (define-public emacs-deadgrep
-  (let ((commit "caeb37b8d6ab83f0eba353d6bbb29678190d4419")
+  ;; We prefer a newer commit (four commits newer than release) because of a
-        (version "0.7")
+  ;; bugfix for globbing.
+  (let ((commit "329119c65126f7917d3910bc584f4191ba8f21ac")
         (revision "1"))
     (package
       (name "emacs-deadgrep")
-      (version (git-version version revision commit))
+      (version (git-version "0.8" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -13759,7 +14002,7 @@ accept and reject GitHub pull requests.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "158fqha8nilwfzmw15lcsq8b099j8wclzq303md0j4mfr2q2gfvs"))))
+           "0fxf7gq9sjfkgpdfqx10w3l3nd4rwa8kv9plyxk1fqacb3s5m6ai"))))
       (build-system emacs-build-system)
       (inputs
        `(("emacs-dash" ,emacs-dash)
@@ -14142,7 +14385,7 @@ buffers – other modes on the TODO list).
 (define-public emacs-magit-todos
   (package
     (name "emacs-magit-todos")
-    (version "1.2")
+    (version "1.3")
     (source
      (origin
        (method git-fetch)
@@ -14152,7 +14395,7 @@ buffers – other modes on the TODO list).
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "17a18gszbypz82bj36xbfyykc4s9rz83vwmpxvlf65svhd51c0nh"))))
+         "0gfm6wn2a4v5i9lfsvvin0kwpr9n96ddm3z4yf50jd3kg2igzry1"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-async" ,emacs-async)
@@ -16189,7 +16432,7 @@ previewed by scrolling up and down within a @code{dired} buffer.")
 (define-public emacs-counsel-etags
   (package
     (name "emacs-counsel-etags")
-    (version "1.8.4")
+    (version "1.8.7")
     (source
      (origin
        (method git-fetch)
@@ -16199,7 +16442,7 @@ previewed by scrolling up and down within a @code{dired} buffer.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "14my9jvxl26a5yn381h5pi5481y9d9gyk7wnxxd0s4sjc964c5h5"))))
+         "0vjcjspfrz1csnmfi6r7p7f070a496adxkqnsxwx1gx8cpylwp1g"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-ivy" ,emacs-ivy)))
@@ -16632,6 +16875,30 @@ provided.  Those alternative commands are and bound by default to their
 corresponding Evil keys.")
       (license license:expat))))
 
+(define-public emacs-evil-traces
+  (let ((commit "b41b7432b8110378c199a3d25af464083777f453")
+        (revision "1"))
+    (package
+      (name "emacs-evil-traces")
+      (version (git-version "0.0.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mamapanda/evil-traces.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0a15f2saynz9fws1h5s7py3cshsk4xs1kwgwj1m5rsin36g0j6hc"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-evil" ,emacs-evil)))
+      (home-page "https://github.com/mamapanda/evil-traces")
+      (synopsis "Visual hints for @code{evil-ex}")
+      (description "This package adds visual hints to certain @code{ex}
+commands in @code{evil-mode}.")
+      (license license:gpl3+))))
+
 (define-public emacs-xterm-color
   (let ((commit "a452ab38a7cfae97078062ff8885b5d74fd1e5a6")
         (version "1.8")
@@ -16846,6 +17113,29 @@ convert the resulting @code{.epub} to a @code{.mobi} file.  Needs a working
 zip utility (default is @code{zip}).")
     (license license:gpl3+)))
 
+(define-public emacs-ox-hugo
+  (package
+    (name "emacs-ox-hugo")
+    (version "0.8")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/kaushalmodi/ox-hugo.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "11h464cyc28ld0b0zridgm4drydc1qjxbm1y24zrwlkyqqjk6yr7"))))
+    (build-system emacs-build-system)
+    (home-page "https://ox-hugo.scripter.co")
+    (synopsis "Hugo markdown back-end for Org export engine")
+    (description
+     "Ox-hugo is an Org exporter backend that exports Org to Hugo-compatible
+Markdown, Blackfriday, and also generates the front-matter in TOML or YAML
+format.")
+    (license license:gpl3+)))
+
 (define-public emacs-ox-pandoc
   (package
     (name "emacs-ox-pandoc")
@@ -16926,3 +17216,28 @@ time.")
     (description "@code{mastodon.el} is an Emacs client for Mastodon, the
 federated microblogging social network.")
     (license license:gpl3+)))
+
+;; The last release tarball is for version 0.6.  We pick a commit close to
+;; version 0.6.10, which doesn't have a release tarball.
+(define-public emacs-ebdb
+  (let ((commit "2a87f5ed2a53e3a4e91e8c88ba5afc49f5e945df")
+        (revision "0"))
+    (package
+      (name "emacs-ebdb")
+      (version (git-version "0.6.10" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/girzel/ebdb.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0fidy7z0c86dpqiss97sg5s92fd3fj4bdl8pqqdgg2m00jx4mrjz"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/girzel/ebdb")
+      (synopsis "EIEIO port of BBDB, Emacs's contact-management package")
+      (description "EBDB is a contact management/addressbook package for
+Emacs.  It's a re-write of the Insidious Big Brother Database (BBDB) using
+Emacs Lisp's (relatively new) EIEIO object oriented libraries.")
+      (license license:gpl3+))))

gnu/packages/emulators.scm

@@ -119,8 +119,8 @@
 
 ;; Building from recent Git because the official 5.0 release no longer builds.
 (define-public dolphin-emu
-  (let ((commit "2c57e709d0f9e4010a4415de4192de887e37f187")
+  (let ((commit "24718c1a389e4f51db974575cd15c372485b92e2")
-        (revision "5"))
+        (revision "6"))
     (package
       (name "dolphin-emu")
       (version (git-version "5.0" revision commit))
@@ -146,7 +146,7 @@
              #t))
          (sha256
           (base32
-           "0aszfdfvs7yg4bmrd3qxwsiz7hx3mrj29f4aw86bz7h9j7hkh57f"))))
+           "1d92rhnw307j3m6swk6bycb8fyc7vw2hfgakd5hpsc4qw65vxfq8"))))
       (build-system cmake-build-system)
       (arguments
        '(#:tests? #f
@@ -244,12 +244,6 @@ turbo speed, networked multiplayer, and graphical enhancements.")
                (base32
                 "02i648i50dwicv1vaql15rccv4g8h5blf5g6inv67lrfxpbkvlf0"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (add-after
-                   'unpack 'autogen.sh
-                   (lambda _
-                     (invoke "sh" "autogen.sh"))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)))
@@ -1185,7 +1179,7 @@ play them on systems for which they were never designed!")
 (define-public mame
   (package
     (name "mame")
-    (version "0.211")
+    (version "0.212")
     (source
      (origin
        (method git-fetch)
@@ -1195,7 +1189,11 @@ play them on systems for which they were never designed!")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0gbxgncbzmmplijg0c1ibwsb87fbmfvs1kjflh002yyx8yvfw83z"))
+         "0p3zcb9l624dsy2gyv23ppp1k1iwd1vrg8cbn5v4fx1s44mx7f5c"))
+       (patches
+       ;; FIXME: Remove once 0.213 is out.  Applied upstream as
+       ;; 0b5b13cf1e28550b49c387dec93f9801f029e313.
+        (search-patches "mame-rapidjson-fix.patch"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled libraries.

gnu/packages/enchant.scm

@@ -33,7 +33,7 @@
 (define-public enchant
   (package
     (name "enchant")
-    (version "2.2.4")
+    (version "2.2.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/AbiWord/enchant/releases"
@@ -41,7 +41,7 @@
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1p6a3qmrh8bjzds6x7rg9da0ir44gg804jzkf634h39wsa4vdmpm"))))
+                "0iqwzs11i9fvqdxv5kn0svcn2mzymn657qf3j66lg8dx1nh4xkpz"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--disable-static"

gnu/packages/engineering.scm

@@ -11,6 +11,7 @@
 ;;; Copyright © 2018, 2019 Jonathan Brielmaier <jonathan.brielmaier@web.de>
 ;;; Copyright © 2018, 2019 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2019 Tim Stahel <swedneck@swedneck.xyz>
+;;; Copyright © 2019 Jovany Leandro G.C <bit4bit@riseup.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2062,3 +2063,49 @@ purpose circuit simulator and can perform DC and transient analyses, fourier
 analysis and AC analysis.  The engine is designed to do true mixed-mode
 simulation.")
     (license license:gpl3+)))
+
+(define-public cutter
+  (package
+    (name "cutter")
+    (version "1.8.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/radareorg/cutter")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "03f3cdckh51anx9gd1b0ndb2fg7061hqngvygf32ky29mm2m2lyv"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (radare2 (assoc-ref inputs "radare2")))
+               ;; fix pkg-config detection ./src/lib_radare2.pri:PREFIX=/usr/lib
+               ;; override `qmake PREFIX=`
+               (substitute* "./src/lib_radare2.pri"
+                 (("PREFIX") "R2PREFIX")
+                 (("R2PREFIX=/usr") (string-append "R2PREFIX=" radare2)))
+               (invoke "qmake"
+                       (string-append "PREFIX=" out)
+                       "./src/Cutter.pro")))))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("qtbase" ,qtbase)
+       ("qtsvg" ,qtsvg)
+       ("openssl" ,openssl)
+       ("radare2" ,radare2)))
+    (home-page "https://github.com/radareorg/cutter")
+    (synopsis "GUI for radare2 reverse engineering framework")
+    (description "Cutter is a GUI for radare2 reverse engineering framework.
+Its goal is making an advanced andcustomizable reverse-engineering platform
+while keeping the user experience at mind.  Cutter is created by reverse
+engineers for reverse engineers.")
+    (license (list license:cc-by-sa3.0  ;the "Iconic" icon set
+                   license:gpl3+))))    ;everything else

gnu/packages/finance.scm

@@ -13,6 +13,7 @@
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2019 Tanguy Le Carrour <tanguy@bioneland.org>
+;;; Copyright © 2019 Martin Becze <mjbecze@riseup.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -38,6 +39,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system python)
   #:use-module (guix build-system glib-or-gtk)
+  #:use-module (guix build-system go)
   #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
@@ -357,7 +359,7 @@ do so.")
 (define-public electrum
   (package
     (name "electrum")
-    (version "3.3.6")
+    (version "3.3.8")
     (source
      (origin
        (method url-fetch)
@@ -365,7 +367,7 @@ do so.")
                            version "/Electrum-"
                            version ".tar.gz"))
        (sha256
-        (base32 "0am5ki3z0yvhrz16vp2jjy5fkxxqph0mj9qqpbw3kpql65shykwz"))
+        (base32 "1g00cj1pmckd4xis8r032wmraiv3vd3zc803hnyxa2bnhj8z3bg2"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -715,9 +717,6 @@ the Monero GUI client.")
 Ledger Nano as a hardware SSH/GPG agent.")
     (license license:lgpl3)))
 
-(define-public python2-trezor-agent
-  (package-with-python2 python-trezor-agent))
-
 (define-public python-mnemonic
   (package
     (name "python-mnemonic")
@@ -813,9 +812,6 @@ Ledger Blue/Nano S.")
 TREZOR Hardware Wallet.")
     (license license:lgpl3)))
 
-(define-public python2-trezor
-  (package-with-python2 python-trezor))
-
 (define-public python-keepkey
   (package
     (name "python-keepkey")
@@ -965,7 +961,7 @@ Luhn and family of ISO/IEC 7064 check digit algorithms. ")
 (define-public python-duniterpy
   (package
     (name "python-duniterpy")
-    (version "0.54.3")
+    (version "0.55.1")
     (source
      (origin
        (method git-fetch)
@@ -976,7 +972,7 @@ Luhn and family of ISO/IEC 7064 check digit algorithms. ")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1k3rpfc9zxj9z50cr4zjfyzdla9ap5mj1v1rlcriqmflgb5cmiba"))))
+         "07zsbbkzmnvyv5v0vw2d42vw3ar4iqhlidy9376ysk4ldlj1igf7"))))
     (build-system python-build-system)
     (arguments
      ;; Tests fail with "AttributeError: module 'attr' has no attribute 's'".
@@ -1023,7 +1019,7 @@ main features are:
 (define-public silkaj
   (package
     (name "silkaj")
-    (version "0.7.2")
+    (version "0.7.3")
     (source
      (origin
        (method git-fetch)
@@ -1033,7 +1029,7 @@ main features are:
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "059k2kil2l8jcm4wp86w1z7y8p26rww7d3l5fzds0qq2dzvkvzgs"))))
+         "0yk2574yb0d0k0rg7qf0pkmjidblsad04x8hhqpy9k80rvgjcr5w"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f))                    ;no test
@@ -1095,3 +1091,26 @@ financial years, budget estimates, bankcard management and other
 information.")
     (home-page "http://grisbi.org")
     (license license:gpl2+)))
+
+(define-public trezord
+  (package
+    (name "trezord")
+    (version "2.0.17")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/trezor/trezord-go.git")
+              (commit (string-append "v" version))))
+       (sha256
+        (base32
+         "0nqzpq0i3crh0i4r1cppja5sn3rwi1fv9afxzwzv63096x5l30a7"))
+       (file-name (git-file-name name version))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/trezor/trezord-go"))
+    (home-page "https://trezor.io")
+    (synopsis "Trezor Communication Daemon aka Trezor Bridge (written in Go)")
+    (description "This allows a Trezor hardware wallet to communicate to the
+Trezor wallet.")
+    (license license:lgpl3+)))

gnu/packages/fonts.scm

@@ -644,7 +644,7 @@ for use at smaller text sizes")))
 (define-public font-gnu-unifont
   (package
     (name "font-gnu-unifont")
-    (version "12.1.02")
+    (version "12.1.03")
     (source
      (origin
        (method url-fetch)
@@ -654,7 +654,7 @@ for use at smaller text sizes")))
              (string-append "mirror://gnu/unifont/unifont-"
                             version "/unifont-" version ".tar.gz")))
        (sha256
-        (base32 "12wdxnlyz5gl5d7h6pazcz8d7h81fwkng1xrayxsgrzh6bqdq4p8"))))
+        (base32 "10mr3ax19v5pa6a791fk2j3k45fpa8n5r36kq9gs8lk95wfnxmf1"))))
     (build-system gnu-build-system)
     (outputs '("out"   ; TrueType version
                "pcf"   ; PCF (bitmap) version

gnu/packages/fontutils.scm

@@ -637,7 +637,7 @@ definitions.")
 opentype fonts.  You can save fonts in many different outline formats, and
 generate bitmaps.")
    (license license:gpl3+)
-   (home-page "https://fontforge.github.io/en-US/")))
+   (home-page "https://fontforge.github.io")))
 
 (define-public python2-ufolib
   (package

gnu/packages/freedesktop.scm

@@ -723,7 +723,7 @@ multiplexer to the KMS/DRM Linux kernel devices.")
 (define-public exempi
   (package
     (name "exempi")
-    (version "2.5.0")
+    (version "2.5.1")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -731,7 +731,7 @@ multiplexer to the KMS/DRM Linux kernel devices.")
                    name "-" version ".tar.bz2"))
              (sha256
               (base32
-               "06vi7dc2gappwqm3xpfyy5ihxq14bmvj3bd47yk482jlq0jgr0nw"))))
+               "1j4vx054l1c2cggw4aka4iw48jkcf68qk5y064pbqw1k3ddks2qh"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags (list (string-append "--with-boost="
@@ -741,7 +741,7 @@ multiplexer to the KMS/DRM Linux kernel devices.")
     (inputs
      `(("expat" ,expat)
        ("zlib" ,zlib)))
-    (home-page "https://wiki.freedesktop.org/libopenraw/Exempi")
+    (home-page "https://libopenraw.freedesktop.org/exempi/")
     (synopsis "XMP metadata handling library")
     (description "Exempi is an implementation of the Extensible Metadata
 Platform (@dfn{XMP}), which enables embedding metadata in PDF and image

gnu/packages/games.scm

@@ -4974,6 +4974,10 @@ Crowther & Woods, its original authors, in 1995.  It has been known as
        ("luajit" ,luajit)))
     (arguments
      `(#:make-flags '("CC=gcc" "config=release")
+       ;; XXX: Building in parallel occasionally causes this build failure:
+       ;;   ../src/luajit2/src/host/buildvm.c:73:10: fatal error: buildvm_arch.h:
+       ;;   No such file or directory
+       #:parallel-build? #f
        #:phases (modify-phases %standard-phases
                   (delete 'bootstrap)
                   (replace 'configure

gnu/packages/gl.scm

@@ -64,14 +64,14 @@
 (define-public glu
   (package
     (name "glu")
-    (version "9.0.0")
+    (version "9.0.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "ftp://ftp.freedesktop.org/pub/mesa/glu/glu-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0r72yyhj09x3krn3kn629jqbwyq50ji8w5ri2pn6zwrk35m4g1s3"))))
+                "1xqhk9bn10nbvffw3r4p4rjslwz1l7gaycc0x2pqkr2irp7q9x7n"))))
     (build-system gnu-build-system)
     (propagated-inputs
      `(("mesa" ,mesa))) ; according to glu.pc
@@ -227,7 +227,7 @@ also known as DXTn or DXTC) for Mesa.")
 (define-public mesa
   (package
     (name "mesa")
-    (version "19.1.1")
+    (version "19.1.4")
     (source
       (origin
         (method url-fetch)
@@ -239,7 +239,7 @@ also known as DXTn or DXTC) for Mesa.")
                                   version "/mesa-" version ".tar.xz")))
         (sha256
          (base32
-          "10amy5sdmpjbskr3xazgk0jyli8xpgi0y1nsmjr76hx8nhb4n4bj"))
+          "1yvb7ja09i36zjifpyrf8jmbm9z0wqs2w3x8dlmxkkzdv6knilm6"))
         (patches
          (search-patches "mesa-skip-disk-cache-test.patch"))))
     (build-system meson-build-system)
@@ -291,7 +291,7 @@ also known as DXTn or DXTC) for Mesa.")
               ;; TODO: Fix svga driver for aarch64 and armhf.
               '("-Dgallium-drivers=etnaviv,freedreno,nouveau,r300,r600,swrast,tegra,v3d,vc4,virgl"))
              (_
-              '("-Dgallium-drivers=nouveau,r300,r600,radeonsi,svga,swrast,virgl")))
+              '("-Dgallium-drivers=iris,nouveau,r300,r600,radeonsi,svga,swrast,virgl")))
          ;; Enable various optional features.  TODO: opencl requires libclc,
          ;; omx requires libomxil-bellagio
          "-Dplatforms=x11,drm,surfaceless,wayland"
@@ -308,11 +308,8 @@ also known as DXTn or DXTC) for Mesa.")
 
          ;; Enable Vulkan on i686-linux and x86-64-linux.
          ,@(match (%current-system)
-             ("x86_64-linux"
+             ((or "i686-linux" "x86_64-linux")
               '("-Dvulkan-drivers=intel,amd"))
-             ;; TODO: Fix intel driver on i686-linux.
-             ("i686-linux"
-              '("-Dvulkan-drivers=amd"))
              (_
               '("-Dvulkan-drivers=auto")))
 

gnu/packages/gnome.scm

@@ -38,6 +38,7 @@
 ;;; Copyright © 2019 Florian Pelz <pelzflorian@pelzflorian.de>
 ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2019 Jelle Licht <jlicht@fsfe.org>
+;;; Copyright © 2019 Jonathan Frederickson <jonathan@terracrypt.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -5538,6 +5539,57 @@ Compatible with Cisco VPN concentrators configured to use IPsec.")
     (license license:gpl2+)
     (properties `((upstream-name . "NetworkManager-vpnc")))))
 
+(define-public network-manager-openconnect
+  (package
+    (name "network-manager-openconnect")
+    (version "1.2.6")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://gnome/sources/NetworkManager-openconnect/"
+                    (version-major+minor version)
+                    "/NetworkManager-openconnect-" version ".tar.xz"))
+              (sha256
+               (base32
+                "0nlp290nkawc4wqm978n4vhzg3xdqi8kpjjx19l855vab41rh44m"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags '("--enable-absolute-paths" "--localstatedir=/var")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'configure 'patch-path
+           (lambda* (#:key inputs outputs #:allow-other-keys #:rest args)
+             (let* ((openconnect (string-append (assoc-ref inputs "openconnect")
+                                         "/sbin/openconnect"))
+                    (modprobe (string-append (assoc-ref inputs "kmod")
+                                             "/bin/modprobe"))
+                    (pretty-ovpn (string-append "\"" openconnect "\"")))
+               (substitute* "src/nm-openconnect-service.c"
+                 (("\"/usr/local/sbin/openconnect\"") pretty-ovpn)
+                 (("\"/usr/sbin/openconnect\"") pretty-ovpn)
+                 (("/sbin/modprobe") modprobe)))
+             #t)))))
+    (native-inputs
+     `(("intltool" ,intltool)
+       ("network-manager-applet" ,network-manager-applet) ;for libnma
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("gcr" ,gcr)
+       ("gtk+" ,gtk+)
+       ("kmod" ,kmod)
+       ("libsecret" ,libsecret)
+       ("libxml2" ,libxml2)
+       ("network-manager" ,network-manager)
+       ("openconnect" ,openconnect)))
+    (home-page "https://wiki.gnome.org/Projects/NetworkManager/VPN")
+    (synopsis "OpenConnect plug-in for NetworkManager")
+    (description
+     "This extension of NetworkManager allows it to take care of connections
+to @acronym{VPNs, virtual private networks} via OpenConnect, an open client for
+Cisco's AnyConnect SSL VPN.")
+    (license license:gpl2+)
+    (properties `((upstream-name . "NetworkManager-openconnect")))))
+
 (define-public mobile-broadband-provider-info
   (package
     (name "mobile-broadband-provider-info")
@@ -8175,15 +8227,18 @@ advanced image management tool")
     (inputs
      `(("cairo" ,cairo)
        ("gobject-introspection" ,gobject-introspection)
+       ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
        ("python2-pycairo" ,python2-pycairo)
        ("python2-pygobject" ,python2-pygobject)
        ("python2-psutil" ,python2-psutil)
        ("vte" ,vte)))
-    (propagated-inputs
-     ;; Terminator refuses to start when these are not present.
-     `(("gsettings-desktop-schemas" ,gsettings-desktop-schemas)))
     (arguments
-     `(#:python ,python-2                          ;Python 3 not supported
+     `(#:python ,python-2                          ; Python 3 isn't supported
+       #:imported-modules ((guix build glib-or-gtk-build-system)
+                           ,@%python-build-system-modules)
+       #:modules ((guix build python-build-system)
+                  ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
+                  (guix build utils))
        #:phases
        (modify-phases %standard-phases
          (add-after
@@ -8194,10 +8249,60 @@ advanced image management tool")
               (wrap-program prog
                 `("PYTHONPATH" = (,(getenv "PYTHONPATH")))
                 `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH"))))
-              #t))))))
+              #t)))
+         (add-after 'wrap-program 'glib-or-gtk-wrap
+           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
     (home-page "https://gnometerminator.blogspot.com/")
     (synopsis "Store and run multiple GNOME terminals in one window")
     (description
      "Terminator allows you to run multiple GNOME terminals in a grid and
 +tabs, and it supports drag and drop re-ordering of terminals.")
     (license license:gpl2)))
+
+(define-public libhandy
+  (package
+    (name "libhandy")
+    (version "0.0.10")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://source.puri.sm/Librem5/libhandy")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1702hbdqhfpgw0c4vj2ag08vgl83byiryrbngbq11b9azmj3jhzs"))))
+    (build-system meson-build-system)
+    (arguments
+     `(#:configure-flags
+       '("-Dglade_catalog=disabled"
+         "-Dgtk_doc=true")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-broken-test
+           (lambda _
+             ;; This test fails for unknown reasons
+             (substitute* "tests/meson.build"
+               (("'test-dialog',") ""))
+             #t))
+         (add-before 'check 'pre-check
+           (lambda _
+             ;; Tests require a running X server.
+             (system "Xvfb :1 &")
+             (setenv "DISPLAY" ":1")
+             #t)))))
+    (inputs
+     `(("gtk+" ,gtk+)))
+    (native-inputs
+     `(("glib:bin" ,glib "bin")
+       ("gobject-introspection" ,gobject-introspection) ; for g-ir-scanner
+       ("vala" ,vala)
+       ("gtk-doc" ,gtk-doc)
+       ("pkg-config" ,pkg-config)
+       ("gettext" ,gettext-minimal)
+       ("xorg-server" ,xorg-server)))
+    (home-page "https://source.puri.sm/Librem5/libhandy")
+    (synopsis "Library full of GTK+ widgets for mobile phones")
+    (description "The aim of the handy library is to help with developing user
+intefaces for mobile devices using GTK+.")
+    (license license:lgpl2.1+)))

gnu/packages/golang.scm

@@ -1218,8 +1218,8 @@ for a variety of protocols to proxy network data.")
       (license license:bsd-3))))
 
 (define-public go-golang-org-x-sys-unix
-  (let ((commit "5ed2794edfdc1c54dfb61d619c5944285f35d444")
+  (let ((commit "04f50cda93cbb67f2afa353c52f342100e80e625")
-        (revision "3"))
+        (revision "4"))
     (package
       (name "go-golang-org-x-sys-unix")
       (version (git-version "0.0.0" revision commit))
@@ -1231,7 +1231,7 @@ for a variety of protocols to proxy network data.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1qy8hmv5nwpcywk7sh1pg0s32jwpd4ykh492xzl4mmxy8galwsr5"))))
+                  "0hmfsz9y1ingwsn482hlzzmzs7kr3cklm0ana0mbdk70isw2bxnw"))))
       (build-system go-build-system)
       (arguments
        `(#:import-path "golang.org/x/sys/unix"
@@ -3617,7 +3617,7 @@ error handling primitives in Go.")
 (define-public go-github-com-maruel-panicparse
   (package
     (name "go-github-com-maruel-panicparse")
-    (version "1.2.1")
+    (version "1.3.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3626,7 +3626,7 @@ error handling primitives in Go.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "05hf68ifb7ww4rpmxyywbj9r0kyap45p1273ncq4qy2ydv042l8j"))))
+                "13qkn7f64yln8jdmma37h6ra4c7anxkp3vfgvfyb6lb07dpr1ibq"))))
     (build-system go-build-system)
     (arguments
      '(#:import-path "github.com/maruel/panicparse"))

gnu/packages/graphics.scm

@@ -160,9 +160,7 @@
      "Blender is a 3D graphics creation suite.  It supports the entirety of
 the 3D pipeline—modeling, rigging, animation, simulation, rendering,
 compositing and motion tracking, even video editing and game creation.  The
-application can be customized via its API for Python scripting.
+application can be customized via its API for Python scripting.")
-
-WARNING: This is a release candidate build of Blender.")
     (license license:gpl2+)))
 
 (define-public blender-2.79

gnu/packages/gtk.scm

@@ -729,9 +729,7 @@ application suites.")
 (define-public gtk+
   (package (inherit gtk+-2)
    (name "gtk+")
-   ;; NOTE: When updating the version of 'gtk+', the hash of 'mate-themes' in
+   (version "3.24.10")
-   ;;       mate.scm will also need to be updated.
-   (version "3.24.9")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnome/sources/" name "/"
@@ -739,7 +737,7 @@ application suites.")
                                 name "-" version ".tar.xz"))
             (sha256
              (base32
-              "0dg6jf2763sp740ls6b5y86b5b9zhz3zj0sbmar2xpws1lkv0zjp"))
+              "00qvq1r96ikdalv7xzgng1kad9i0rcahqk01gwhxl3xrw83z3a1m"))
             (patches (search-patches "gtk3-respect-GUIX_GTK3_PATH.patch"
                                      "gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch"))))
    (outputs '("out" "bin" "doc"))

gnu/packages/guile-xyz.scm

@@ -907,27 +907,30 @@ tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
 (define-public guile-email
   (package
     (name "guile-email")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
-             "https://git.systemreboot.net/guile-email/snapshot/guile-email-"
+             "https://guile-email.systemreboot.net/releases/guile-email-"
-             version ".tar.xz"))
+             version ".tar.lz"))
        (sha256
         (base32
-         "0p2v8q2kkz8m6vf2rsjvz3dj1mvnx7dxakjf72dwkndbgk3rp79f"))))
+         "05pm0rwdxhjdlpmvhn0kyfslph6j5m1gv76givs0hshb30nirl2x"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("autoconf" ,autoconf)
+       ("lzip" ,lzip)))
-       ("automake" ,automake)))
     (inputs
      `(("guile" ,guile-2.2)))
-    (home-page "https://git.systemreboot.net/guile-email")
+    (arguments
+     '(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ; to prevent guild warnings
+    (home-page "https://guile-email.systemreboot.net")
     (synopsis "Guile email parser")
-    (description "This package provides an email parser written in pure
+    (description "guile-email is a collection of email utilities implemented
-Guile.")
+in pure guile.  It supports parsing MIME (Multipurpose Internet Mail
+Extensions) compliant email messages and reading emails from the mbox
+format.")
     (license license:agpl3+)))
 
 (define-public guile-debbugs-next

gnu/packages/guile.scm

@@ -261,29 +261,27 @@ without requiring the source code to be rewritten.")
 
 (define-public guile-next
   ;; This is the upcoming Guile 3.0, with JIT support.
-  (let ((commit "6f3357b0df64c4be17e72079864c09a542f1c779")
+  (package
-        (revision "1"))
+    (inherit guile-2.2)
-    (package
+    (name "guile-next")
-      (inherit guile-2.2)
+    (version "2.9.3")
-      (name "guile-next")
+    (source (origin
-      (version "2.9.2")
+              (inherit (package-source guile-2.2))
-      (source (origin
+              (uri (string-append "ftp://alpha.gnu.org/gnu/guile/guile-"
-                (inherit (package-source guile-2.2))
+                                  version ".tar.xz"))
-                (uri (string-append "ftp://alpha.gnu.org/gnu/guile/guile-"
+              (sha256
-                                    version ".tar.xz"))
+               (base32
-                (sha256
+                "14990wcpysgw58kij03wbgiggmi5z94jmy7wdcqnn6ny7cimkkgr"))))
-                 (base32
+    (native-search-paths
-                  "1w358df2wmcyzk2ziqrj2zhwqisaqraqfa3008ay23nf1a7bw0z4"))))
+     (list (search-path-specification
-      (native-search-paths
+            (variable "GUILE_LOAD_PATH")
-       (list (search-path-specification
+            (files '("share/guile/site/3.0")))
-              (variable "GUILE_LOAD_PATH")
+           (search-path-specification
-              (files '("share/guile/site/3.0")))
+            (variable "GUILE_LOAD_COMPILED_PATH")
-             (search-path-specification
+            (files '("lib/guile/3.0/site-ccache"
-              (variable "GUILE_LOAD_COMPILED_PATH")
+                     "share/guile/site/3.0")))))
-              (files '("lib/guile/3.0/site-ccache"
+    (properties '((ftp-server . "alpha.gnu.org")
-                       "share/guile/site/3.0")))))
+                  (upstream-name . "guile")))))
-      (properties '((ftp-server . "alpha.gnu.org")
-                    (upstream-name . "guile"))))))
 
 (define (make-guile-readline guile)
   (package

gnu/packages/haskell-apps.scm

@@ -6,6 +6,7 @@
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
+;;; Copyright © 2019 Kyle Meyer <kyle@kyleam.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -142,7 +143,7 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
 (define-public git-annex
   (package
     (name "git-annex")
-    (version "6.20180926")
+    (version "7.20190708")
     (source
      (origin
        (method url-fetch)
@@ -150,15 +151,20 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
                            "git-annex/git-annex-" version ".tar.gz"))
        (sha256
         (base32
-         "1251rj8h63y30sfqk0zh670yhz14p256y59n3590pg015pf3575d"))))
+         "18s563swrp8mx479995pdhhmn40y3xwlbm1z3w63qsnjqmj7zlij"))))
     (build-system haskell-build-system)
     (arguments
      `(#:configure-flags
        '("--flags=-Android -Assistant -Pairing -S3 -Webapp -WebDAV")
        #:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'patch-shell
+         (add-before 'configure 'patch-shell-for-tests
            (lambda _
+             ;; Shell.hs defines "/bin/sh" that is used in Git hooks.  We
+             ;; shouldn't patch hooks with Guix's current bash because the
+             ;; hooks can exist after that bash is garbage collected, but
+             ;; let's temporarily patch it so that we can run the tests.
+             (copy-file "Utility/Shell.hs" "/tmp/Shell.hs")
              (substitute* "Utility/Shell.hs"
                (("/bin/sh") (which "sh")))
              #t))
@@ -192,6 +198,11 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
                (symlink "git-annex" "git-annex-shell"))
              (invoke "git-annex" "test")
              #t))
+         (add-after 'check 'unpatch-shell-and-rebuild
+           (lambda args
+             ;; Undo `patch-shell-for-tests'.
+             (copy-file "/tmp/Shell.hs" "Utility/Shell.hs")
+             (apply (assoc-ref %standard-phases 'build) args)))
          (add-after 'install 'install-symlinks
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -208,6 +219,7 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
        ("ghc-bloomfilter" ,ghc-bloomfilter)
        ("ghc-byteable" ,ghc-byteable)
        ("ghc-case-insensitive" ,ghc-case-insensitive)
+       ("ghc-concurrent-output" ,ghc-concurrent-output)
        ("ghc-crypto-api" ,ghc-crypto-api)
        ("ghc-cryptonite" ,ghc-cryptonite)
        ("ghc-data-default" ,ghc-data-default)

gnu/packages/haskell-check.scm

@@ -811,7 +811,7 @@ implementations of cryptographic ciphers.")
          "0xz10ycdm5vk9nrcym1fi83k19frfwqz18bz8bnpzwvaj0j41yfj"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-ansi-terminal" ,ghc-ansi-terminal-0.8)
+     `(("ghc-ansi-terminal" ,ghc-ansi-terminal)
        ("ghc-async" ,ghc-async)
        ("ghc-concurrent-output" ,ghc-concurrent-output)
        ("ghc-exceptions" ,ghc-exceptions)

gnu/packages/haskell-crypto.scm

@@ -25,6 +25,8 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages haskell)
   #:use-module (gnu packages haskell-check)
+  #:use-module (gnu packages haskell-xyz)
+  #:use-module (gnu packages tls)
   #:use-module (guix build-system haskell)
   #:use-module (guix download)
   #:use-module ((guix licenses) #:prefix license:)
@@ -775,3 +777,64 @@ Ephemeral (Elliptic curve and regular) Diffie Hellman key exchanges, and many
 extensions.")
     (license license:bsd-3)))
 
+(define-public ghc-hsopenssl
+  (package
+    (name "ghc-hsopenssl")
+    (version "0.11.4.15")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "HsOpenSSL/HsOpenSSL-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0idmak6d8mpbxphyq9hkxkmby2wnzhc1phywlgm0zw6q47pwxgff"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-network" ,ghc-network)
+       ("openssl" ,openssl)))
+    (arguments
+     `(#:cabal-revision
+       ("1" "0bkcw2pjfgv1bhgkrpncvwq9czfr7cr4ak14n0v8c2y33i33wk5z")))
+    (home-page "https://github.com/vshabanov/HsOpenSSL")
+    (synopsis "Partial OpenSSL binding for Haskell")
+    (description "HsOpenSSL is an OpenSSL binding for Haskell.  It can
+generate RSA and DSA keys, read and write PEM files, generate message
+digests, sign and verify messages, encrypt and decrypt messages.  It has
+also some capabilities of creating SSL clients and servers.  This
+package is in production use by a number of Haskell based systems and
+stable.  You may also be interested in the tls package,
+@uref{http://hackage.haskell.org/package/tls}, which is a pure Haskell
+implementation of SSL.")
+    (license license:public-domain)))
+
+(define-public ghc-openssl-streams
+  (package
+    (name "ghc-openssl-streams")
+    (version "1.2.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "openssl-streams/openssl-streams-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0pwghr7ygv59k572xsj1j97rilkbjz66qaiyj0ra2wfg6pl70wfw"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-hsopenssl" ,ghc-hsopenssl)
+       ("ghc-io-streams" ,ghc-io-streams)
+       ("ghc-network" ,ghc-network)))
+    (native-inputs
+     `(("ghc-hunit" ,ghc-hunit)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))
+    (arguments
+     `(#:cabal-revision
+       ("2" "1004kgdryflpkp19dv4ikilhcn0xbfc5dsp6v3ib34580pcfj7wy")))
+    (home-page "http://hackage.haskell.org/package/openssl-streams")
+    (synopsis "OpenSSL network support for io-streams")
+    (description "This library contains io-streams routines for secure
+networking using OpenSSL (by way of HsOpenSSL).")
+    (license license:bsd-3)))

gnu/packages/haskell-web.scm

@@ -28,6 +28,7 @@
   #:use-module (gnu packages haskell)
   #:use-module (gnu packages haskell-check)
   #:use-module (gnu packages haskell-crypto)
+  #:use-module (gnu packages haskell-xyz)
   #:use-module (guix build-system haskell)
   #:use-module (guix download)
   #:use-module ((guix licenses) #:prefix license:)
@@ -1294,3 +1295,171 @@ derivations of regular expressions.")
      "The Haskell XML Toolbox bases on the ideas of HaXml and HXML, but
 introduces a more general approach for processing XML with Haskell.")
     (license license:expat)))
+
+(define-public ghc-http-common
+  (package
+    (name "ghc-http-common")
+    (version "0.8.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "http-common/http-common-" version ".tar.gz"))
+       (sha256
+        (base32
+         "14s5a178sb2vm5k00rs21760mds5dz2gs10k9iyn22h01mxyf599"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-base64-bytestring" ,ghc-base64-bytestring)
+       ("ghc-blaze-builder" ,ghc-blaze-builder)
+       ("ghc-case-insensitive" ,ghc-case-insensitive)
+       ("ghc-network" ,ghc-network)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)))
+    (home-page "https://github.com/afcowie/http-streams/")
+    (synopsis "Common types for HTTP clients and servers")
+    (description "Base types used by a variety of HTTP clients and
+servers.  See http-streams @code{Network.Http.Client} or pipes-http
+@code{Pipes.Http.Client} for full documentation.  You can import
+@code{Network.Http.Types} if you like, but both http-streams and
+pipes-http re-export this package's types and functions.")
+    (license license:bsd-3)))
+
+(define-public ghc-http-streams
+  (package
+    (name "ghc-http-streams")
+    (version "0.8.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "http-streams/http-streams-" version ".tar.gz"))
+       (sha256
+        (base32
+         "18vxd35n7s3z4gjvad94bknc8z1w9d7ccgphnhsxlz5cackizmxq"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-attoparsec" ,ghc-attoparsec)
+       ("ghc-base64-bytestring" ,ghc-base64-bytestring)
+       ("ghc-blaze-builder" ,ghc-blaze-builder)
+       ("ghc-case-insensitive" ,ghc-case-insensitive)
+       ("ghc-io-streams" ,ghc-io-streams)
+       ("ghc-hsopenssl" ,ghc-hsopenssl)
+       ("ghc-openssl-streams" ,ghc-openssl-streams)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-aeson" ,ghc-aeson)
+       ("ghc-http-common" ,ghc-http-common)
+       ("ghc-network-uri" ,ghc-network-uri)
+       ("ghc-network" ,ghc-network)))
+    (arguments
+     `(#:tests? #f)) ; tests rely on an outdated version of snap-server
+    (home-page "https://github.com/afcowie/http-streams/")
+    (synopsis "HTTP client using io-streams")
+    (description "An HTTP client using the Snap Framework's io-streams
+library to handle the streaming IO.  The API is optimized for ease of
+use for the rather common case of code needing to query web services and
+deal with the result.")
+    (license license:bsd-3)))
+
+(define-public ghc-snap-core
+  (package
+    (name "ghc-snap-core")
+    (version "1.0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "snap-core/snap-core-" version ".tar.gz"))
+       (sha256
+        (base32
+         "136q7l4hd5yn5hb507q1ziqx124ma1lkzh5dx0n150p8dx3rhhsc"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-old-locale" ,ghc-old-locale)
+       ("ghc-hunit" ,ghc-hunit)
+       ("ghc-attoparsec" ,ghc-attoparsec)
+       ("ghc-bytestring-builder" ,ghc-bytestring-builder)
+       ("ghc-case-insensitive" ,ghc-case-insensitive)
+       ("ghc-lifted-base" ,ghc-lifted-base)
+       ("ghc-io-streams" ,ghc-io-streams)
+       ("ghc-hashable" ,ghc-hashable)
+       ("ghc-monad-control" ,ghc-monad-control)
+       ("ghc-random" ,ghc-random)
+       ("ghc-readable" ,ghc-readable)
+       ("ghc-regex-posix" ,ghc-regex-posix)
+       ("ghc-transformers-base" ,ghc-transformers-base)
+       ("ghc-unix-compat" ,ghc-unix-compat)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-vector" ,ghc-vector)
+       ("ghc-network-uri" ,ghc-network-uri)
+       ("ghc-network" ,ghc-network)))
+    (native-inputs
+     `(("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-parallel" ,ghc-parallel)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
+       ("ghc-zlib" ,ghc-zlib)))
+    (arguments
+     `(#:cabal-revision
+       ("3" "0wlhn33r7c9g7j23y006ddq9d87lkmianvvfrbl8jd8mvjvj2gfa")))
+    (home-page "http://snapframework.com/")
+    (synopsis "Haskell Web Framework (core interfaces and types)")
+    (description "Snap is a simple and fast web development framework
+and server written in Haskell.  For more information, you can visit the
+Snap project website at @uref{http://snapframework.com/}.  This library
+contains the core definitions and types for the Snap framework.")
+    (license license:bsd-3)))
+
+(define-public ghc-snap-server
+  (package
+    (name "ghc-snap-server")
+    (version "1.1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "snap-server/snap-server-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0vvw9n8xs272qdlrf3dxhnva41zh3awi7pf022rrjj75lj8a77i4"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-attoparsec" ,ghc-attoparsec)
+       ("ghc-blaze-builder" ,ghc-blaze-builder)
+       ("ghc-bytestring-builder" ,ghc-bytestring-builder)
+       ("ghc-case-insensitive" ,ghc-case-insensitive)
+       ("ghc-clock" ,ghc-clock)
+       ("ghc-io-streams" ,ghc-io-streams)
+       ("ghc-io-streams-haproxy" ,ghc-io-streams-haproxy)
+       ("ghc-lifted-base" ,ghc-lifted-base)
+       ("ghc-network" ,ghc-network)
+       ("ghc-old-locale" ,ghc-old-locale)
+       ("ghc-snap-core" ,ghc-snap-core)
+       ("ghc-unix-compat" ,ghc-unix-compat)
+       ("ghc-vector" ,ghc-vector)))
+    (native-inputs
+     `(("ghc-base16-bytestring" ,ghc-base16-bytestring)
+       ("ghc-monad-control" ,ghc-monad-control)
+       ("ghc-random" ,ghc-random)
+       ("ghc-threads" ,ghc-threads)
+       ("ghc-hunit" ,ghc-hunit)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-http-streams" ,ghc-http-streams)
+       ("ghc-http-common" ,ghc-http-common)
+       ("ghc-parallel" ,ghc-parallel)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
+    (arguments
+     `(#:cabal-revision
+       ("3" "0a9d3nqb5rvgm25nak68lp6yj9m6cwhbgdbg5l7ib5i2czcg7yjh")))
+    (home-page "http://snapframework.com/")
+    (synopsis "Web server for the Snap Framework")
+    (description "Snap is a simple and fast web development framework
+and server written in Haskell.  For more information, you can visit the
+Snap project website at @uref{http://snapframework.com/}.  The Snap HTTP
+server is a high performance web server library written in Haskell.
+Together with the snap-core library upon which it depends, it provides a
+clean and efficient Haskell programming interface to the HTTP
+protocol.")
+    (license license:bsd-3)))

gnu/packages/haskell-xyz.scm

@@ -0,0 +1,276 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Robert Vollmert <rob@vllmrt.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages haskell-xyz)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages haskell)
+  #:use-module (gnu packages haskell-check)
+  #:use-module (guix build-system haskell)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages))
+
+(define-public ghc-concurrent-extra
+  (package
+    (name "ghc-concurrent-extra")
+    (version "0.7.0.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "concurrent-extra/concurrent-extra-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1y8xk460fvnw0idzdiylmm874sjny4q9jxb1js9fjz8lw2wns3h4"))))
+    (build-system haskell-build-system)
+    (arguments
+     ;; XXX: The ReadWriteLock 'stressTest' fails.
+     `(#:tests? #f))
+    (inputs
+     `(("ghc-unbounded-delays" ,ghc-unbounded-delays)))
+    (native-inputs
+     `(("ghc-async" ,ghc-async)
+       ("ghc-hunit" ,ghc-hunit)
+       ("ghc-random" ,ghc-random)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))
+    (home-page "https://github.com/basvandijk/concurrent-extra")
+    (synopsis "Extra concurrency primitives")
+    (description "This Haskell library offers (among other things) the
+following selection of synchronisation primitives:
+
+@itemize
+@item @code{Broadcast}: Wake multiple threads by broadcasting a value.
+@item @code{Event}: Wake multiple threads by signalling an event.
+@item @code{Lock}: Enforce exclusive access to a resource.  Also known
+as a binary semaphore or mutex.  The package additionally provides an
+alternative that works in the STM monad.
+@item @code{RLock}: A lock which can be acquired multiple times by the
+same thread.  Also known as a reentrant mutex.
+@item @code{ReadWriteLock}: Multiple-reader, single-writer locks.  Used
+to protect shared resources which may be concurrently read, but only
+sequentially written.
+@item @code{ReadWriteVar}: Concurrent read, sequential write variables.
+@end itemize
+
+Please consult the API documentation of the individual modules for more
+detailed information.
+
+This package was inspired by the concurrency libraries of Java and
+Python.")
+    (license license:bsd-3)))
+
+(define-public ghc-io-streams
+  (package
+    (name "ghc-io-streams")
+    (version "1.5.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "io-streams/io-streams-" version ".tar.gz"))
+       (sha256
+        (base32
+         "12rcdg2d70644bvn838fxcjkssqj8pssnx5y657si5rijcbkgjsx"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-attoparsec" ,ghc-attoparsec)
+       ("ghc-bytestring-builder" ,ghc-bytestring-builder)
+       ("ghc-network" ,ghc-network)
+       ("ghc-primitive" ,ghc-primitive)
+       ("ghc-vector" ,ghc-vector)
+       ("ghc-zlib-bindings" ,ghc-zlib-bindings)))
+    (native-inputs
+     `(("ghc-hunit" ,ghc-hunit)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
+       ("ghc-zlib" ,ghc-zlib)))
+    (arguments
+     `(#:cabal-revision
+       ("2" "1mcab95d6hm098myh9gp7sh10srigjphgvm8s9pfs7jg5hzghy14")))
+    (home-page "http://hackage.haskell.org/package/io-streams")
+    (synopsis "Simple and composable stream I/O")
+    (description "This library contains simple and easy-to-use
+primitives for I/O using streams.")
+    (license license:bsd-3)))
+
+(define-public ghc-io-streams-haproxy
+  (package
+    (name "ghc-io-streams-haproxy")
+    (version "1.0.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "io-streams-haproxy/io-streams-haproxy-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "11nh9q158mgnvvb23s5ffg87lkhl5smk039yl43jghxmb214z0bp"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-attoparsec" ,ghc-attoparsec)
+       ("ghc-io-streams" ,ghc-io-streams)
+       ("ghc-network" ,ghc-network)))
+    (native-inputs
+     `(("ghc-hunit" ,ghc-hunit)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))
+    (arguments
+     `(#:cabal-revision
+       ("4" "06c51a057n5bc9xfbp2m4jz5ds4z1xvmsx5mppch6qfwbz7x5i9l")))
+    (home-page "http://snapframework.com/")
+    (synopsis "HAProxy protocol 1.5 support for io-streams")
+    (description "HAProxy protocol version 1.5 support
+(see @uref{http://haproxy.1wt.eu/download/1.5/doc/proxy-protocol.txt})
+for applications using io-streams.  The proxy protocol allows information
+about a networked peer (like remote address and port) to be propagated
+through a forwarding proxy that is configured to speak this protocol.")
+    (license license:bsd-3)))
+
+(define-public ghc-language-glsl
+  (package
+    (name "ghc-language-glsl")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "language-glsl/language-glsl-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0hdg67ainlqpjjghg3qin6fg4p783m0zmjqh4rd5gyizwiplxkp1"))))
+    (build-system haskell-build-system)
+    (inputs `(("ghc-prettyclass" ,ghc-prettyclass)))
+    (arguments
+     `(#:tests? #f
+       #:cabal-revision
+       ("1" "10ac9pk4jy75k03j1ns4b5136l4kw8krr2d2nw2fdmpm5jzyghc5")))
+    (home-page "http://hackage.haskell.org/package/language-glsl")
+    (synopsis "GLSL abstract syntax tree, parser, and pretty-printer")
+    (description "This package is a Haskell library for the
+representation, parsing, and pretty-printing of GLSL 1.50 code.")
+    (license license:bsd-3)))
+
+(define-public ghc-prettyclass
+  (package
+    (name "ghc-prettyclass")
+    (version "1.0.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "prettyclass/prettyclass-" version ".tar.gz"))
+       (sha256
+        (base32
+         "11l9ajci7nh1r547hx8hgxrhq8mh5gdq30pdf845wvilg9p48dz5"))))
+    (build-system haskell-build-system)
+    (home-page "http://hackage.haskell.org/package/prettyclass")
+    (synopsis "Pretty printing class similar to Show")
+    (description "This package provides a pretty printing class similar
+to @code{Show}, based on the HughesPJ pretty printing library.  It
+provides the pretty printing class and instances for the Prelude
+types.")
+    (license license:bsd-3)))
+
+(define-public ghc-readable
+  (package
+    (name "ghc-readable")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "readable/readable-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1ja39cg26wy2fs00gi12x7iq5k8i366pbqi3p916skfa5jnkfc3h"))))
+    (build-system haskell-build-system)
+    (home-page "https://github.com/mightybyte/readable")
+    (synopsis "Type class for reading from Text and ByteString")
+    (description "This package provides a @code{Readable} type class for
+reading data types from @code{ByteString} and @code{Text}.  It also
+includes efficient implementations for common data types.")
+    (license license:bsd-3)))
+
+(define-public ghc-threads
+  (package
+    (name "ghc-threads")
+    (version "0.5.1.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "threads/threads-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0bjnjhnq3km6xqk0fn1fgyz5xdw4h6lylbwwbcmkkfzwcz0c76hk"))))
+    (build-system haskell-build-system)
+    (native-inputs
+     `(("ghc-concurrent-extra" ,ghc-concurrent-extra)
+       ("ghc-hunit" ,ghc-hunit)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))
+    (home-page "https://github.com/basvandijk/threads")
+    (synopsis "Fork threads and wait for their result")
+    (description "This package provides functions to fork threads and
+wait for their result, whether it's an exception or a normal value.
+Besides waiting for the termination of a single thread this package also
+provides functions to wait for a group of threads to terminate.  This
+package is similar to the @code{threadmanager}, @code{async} and
+@code{spawn} packages.  The advantages of this package are:
+
+@itemize
+@item Simpler API.
+@item More efficient in both space and time.
+@item No space-leak when forking a large number of threads.
+@item Correct handling of asynchronous exceptions.
+@item GHC specific functionality like @code{forkOn} and
+@code{forkIOWithUnmask}.
+@end itemize")
+    (license license:bsd-3)))
+
+(define-public ghc-zlib-bindings
+  (package
+    (name "ghc-zlib-bindings")
+    (version "0.1.1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "zlib-bindings/zlib-bindings-" version ".tar.gz"))
+       (sha256
+        (base32
+         "02ciywlz4wdlymgc3jsnicz9kzvymjw1www2163gxidnz4wb8fy8"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-zlib" ,ghc-zlib)))
+    (native-inputs
+     `(("ghc-hspec" ,ghc-hspec)
+       ("ghc-quickcheck" ,ghc-quickcheck)))
+    (arguments
+     `(#:cabal-revision
+       ("2" "0fq49694gqkab8m0vq4i879blswczwd66n7xh4r4gwiahf0ryvqc")))
+    (home-page "https://github.com/snapframework/zlib-bindings")
+    (synopsis "Low-level bindings to the @code{zlib} package")
+    (description "This package provides low-level bindings to the
+@code{zlib} package.")
+    (license license:bsd-3)))

gnu/packages/haskell.scm

@@ -73,6 +73,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix utils)
+  #:use-module (ice-9 match)
   #:use-module (ice-9 regex)
   #:use-module ((srfi srfi-1) #:select (alist-delete)))
 
@@ -440,7 +441,7 @@ interactive environment for the functional language Haskell.")
 interactive environment for the functional language Haskell.")
     (license license:bsd-3)))
 
-(define-public ghc-8
+(define-public ghc-8.4
   (package (inherit ghc-8.0)
     (name "ghc")
     (version "8.4.3")
@@ -572,6 +573,53 @@ interactive environment for the functional language Haskell.")
                                 (file-pattern ".*\\.conf\\.d$")
                                 (file-type 'directory))))))
 
+(define-public ghc-8.6
+  (package (inherit ghc-8.4)
+    (name "ghc")
+    (version "8.6.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://www.haskell.org/ghc/dist/"
+                           version "/" name "-" version "-src.tar.xz"))
+       (sha256
+        (base32 "0qg3zsmbk4rkwkc3jpas3zs74qaxmw4sp4v1mhsbj0a0dzls2jjd"))))
+    (native-inputs
+     `(;; GHC 8.6.5 must be built with GHC >= 8.2.
+       ("ghc-bootstrap" ,ghc-8.4)
+       ("ghc-testsuite"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append
+                 "https://www.haskell.org/ghc/dist/"
+                 version "/" name "-" version "-testsuite.tar.xz"))
+           (sha256
+            (base32
+             "0pw9r91g2np3i806g2f4f8z4jfdd7mx226cmdizk4swa7av1qf91"))))
+       ,@(filter (match-lambda
+                   (("ghc-bootstrap" . _) #f)
+                   (("ghc-testsuite" . _) #f)
+                   (_ #t))
+                 (package-native-inputs ghc-8.4))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments ghc-8.4)
+       ((#:make-flags make-flags ''())
+        `(cons "EXTRA_RUNTEST_OPTS=--skip-perf-tests"
+               ,make-flags))
+       ((#:phases phases '%standard-phases)
+        `(modify-phases ,phases
+           ;; These two tests refer to the root user, which doesn't exist
+           ;; (see <https://bugs.gnu.org/36692>).
+           (add-after 'unpack-testsuite 'skip-tests
+             (lambda _
+               (substitute* "libraries/unix/tests/all.T"
+                 (("^test\\('T8108'") "# guix skipped: test('T8108'"))
+               (substitute* "libraries/unix/tests/libposix/all.T"
+                 (("^test\\('posix010'") "# guix skipped: test('posix010'"))
+               #t))))))))
+
+(define-public ghc-8 ghc-8.4)
+
 (define-public ghc ghc-8)
 
 (define-public ghc-hostname
@@ -1054,28 +1102,6 @@ the ‘haddock’ package.")
 documentation-generation tool for Haskell libraries.")
     (license license:bsd-3)))
 
-(define-public ghc-haddock-test
-  (package
-    (name "ghc-haddock-test")
-    (version "0.0.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/"
-                           "haddock-test/haddock-test-"
-                           version ".tar.gz"))
-       (sha256
-        (base32
-         "1ax8fnfrwx66csj952f3virxzapipan9da7z5l1zc12nqkifbs7w"))))
-    (build-system haskell-build-system)
-    (inputs
-     `(("ghc-xml" ,ghc-xml)
-       ("ghc-syb" ,ghc-syb)))
-    (home-page "http://www.haskell.org/haddock/")
-    (synopsis "Test utilities for Haddock")
-    (description "This package provides test utilities for Haddock.")
-    (license license:bsd-3)))
-
 (define-public ghc-haddock
   (package
     (name "ghc-haddock")
@@ -2903,30 +2929,6 @@ Haskell library @code{regex-base}.")
 @code{regex-posix} to replace @code{Text.Regex}.")
     (license license:bsd-3)))
 
-(define-public ghc-regex-tdfa-rc
-  (package
-    (name "ghc-regex-tdfa-rc")
-    (version "1.1.8.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://hackage.haskell.org/package/regex-tdfa-rc/regex-tdfa-rc-"
-             version
-             ".tar.gz"))
-       (sha256
-        (base32
-         "1vi11i23gkkjg6193ak90g55akj69bhahy542frkwb68haky4pp3"))))
-    (build-system haskell-build-system)
-    (inputs
-     `(("ghc-regex-base" ,ghc-regex-base)))
-    (home-page
-     "https://hackage.haskell.org/package/regex-tdfa")
-    (synopsis "Tagged DFA regex engine for Haskell")
-    (description "A new all-Haskell \"tagged\" DFA regex engine, inspired by
-@code{libtre} (fork by Roman Cheplyaka).")
-    (license license:bsd-3)))
-
 (define-public ghc-regex-tdfa-text
   (package
     (name "ghc-regex-tdfa-text")
@@ -3041,6 +3043,7 @@ the parsers provided by @code{parsec}, @code{attoparsec} and @code{base}'s
                (base32
                 "0hznd8i65s81xy13i2qc7cvipw3lfb2yhkv53apbdsh6sbljz5sk"))))
     (build-system haskell-build-system)
+    (arguments `(#:tests? #f)) ; doctest suite fails to build on i686
     (inputs
      `(("ghc-reducers" ,ghc-reducers)
        ("ghc-semigroups" ,ghc-semigroups)
@@ -3990,7 +3993,7 @@ instances of the @code{Pretty} class.")
          "0gnb4mkqryv08vncxnj0bzwcnd749613yw3cxfzw6y3nsldp4c56"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-ansi-terminal" ,ghc-ansi-terminal-0.8)))
+     `(("ghc-ansi-terminal" ,ghc-ansi-terminal)))
     (home-page "https://github.com/ekmett/ansi-wl-pprint")
     (synopsis "Wadler/Leijen Pretty Printer for colored ANSI terminal output")
     (description "This is a pretty printing library based on Wadler's paper
@@ -4235,7 +4238,7 @@ interface.")
 (define-public ghc-ansi-terminal
   (package
     (name "ghc-ansi-terminal")
-    (version "0.9.1")
+    (version "0.8.0.4")
     (source
      (origin
        (method url-fetch)
@@ -4245,7 +4248,7 @@ interface.")
              ".tar.gz"))
        (sha256
         (base32
-         "1yr0ld0kqns3w3j9gl62bdwshvyazidx4dv1qkvq19ivnf08w23l"))))
+         "0428gq8m3fdnb7ldcsyk97qcch76hcxbgh2666p6f76fs2qbhg7b"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-colour" ,ghc-colour)))
@@ -4256,21 +4259,6 @@ allows cursor movement, screen clearing, color output showing or hiding the
 cursor, and changing the title.")
     (license license:bsd-3)))
 
-(define-public ghc-ansi-terminal-0.8
-  (package (inherit ghc-ansi-terminal)
-           (name "ghc-ansi-terminal")
-           (version "0.8.0.4")
-           (source
-            (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://hackage.haskell.org/package/ansi-terminal/ansi-terminal-"
-                    version
-                    ".tar.gz"))
-              (sha256
-               (base32
-                "0428gq8m3fdnb7ldcsyk97qcch76hcxbgh2666p6f76fs2qbhg7b"))))))
-
 (define-public ghc-vault
   (package
     (name "ghc-vault")
@@ -5909,35 +5897,6 @@ within an enclosed computation, while remaining responsive to (external)
 asynchronous exceptions.")
     (license license:expat)))
 
-(define-public ghc-packedstring
-  (package
-    (name "ghc-packedstring")
-    (version "0.1.0.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://hackage.haskell.org/package/"
-                                  "packedstring/packedstring-"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "1x78pzzdlnpcmh9p37rlf8m5cxf3yqm2alf3whl4zpr9w25r0qj8"))))
-    (build-system haskell-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'enable-extension
-          (lambda _
-            ;; This package won't compile without the StandaloneDeriving
-            ;; extension.
-            (substitute* "packedstring.cabal"
-              (("CPP") "CPP, StandaloneDeriving"))
-            #t)))))
-    (home-page "https://hackage.haskell.org/package/packedstring")
-    (synopsis "Library for packed strings")
-    (description
-     "This deprecated library provides an implementation of packed strings.")
-    (license license:bsd-3)))
-
 (define-public ghc-th-abstraction
   (package
     (name "ghc-th-abstraction")
@@ -6252,6 +6211,9 @@ back-ends.")
                (base32
                 "0cbsyh4ilvjzq1q7pxls43k6pdqxg1l85xzibcwpbvmlvrizh86w"))))
     (build-system haskell-build-system)
+    ;; The tests are broken on i686.  They are fixed in 0.10.3.0.
+    ;; See https://github.com/snoyberg/yaml/issues/158
+    (arguments `(#:tests? #f))
     (inputs
      `(("ghc-conduit" ,ghc-conduit)
        ("ghc-resourcet" ,ghc-resourcet)
@@ -11278,6 +11240,9 @@ imported with the correct Haskell types.")
         (base32
          "1931m23iqb4wddpdidm4ph746zpaw41kkjzmb074j7yyfpk7x1jv"))))
     (build-system haskell-build-system)
+    ;; Tests fail on i686.
+    ;; See https://github.com/vimus/libmpd-haskell/issues/112
+    (arguments `(#:tests? #f))
     (inputs
      `(("ghc-attoparsec" ,ghc-attoparsec)
        ("ghc-old-locale" ,ghc-old-locale)
@@ -11821,7 +11786,7 @@ default)
 (define-public ghc-validation
   (package
     (name "ghc-validation")
-    (version "1.1")
+    (version "1")
     (source
      (origin
        (method url-fetch)
@@ -11831,18 +11796,11 @@ default)
              ".tar.gz"))
        (sha256
         (base32
-         "1acj7mh3581ks405xswxw6667z7y1y0slisg6jvp6chc191ji9l5"))))
+         "08drmdvyzg2frbb26icy1mlz52xv0l6gi3v8gb7xp0vrcci5libh"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:phases
+     `(#:cabal-revision
-       (modify-phases %standard-phases
+       ("1" "1x1g4nannz81j1h64l1m3ancc96zc57d1bjhj1wk7bwn1xxbi5h3")))
-         (add-after 'unpack 'add-setup-script
-           (lambda _
-             ;; The usual "Setup.hs" script is missing from the source.
-             (with-output-to-file "Setup.hs"
-               (lambda ()
-                 (format #t "import Distribution.Simple~%")
-                 (format #t "main = defaultMain~%"))))))))
     (inputs
      `(("ghc-semigroups" ,ghc-semigroups)
        ("ghc-semigroupoids" ,ghc-semigroupoids)
@@ -11875,7 +11833,7 @@ example of, \"An applicative functor that is not a monad.\"")
 (define-public ghc-concurrent-output
   (package
     (name "ghc-concurrent-output")
-    (version "1.10.10")
+    (version "1.10.9")
     (source
      (origin
        (method url-fetch)
@@ -11885,7 +11843,7 @@ example of, \"An applicative functor that is not a monad.\"")
              ".tar.gz"))
        (sha256
         (base32
-         "1wnjxnwbc3l853kiiijagzjyb6fmhz3lmkwls24plbximl1qrr22"))))
+         "0mwf155w89nbbkjln7hhbn8k3f8p0ylcvgrg31cm7ijpx4499i4c"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-async" ,ghc-async)

gnu/packages/image.scm

@@ -577,9 +577,6 @@ collection of tools for doing simple manipulations of TIFF images.")
     (arguments
      '(#:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _
-             (invoke "sh" "autobuild")))
          (add-after 'unpack 'patch-reg-wrapper
            (lambda _
              (substitute* "prog/reg_wrapper.sh"
@@ -1004,7 +1001,7 @@ language bindings to VIGRA.")
 (define-public libwebp
   (package
     (name "libwebp")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
      (origin
        ;; No tarballs are provided for >0.6.1.
@@ -1015,7 +1012,7 @@ language bindings to VIGRA.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1ay0sai7f74dyk2gi975qfllmq534vnsx456npf16583mqb6ib2q"))))
+         "1l8h9d3z3kla567ilmymrgg8vc2n763g8qss1hah8dg832hbqkxf"))))
     (build-system gnu-build-system)
     (inputs
      `(("freeglut" ,freeglut)
@@ -1074,14 +1071,14 @@ channels.")
 (define-public exiv2
   (package
     (name "exiv2")
-    (version "0.27.1")
+    (version "0.27.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.exiv2.org/builds/exiv2-" version
                            "-Source.tar.gz"))
        (sha256
-        (base32 "109hbfk63dh14fz20ivq20gcclb9jj9jmh48w4lcn6zxh1ljh9gi"))))
+        (base32 "0gqminvj14xm3rgbnydbywf22608js80rp7nmxxk4497j5mzali6"))))
     (build-system cmake-build-system)
     (arguments '(#:tests? #f))          ; no test suite
     (propagated-inputs
@@ -1206,12 +1203,6 @@ ISO/IEC 15444-1).")
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
        ("libtool" ,libtool)))
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     (synopsis "Scaling, colorspace conversion, and dithering library")
     (description "Zimg implements the commonly required image processing basics
 of scaling, colorspace conversion, and depth conversion.  A simple API enables

gnu/packages/imagemagick.scm

@@ -48,14 +48,14 @@
     ;; The 7 release series has an incompatible API, while the 6 series is still
     ;; maintained. Don't update to 7 until we've made sure that the ImageMagick
     ;; users are ready for the 7-series API.
-    (version "6.9.10-51")
+    (version "6.9.10-58")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://imagemagick/ImageMagick-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "03c5r14ycp7mmlk6pryfcnpvjjnghk3z7dbjd1b7m1bgzmw21jhj"))))
+               "1hrd408lqgwg70aaif8g60lipwsplsg61722kpmx7a08pygs46hf"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")

gnu/packages/kde.scm

@@ -320,7 +320,7 @@ plugins, as well as code to create plugins, or complete applications.")
 (define-public krita
   (package
     (name "krita")
-    (version "4.2.2")
+    (version "4.2.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -329,7 +329,7 @@ plugins, as well as code to create plugins, or complete applications.")
                     "/krita-" version ".tar.gz"))
               (sha256
                (base32
-                "1pzk5bqp3kh22djhvsvmsc7ybirs4hsnkpg1y9677m2gxwbqnnps"))))
+                "1f14r2mrqasl6nr3sss0xy2h8xlxd5wdcjcd64m9nz2gwlm39r7w"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f

gnu/packages/libevent.scm

@@ -41,7 +41,7 @@
 (define-public libevent
   (package
     (name "libevent")
-    (version "2.1.10")
+    (version "2.1.11")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -49,7 +49,7 @@
                     version "-stable/libevent-" version "-stable.tar.gz"))
               (sha256
                (base32
-                "1c25928gdv495clxk2v1d4gkr5py7ack4gx2n7d13frnld0syr78"))))
+                "0g988zqm45sj1hlhhz4il5z4dpi5dl74hzjwzl4md37a09iaqnx6"))))
     (build-system gnu-build-system)
     (arguments
      ;; This skips some of the tests which fail on armhf and aarch64.

gnu/packages/linux.scm

@@ -349,42 +349,42 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                         "linux-" version ".tar.xz"))
     (sha256 hash)))
 
-(define-public linux-libre-5.2-version "5.2.4")
+(define-public linux-libre-5.2-version "5.2.8")
 (define-public linux-libre-5.2-pristine-source
   (let ((version linux-libre-5.2-version)
-        (hash (base32 "0hzfayq79bksng09ngw3k3h3zkd6ndfn059rvwpznypy1fg8pkdi")))
+        (hash (base32 "0dv91zfjkil29lp2l35lswkrhrqbc4kjh965ciaqwih1rh3cs9x1")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.2)))
 
-(define-public linux-libre-4.19-version "4.19.62")
+(define-public linux-libre-4.19-version "4.19.66")
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "1p6s1ksrsq3za7644j0qf9brf6brwq39jxpfln5ypmyfi5qn9gh7")))
+        (hash (base32 "0r6vzarmi77fhivd1n6f667sgcw8zd54ykmhmp6rd52bbkhsp0f9")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
 
-(define-public linux-libre-4.14-version "4.14.134")
+(define-public linux-libre-4.14-version "4.14.138")
 (define-public linux-libre-4.14-pristine-source
   (let ((version linux-libre-4.14-version)
-        (hash (base32 "0b9xj1rwr5fpw2giirfghzxxc0wp1hwf4nqvalx314pxxysyf88b")))
+        (hash (base32 "0yw39cqpk6g42q0xcv2aq8yyzsi0kzx9nvlfbw0iyg58wcfvsl7j")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))
 
-(define-public linux-libre-4.9-version "4.9.186")
+(define-public linux-libre-4.9-version "4.9.189")
 (define-public linux-libre-4.9-pristine-source
   (let ((version linux-libre-4.9-version)
-        (hash (base32 "0sjbp7m6d625rw06wv34a0805d1lgldii4pxiqfpja871m1q8914")))
+        (hash (base32 "1cyhwnxkjd0qa5d48657yppjnzbi830q0p25jjv2dxs629k4bnck")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.9)))
 
-(define-public linux-libre-4.4-version "4.4.186")
+(define-public linux-libre-4.4-version "4.4.189")
 (define-public linux-libre-4.4-pristine-source
   (let ((version linux-libre-4.4-version)
-        (hash (base32 "113rjf8842glzi23y1g1yrwncihv2saah6wz0r726r06bk9p64hb")))
+        (hash (base32 "0nc8v62gw89m3ykqg6nqf749fzm8y1n481ns8vny4gbinyikjhlp")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.4)))
@@ -1397,15 +1397,18 @@ Zerofree requires the file system to be unmounted or mounted read-only.")
 (define-public strace
   (package
     (name "strace")
-    (version "5.1")
+    (version "5.2")
     (home-page "https://strace.io")
     (source (origin
              (method url-fetch)
              (uri (string-append home-page "/files/" version
                                  "/strace-" version ".tar.xz"))
+             ;; XXX Remove the 'regenerate-tests' phase below when
+             ;; "strace-ipc-tests.patch" is no longer applied.
+             (patches (search-patches "strace-ipc-tests.patch"))
              (sha256
               (base32
-               "12wsga1v3rab24gr0mpfip7j7gwr90m8f9h6fviqxa3xgnwl38zm"))))
+               "1li49i75wrdw91hchyyd8spnzfcmxcfyfb5g9zbaza89aq4bq4ym"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -1414,7 +1417,14 @@ Zerofree requires the file system to be unmounted or mounted read-only.")
            (lambda _
              (substitute* "strace.c"
                (("/bin/sh") (which "sh")))
-             #t)))
+             #t))
+         (add-before 'configure 'regenerate-tests
+           ;; XXX Remove this phase when "strace-ipc-tests.patch" is no longer
+           ;; applied in the 'source' field above.  This phase is needed to
+           ;; regenerate many other files from tests/gen_tests.in, which is
+           ;; modified by the aforementioned patch.
+           (lambda _
+             (invoke "tests/gen_tests.sh"))))
        ;; Don't fail if the architecture doesn't support different personalities.
        #:configure-flags '("--enable-mpers=check")
        ;; See <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=32459>.
@@ -4613,7 +4623,7 @@ are exceeded.")
 (define-public mtd-utils
   (package
     (name "mtd-utils")
-    (version "2.0.2")
+    (version "2.1.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4621,17 +4631,19 @@ are exceeded.")
                     "mtd-utils-" version ".tar.bz2"))
               (sha256
                (base32
-                "1f30jszknc5v6ykmil8ajxgksmcg54q3rsp84jsancp9x0dycggv"))))
+                "1lijl89l7hljx8xx70vrz9srd3h41v5gh4b0lvqnlv831yvyh5cd"))))
     (arguments
      '(#:configure-flags '("--enable-unit-tests")))
     (native-inputs
      `(("cmocka" ,cmocka)
        ("pkg-config" ,pkg-config)))
     (inputs
-     `(("acl" ,acl) ; for XATTR
+     `(("acl" ,acl)                     ; extended attributes (xattr)
        ("libuuid" ,util-linux)
        ("lzo" ,lzo)
-       ("zlib" ,zlib)))
+       ("openssl" ,openssl)             ; optional crypto support
+       ("zlib" ,zlib)
+       ("zstd" ,zstd "lib")))
     (build-system gnu-build-system)
     (synopsis "MTD Flash Storage Utilities")
     (description "This package provides utilities for testing, partitioning, etc

gnu/packages/lisp.scm

@@ -6563,7 +6563,24 @@ This system contains the CFFI foreign slot access extension.")))
        ("trivia.cffi" ,sbcl-trivia.cffi)
        ("optima" ,sbcl-optima)))
     (arguments
-     `(#:test-asd-file "trivia.test.asd"))
+     `(#:test-asd-file "trivia.test.asd"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'create-asd 'remove-component
+           ;; XXX: The original .asd has no components, but our build system
+           ;; creates an entry nonetheless.  We need to remove it for the
+           ;; generated .asd to load properly.  See trivia.trivial for a
+           ;; similar problem.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (asd (string-append out "/lib/" (%lisp-type) "/trivia.asd")))
+               (substitute* asd
+                 (("  :components
+")
+                  ""))
+               (substitute* asd
+                 ((" *\\(\\(:compiled-file \"trivia--system\"\\)\\)")
+                  ""))))))))
     (description "Trivia is a pattern matching compiler that is compatible
 with Optima, another pattern matching library for Common Lisp.  It is meant to
 be faster and more extensible than Optima.")))
@@ -6598,3 +6615,38 @@ various string metrics in Common Lisp:
 @item Overlap coefficient
 @end itemize\n")
     (license license:x11)))
+
+(define-public sbcl-cl-str
+  (let ((commit "3d5ec86e3a0199e5973aacde951086dfd754b5e5"))
+    (package
+      (name "sbcl-cl-str")
+      (version (git-version "0.8" "1" commit))
+      (home-page "https://github.com/vindarel/cl-str")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url home-page)
+                      (commit commit)))
+                (sha256
+                 (base32 "0szzzbygw9h985yxz909vvqrp69pmpcpahn7hn350lnyjislk9ga"))
+                (file-name (git-file-name name version))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("cl-ppcre" ,sbcl-cl-ppcre)
+         ("cl-ppcre-unicode" ,sbcl-cl-ppcre-unicode)))
+      (native-inputs
+       `(("prove" ,sbcl-prove)
+         ("prove-asdf" ,sbcl-prove-asdf)))
+      (arguments
+       `(#:asd-file "str.asd"
+         #:asd-system-name "str"
+         #:test-asd-file "str.test.asd"))
+      (synopsis "Modern, consistent and terse Common Lisp string manipulation library")
+      (description "A modern and consistent Common Lisp string manipulation
+library that focuses on modernity, simplicity and discoverability:
+@code{(str:trim s)} instead of @code{(string-trim '(#\\Space ...) s)}), or
+@code{str:concat strings} instead of an unusual format construct; one
+discoverable library instead of many; consistency and composability, where
+@code{s} is always the last argument, which makes it easier to feed pipes and
+arrows.")
+      (license license:expat))))

gnu/packages/machine-learning.scm

@@ -193,7 +193,7 @@ classification.")
                 (uri (svn-reference
                       (url "http://svn.code.sf.net/p/ghmm/code/trunk")
                       (revision svn-revision)))
-                (file-name (string-append name "-" version))
+                (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
                   "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
@@ -250,10 +250,7 @@ classification.")
                   (string-append indent
                                  "@unittest.skip(\"Disabled by Guix\")\n"
                                  line)))
-               #t))
+               #t)))))
-           (add-after 'disable-broken-tests 'autogen
-             (lambda _
-               (invoke "bash" "autogen.sh"))))))
       (inputs
        `(("python" ,python-2) ; only Python 2 is supported
          ("libxml2" ,libxml2)))
@@ -820,8 +817,14 @@ computing environments.")
              (setenv "HOME" "/tmp")
 
              (invoke "pytest" "sklearn" "-m" "not network")))
-         ;; FIXME: This fails with permission denied
+         (add-before 'reset-gzip-timestamps 'make-files-writable
-         (delete 'reset-gzip-timestamps))))
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Make sure .gz files are writable so that the
+             ;; 'reset-gzip-timestamps' phase can do its work.
+             (let ((out (assoc-ref outputs "out")))
+               (for-each make-file-writable
+                         (find-files out "\\.gz$"))
+               #t))))))
     (inputs
      `(("openblas" ,openblas)))
     (native-inputs

gnu/packages/mail.scm

@@ -1051,7 +1051,7 @@ useful features.")
     (arguments
       '(#:phases
         (modify-phases %standard-phases
-          (add-after 'unpack 'autogen
+          (replace 'bootstrap
             (lambda _
               (setenv "NOCONFIGURE" "true")
               (invoke "sh" "autogen.sh"))))
@@ -1365,12 +1365,7 @@ It supports mbox/Maildir and its own dbox/mdbox formats.")
      `(#:tests? #f ;No tests exist.
        #:configure-flags (list (string-append "--with-dovecot="
                                               (assoc-ref %build-inputs "dovecot")
-                                              "/lib/dovecot"))
+                                              "/lib/dovecot"))))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     (home-page "https://0xacab.org/riseuplabs/trees")
     (synopsis "NaCL-based Dovecot email storage encryption plugin")
     (description
@@ -1421,12 +1416,7 @@ using libsodium sealed boxes.
        `(#:tests? #f ;No tests exist.
          #:configure-flags (list (string-append "--with-dovecot="
                                                 (assoc-ref %build-inputs "dovecot")
-                                                "/lib/dovecot"))
+                                                "/lib/dovecot"))))
-         #:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'autogen
-             (lambda _
-               (invoke "sh" "autogen.sh"))))))
       (home-page "https://github.com/LuckyFellow/dovecot-libsodium-plugin")
       (synopsis "Libsodium password hashing schemes plugin for Dovecot")
       (description

gnu/packages/man.scm

@@ -162,7 +162,7 @@ the traditional flat-text whatis databases.")
 (define-public man-pages
   (package
     (name "man-pages")
-    (version "5.01")
+    (version "5.02")
     (source
      (origin
        (method url-fetch)
@@ -172,7 +172,7 @@ the traditional flat-text whatis databases.")
               (string-append "mirror://kernel.org/linux/docs/man-pages/Archive/"
                              "man-pages-" version ".tar.xz")))
        (sha256
-        (base32 "09xn8d8xxwgms6h1bvjlgn3mxz51vxf3ra0ry9f5dqi29qry3z3x"))))
+        (base32 "1s4pdz2pwf0kvhdwx2s6lqn3xxzi38yz5jfyq5ymdmswc9gaiyn2"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases (delete 'configure))

gnu/packages/maths.scm

@@ -325,7 +325,7 @@ enough to be used effectively as a scientific calculator.")
 (define-public double-conversion
   (package
     (name "double-conversion")
-    (version "3.1.4")
+    (version "3.1.5")
     (home-page "https://github.com/google/double-conversion")
     (source (origin
               (method git-fetch)
@@ -334,7 +334,7 @@ enough to be used effectively as a scientific calculator.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "13xwcqk2c0q8c1siw566clxcpvp0xrxvb72mra42wa3nvq9wlsv6"))))
+                "0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv"))))
     (build-system cmake-build-system)
     (arguments
      '(#:test-target "test"
@@ -4333,14 +4333,14 @@ are noisy or are discontinuous at the solution.")
 (define-public r-desolve
   (package
     (name "r-desolve")
-    (version "1.21")
+    (version "1.24")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "deSolve" version))
         (sha256
          (base32
-          "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
+          "0hkvspq0fp8j64l9zayab2l2nazazhwfgfym0jllh0xv5a12r99s"))))
     (properties `((upstream-name . "deSolve")))
     (build-system r-build-system)
     (native-inputs

gnu/packages/mp3.scm

@@ -65,7 +65,8 @@
               "14460zhacxhswnzb36qfpd1f2wbk10qvksvm6wyq5hpvdgnw7ymv"))
             (patches (search-patches "libmad-armv7-thumb-pt1.patch"
                                      "libmad-armv7-thumb-pt2.patch"
-                                     "libmad-frame-length.patch"
+                                     "libmad-md_size.patch"
+                                     "libmad-length-check.patch"
                                      "libmad-mips-newgcc.patch"))))
    (build-system gnu-build-system)
    (arguments

gnu/packages/mpd.scm

@@ -90,7 +90,7 @@ interfacing MPD in the C, C++ & Objective C languages.")
 (define-public mpd
   (package
     (name "mpd")
-    (version "0.21.11")
+    (version "0.21.13")
     (source (origin
               (method url-fetch)
               (uri
@@ -99,7 +99,7 @@ interfacing MPD in the C, C++ & Objective C languages.")
                               "/mpd-" version ".tar.xz"))
               (sha256
                (base32
-                "1gbcg8icm0pp918jw1lx1j066m39zg9wyqjla328ic848j5zhbnk"))))
+                "1sjyhmq50nlccwmd8xn7m0bk8xvyixvfyr24v9dy3g86hhk0pdwm"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags '("-Ddocumentation=true"))) ;the default is 'false'...

gnu/packages/multiprecision.scm

@@ -64,12 +64,11 @@
                           (else '())))))
    (synopsis "Multiple-precision arithmetic library")
    (description
-    "@dfn{GMP} (the GNU Multiple Precision Arithmetic Library) is a library for
+    "The @acronym{GMP, the GNU Multiple Precision Arithmetic} library performs
-arbitrary-precision arithmetic, operating on signed integers, rational numbers
+arbitrary-precision arithmetic on signed integers, rational numbers and floating
-and floating point numbers.  The precision is only limited by the available
+point numbers.  The precision is only limited by the available memory.
-memory.  The library is highly optimized, with a design focus on execution
+The library is highly optimized, with a design focus on execution speed.
-speed.  It is aimed at use in, for example, cryptography and computational
+It is aimed at use in, for example, cryptography and computational algebra.")
-algebra.")
    (license lgpl3+)
    (home-page "https://gmplib.org/")))
 
@@ -105,7 +104,7 @@ algebra.")
    (propagated-inputs `(("gmp" ,gmp)))            ; <mpfr.h> refers to <gmp.h>
    (synopsis "C library for arbitrary-precision floating-point arithmetic")
    (description
-    "GNU@tie{}@dfn{MPFR} (Multiple Precision Floating-Point Reliably) is a C
+    "GNU@tie{}@acronym{MPFR, Multiple Precision Floating-Point Reliably} is a C
 library for performing multiple-precision, floating-point computations with
 correct rounding.")
    (license lgpl3+)
@@ -128,8 +127,8 @@ correct rounding.")
                         ("mpfr" ,mpfr)))
    (synopsis "C library for arbitrary-precision complex arithmetic")
    (description
-    "GNU@tie{}@dfn{MPC} (Multiple Precision Complex library) is a C library for
+    "GNU@tie{}@acronym{MPC, Multiple Precision Complex library} is a C library
-performing arithmetic on complex numbers.  It supports arbitrarily high
+for performing arithmetic on complex numbers.  It supports arbitrarily high
 precision and correctly rounds the results.")
    (license lgpl3+)
    (home-page "http://multiprecision.org/mpc/")))
@@ -150,11 +149,11 @@ precision and correctly rounds the results.")
                          ("mpfr" ,mpfr)))
     (synopsis "C library for arbitrary-precision interval arithmetic")
     (description
-     "@dfn{MPFI} (Multiple Precision Floating-point Interval) is a portable C
+     "@acronym{MPFI, Multiple Precision Floating-point Interval} is a portable C
 library for arbitrary-precision interval arithmetic, with intervals represented
-using MPFR reliable floating-point numbers.  It's based on the @dfn{GMP} (GNU
+using MPFR reliable floating-point numbers.  It's based on the @acronym{GMP, GNU
-Multiple Precision Arithmetic) and GNU@tie{}@dfn{MPFR} (Multiple Precision
+Multiple Precision Arithmetic} and GNU@tie{}@acronym{MPFR, Multiple Precision
-Floating-Point Reliably) libraries.
+Floating-Point Reliably} libraries.
 
 The purpose of arbitrary-precision interval arithmetic is to get results that
 are both guaranteed, thanks to interval computation, and accurate, thanks to

gnu/packages/networking.scm

@@ -592,14 +592,14 @@ of the same name.")
 (define-public wireshark
   (package
     (name "wireshark")
-    (version "3.0.2")
+    (version "3.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.wireshark.org/download/src/wireshark-"
                            version ".tar.xz"))
        (sha256
-        (base32 "0fz5lbyiw4a27fqc4ndi1w20bpcb6wi9k7vjv29l9fhd99kca7ky"))))
+        (base32 "0711jilp9sbgi46d105m3galw8n4wk5yncawi08031qxg2f754mg"))))
     (build-system cmake-build-system)
     (arguments
      `(#:phases

gnu/packages/nss.scm

@@ -70,7 +70,7 @@ in the Mozilla clients.")
 (define-public nss
   (package
     (name "nss")
-    (version "3.44.1")
+    (version "3.45")
     (source (origin
               (method url-fetch)
               (uri (let ((version-with-underscores
@@ -81,9 +81,10 @@ in the Mozilla clients.")
                       "nss-" version ".tar.gz")))
               (sha256
                (base32
-                "1y0jvva4s3j7cjz22kqw2lsml0an1295bgpc2raf7kc9r60cpr7w"))
+                "12sfq9xvpwpc22qnjsg1if1lmchiy33byrh92wn91phz7li0abqi"))
               ;; Create nss.pc and nss-config.
               (patches (search-patches "nss-pkgconfig.patch"
+                                       "nss-freebl-stubs.patch"
                                        "nss-increase-test-timeout.patch"))))
     (build-system gnu-build-system)
     (outputs '("out" "bin"))

gnu/packages/package-management.scm

@@ -561,16 +561,16 @@ transactions from C or Python.")
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "116")
+    (version "120")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://salsa.debian.org/reproducible-builds/diffoscope.git")
-                    (commit "116")))
+                    (commit "120")))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1anz2c112y0w21mh7xp6bs6z7v10dcy1i25nypkvqy3j929m0g28"))))
+                "07z9yclvfkw4326739l2ywzzihax5vdijiaqqpfix9rz1rb923aa"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -1023,7 +1023,7 @@ the boot loader configuration.")
 (define-public flatpak
   (package
    (name "flatpak")
-   (version "1.2.4")
+   (version "1.4.2")
    (source
     (origin
      (method url-fetch)
@@ -1031,7 +1031,7 @@ the boot loader configuration.")
                          version "/flatpak-" version ".tar.xz"))
      (sha256
       (base32
-       "1qf3ys84fzv11z6f6li59rxjdjbyrv7cyi9539k73r9i9pckjr8v"))))
+       "08nmpp26mgv0vp3mlwk97rnp0j7i108h4hr9nllja19sjxnrlygj"))))
 
    ;; Wrap 'flatpak' so that GIO_EXTRA_MODULES is set, thereby allowing GIO to
    ;; find the TLS backend in glib-networking.
@@ -1059,6 +1059,7 @@ the boot loader configuration.")
    (inputs `(("appstream-glib" ,appstream-glib)
              ("bubblewrap" ,bubblewrap)
              ("dconf" ,dconf)
+             ("fuse" ,fuse)
              ("gdk-pixbuf" ,gdk-pixbuf)
              ("gpgme" ,gpgme)
              ("json-glib" ,json-glib)

gnu/packages/patches/emacs-dired-toggle-sudo-emacs-26.patch

@@ -0,0 +1,49 @@
+From 3c0f4b27a079b90dc632f5061a81ce28cef24801 Mon Sep 17 00:00:00 2001
+From: eryx67 <eryx67@gmail.com>
+Date: Thu, 29 Nov 2018 10:30:20 +0500
+Subject: [PATCH] fix for latest emacs
+
+---
+ dired-toggle-sudo.el | 11 +++++++----
+ 1 file changed, 7 insertions(+), 4 deletions(-)
+
+diff --git a/dired-toggle-sudo.el b/dired-toggle-sudo.el
+index 386921b..fe5898e 100644
+--- a/dired-toggle-sudo.el
++++ b/dired-toggle-sudo.el
+@@ -37,17 +37,20 @@
+ unless SUDO-USER is provided."
+   (let* (;; Handle the case of local files. `tramp-dissect-file-name' does
+ 	 ;; not raise an error anymore.
+-	 (path (if (tramp-tramp-file-p path) path (concat "/:" path)))
++	 ;;(path (if (tramp-tramp-file-p path) path (concat "/-::" path)))
+ 	 (file-vec (or (ignore-errors (tramp-dissect-file-name
+ 				       path))
+ 		       (tramp-dissect-file-name
+-			(concat "/:" path) 1)))
++			(concat "/-::" path) 1)))
+ 	 (method  (tramp-file-name-method file-vec))
+ 	 (user (tramp-file-name-user file-vec))
+ 	 (host  (tramp-file-name-host file-vec))
++         (domain  (tramp-file-name-domain file-vec))
++         (port  (tramp-file-name-port file-vec))
+ 	 (localname (expand-file-name
+ 		     (tramp-file-name-localname file-vec))))
+-    (when (string= system-name host)
++    (when (or (string= (system-name) host)
++              (string= "-" host))
+       (setq host nil))
+     (cond
+      ;; remote directory -> sudo
+@@ -67,7 +70,7 @@ unless SUDO-USER is provided."
+       (setq method "sudo" user sudo-user)))
+     (replace-regexp-in-string
+      "^/:/" "/"
+-     (tramp-make-tramp-file-name method user host localname))))
++     (tramp-make-tramp-file-name method domain user host port localname))))
+ 
+ (defun dired-toggle-sudo-find (fname)
+   "Create a new buffer for file name FNAME."
+-- 
+2.22.0
+

gnu/packages/patches/flac-CVE-2017-6888.patch

@@ -1,29 +0,0 @@
-https://git.xiph.org/?p=flac.git;a=patch;h=4f47b63e9c971e6391590caf00a0f2a5ed612e67
-
-From 4f47b63e9c971e6391590caf00a0f2a5ed612e67 Mon Sep 17 00:00:00 2001
-From: Erik de Castro Lopo <erikd@mega-nerd.com>
-Date: Sat, 8 Apr 2017 18:34:49 +1000
-Subject: [PATCH] stream_decoder.c: Fix a memory leak
-
-Leak reported by Secunia Research.
----
- src/libFLAC/stream_decoder.c | 3 +++
- 1 file changed, 3 insertions(+)
-
-diff --git a/src/libFLAC/stream_decoder.c b/src/libFLAC/stream_decoder.c
-index 14d5fe7f..a5527511 100644
---- a/src/libFLAC/stream_decoder.c
-+++ b/src/libFLAC/stream_decoder.c
-@@ -1753,6 +1753,9 @@ FLAC__bool read_metadata_vorbiscomment_(FLAC__StreamDecoder *decoder, FLAC__Stre
- 					}
- 					memset (obj->comments[i].entry, 0, obj->comments[i].length) ;
- 					if (!FLAC__bitreader_read_byte_block_aligned_no_crc(decoder->private_->input, obj->comments[i].entry, obj->comments[i].length)) {
-+						/* Current i-th entry is bad, so we delete it. */
-+						free (obj->comments[i].entry) ;
-+						obj->comments[i].entry = NULL ;
- 						obj->num_comments = i;
- 						goto skip;
- 					}
--- 
-2.11.0
-

gnu/packages/patches/isc-dhcp-4.4.1-fixes-for-newer-bind.patch

@@ -0,0 +1,100 @@
+These fixes are needed to adapt isc-dhcp-4.4.1 to build
+successfully after its bundled copy of bind has been updated.
+
+It is derived from the following upstream commits:
+
+commit 8194daabfd590f17825f0c61e9534bee5c99cc86
+Author: Thomas Markwalder <tmark@isc.org>
+Date:   Fri Sep 14 13:41:14 2018 -0400
+
+  [master] Added includes of new BIND9 compatibility headers, updated util/bind.sh
+  
+      Merges in rt48072.
+
+commit cc35f84943df44dac2499f3e16e8aaba7d54191d
+Author: Thomas Markwalder <tmark@isc.org>
+Date:   Tue Mar 19 08:36:23 2019 -0400
+
+  [master] Avoid Bind9 python dependency
+  
+      merges [#3,!1] Avoid Bind9 python dependency
+
+--- a/bind/Makefile.in
++++ b/bind/Makefile.in
+@@ -23,7 +23,7 @@ exec_prefix = @exec_prefix@
+ 
+ bindconfig = --without-openssl --without-libxml2 --without-libjson \
+ 	--without-gssapi --disable-threads --without-lmdb \
+-	--includedir=@includedir@ --libdir=@libdir@ \
++	--includedir=@includedir@ --libdir=@libdir@  --without-python\
+ 	@BINDLT@ @BINDIOMUX@ @BINDCONFIG@ --enable-full-report
+ 
+ @BIND_ATF_FALSE@cleandirs = ./lib ./include
+diff --git a/includes/omapip/isclib.h b/includes/omapip/isclib.h
+index 75a87ff6..538b927f 100644
+--- a/includes/omapip/isclib.h
++++ b/includes/omapip/isclib.h
+@@ -48,6 +48,9 @@
+ #include <string.h>
+ #include <netdb.h>
+ 
++#include <isc/boolean.h>
++#include <isc/int.h>
++
+ #include <isc/buffer.h>
+ #include <isc/lex.h>
+ #include <isc/lib.h>
+diff --git a/includes/omapip/result.h b/includes/omapip/result.h
+index 91243e1b..860298f6 100644
+--- a/includes/omapip/result.h
++++ b/includes/omapip/result.h
+@@ -26,6 +26,7 @@
+ #ifndef DHCP_RESULT_H
+ #define DHCP_RESULT_H 1
+ 
++#include <isc/boolean.h>
+ #include <isc/lang.h>
+ #include <isc/resultclass.h>
+ #include <isc/types.h>
+diff --git a/server/dhcpv6.c b/server/dhcpv6.c
+index a7110f98..cde4f617 100644
+--- a/server/dhcpv6.c
++++ b/server/dhcpv6.c
+@@ -1034,7 +1034,8 @@ void check_pool6_threshold(struct reply_state *reply,
+ 				  shared_name,
+ 				  inet_ntop(AF_INET6, &lease->addr,
+ 					    tmp_addr, sizeof(tmp_addr)),
+-				  used, count);
++				  (long long unsigned)(used),
++				  (long long unsigned)(count));
+ 		}
+ 		return;
+ 	}
+@@ -1066,7 +1067,8 @@ void check_pool6_threshold(struct reply_state *reply,
+ 		  "address: %s; high threshold %d%% %llu/%llu.",
+ 		  shared_name,
+ 		  inet_ntop(AF_INET6, &lease->addr, tmp_addr, sizeof(tmp_addr)),
+-		  poolhigh, used, count);
++		  poolhigh, (long long unsigned)(used),
++		  (long long unsigned)(count));
+ 
+ 	/* handle the low threshold now, if we don't
+ 	 * have one we default to 0. */
+@@ -1436,12 +1438,15 @@ pick_v6_address(struct reply_state *reply)
+ 		log_debug("Unable to pick client address: "
+ 			  "no addresses available  - shared network %s: "
+ 			  " 2^64-1 < total, %llu active,  %llu abandoned",
+-			  shared_name, active - abandoned, abandoned);
++			  shared_name, (long long unsigned)(active - abandoned),
++			  (long long unsigned)(abandoned));
+ 	} else {
+ 		log_debug("Unable to pick client address: "
+ 			  "no addresses available  - shared network %s: "
+ 			  "%llu total, %llu active,  %llu abandoned",
+-			  shared_name, total, active - abandoned, abandoned);
++			  shared_name, (long long unsigned)(total),
++			  (long long unsigned)(active - abandoned),
++		          (long long unsigned)(abandoned));
+ 	}
+ 
+ 	return ISC_R_NORESOURCES;

gnu/packages/patches/libmad-frame-length.patch

@@ -1,199 +0,0 @@
-Copied from Debian.
-
-; You can calculate where the next frame will start depending on things
-; like the bitrate. See mad_header_decode().  It seems that when decoding
-; the frame you can go past that boundary.  This attempts to catch those cases,
-; but might not catch all of them.
-; For more info see http://bugs.debian.org/508133
-Index: libmad-0.15.1b/layer12.c
-===================================================================
---- libmad-0.15.1b.orig/layer12.c	2008-12-23 21:38:07.000000000 +0100
-+++ libmad-0.15.1b/layer12.c	2008-12-23 21:38:12.000000000 +0100
-@@ -134,6 +134,12 @@
-   for (sb = 0; sb < bound; ++sb) {
-     for (ch = 0; ch < nch; ++ch) {
-       nb = mad_bit_read(&stream->ptr, 4);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
-       if (nb == 15) {
- 	stream->error = MAD_ERROR_BADBITALLOC;
-@@ -146,6 +152,12 @@
- 
-   for (sb = bound; sb < 32; ++sb) {
-     nb = mad_bit_read(&stream->ptr, 4);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
-     if (nb == 15) {
-       stream->error = MAD_ERROR_BADBITALLOC;
-@@ -162,6 +174,12 @@
-     for (ch = 0; ch < nch; ++ch) {
-       if (allocation[ch][sb]) {
- 	scalefactor[ch][sb] = mad_bit_read(&stream->ptr, 6);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
- # if defined(OPT_STRICT)
- 	/*
-@@ -187,6 +205,12 @@
- 	frame->sbsample[ch][s][sb] = nb ?
- 	  mad_f_mul(I_sample(&stream->ptr, nb),
- 		    sf_table[scalefactor[ch][sb]]) : 0;
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
-       }
-     }
- 
-@@ -195,6 +219,12 @@
- 	mad_fixed_t sample;
- 
- 	sample = I_sample(&stream->ptr, nb);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
- 	for (ch = 0; ch < nch; ++ch) {
- 	  frame->sbsample[ch][s][sb] =
-@@ -403,7 +433,15 @@
-     nbal = bitalloc_table[offsets[sb]].nbal;
- 
-     for (ch = 0; ch < nch; ++ch)
-+    {
-       allocation[ch][sb] = mad_bit_read(&stream->ptr, nbal);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
-+    }
-   }
- 
-   for (sb = bound; sb < sblimit; ++sb) {
-@@ -411,6 +449,13 @@
- 
-     allocation[0][sb] =
-     allocation[1][sb] = mad_bit_read(&stream->ptr, nbal);
-+
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
-   }
- 
-   /* decode scalefactor selection info */
-@@ -419,6 +464,12 @@
-     for (ch = 0; ch < nch; ++ch) {
-       if (allocation[ch][sb])
- 	scfsi[ch][sb] = mad_bit_read(&stream->ptr, 2);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
-     }
-   }
- 
-@@ -442,6 +493,12 @@
-     for (ch = 0; ch < nch; ++ch) {
-       if (allocation[ch][sb]) {
- 	scalefactor[ch][sb][0] = mad_bit_read(&stream->ptr, 6);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
- 	switch (scfsi[ch][sb]) {
- 	case 2:
-@@ -452,11 +509,23 @@
- 
- 	case 0:
- 	  scalefactor[ch][sb][1] = mad_bit_read(&stream->ptr, 6);
-+		if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+		{
-+			stream->error = MAD_ERROR_LOSTSYNC;
-+			stream->sync = 0;
-+			return -1;
-+		}
- 	  /* fall through */
- 
- 	case 1:
- 	case 3:
- 	  scalefactor[ch][sb][2] = mad_bit_read(&stream->ptr, 6);
-+		if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+		{
-+			stream->error = MAD_ERROR_LOSTSYNC;
-+			stream->sync = 0;
-+			return -1;
-+		}
- 	}
- 
- 	if (scfsi[ch][sb] & 1)
-@@ -488,6 +557,12 @@
- 	  index = offset_table[bitalloc_table[offsets[sb]].offset][index - 1];
- 
- 	  II_samples(&stream->ptr, &qc_table[index], samples);
-+		if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+		{
-+			stream->error = MAD_ERROR_LOSTSYNC;
-+			stream->sync = 0;
-+			return -1;
-+		}
- 
- 	  for (s = 0; s < 3; ++s) {
- 	    frame->sbsample[ch][3 * gr + s][sb] =
-@@ -506,6 +581,12 @@
- 	index = offset_table[bitalloc_table[offsets[sb]].offset][index - 1];
- 
- 	II_samples(&stream->ptr, &qc_table[index], samples);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
- 	for (ch = 0; ch < nch; ++ch) {
- 	  for (s = 0; s < 3; ++s) {
-Index: libmad-0.15.1b/layer3.c
-===================================================================
---- libmad-0.15.1b.orig/layer3.c	2008-12-23 21:38:07.000000000 +0100
-+++ libmad-0.15.1b/layer3.c	2008-12-23 21:38:12.000000000 +0100
-@@ -2608,6 +2608,12 @@
-     next_md_begin = 0;
- 
-   md_len = si.main_data_begin + frame_space - next_md_begin;
-+  if (md_len + MAD_BUFFER_GUARD > MAD_BUFFER_MDLEN)
-+  {
-+	stream->error = MAD_ERROR_LOSTSYNC;
-+	stream->sync = 0;
-+	return -1;
-+  }
- 
-   frame_used = 0;
- 

gnu/packages/patches/libmad-length-check.patch

@@ -0,0 +1,819 @@
+Copied from Debian.
+
+From: Kurt Roeckx <kurt@roeckx.be>
+Date: Sun, 28 Jan 2018 19:26:36 +0100
+Subject: Check the size before reading with mad_bit_read
+
+There are various cases where it attemps to read past the end of the buffer
+using mad_bit_read(). Most functions didn't even know the size of the buffer
+they were reading from.
+
+Index: libmad-0.15.1b/bit.c
+===================================================================
+--- libmad-0.15.1b.orig/bit.c
++++ libmad-0.15.1b/bit.c
+@@ -138,6 +138,9 @@ unsigned long mad_bit_read(struct mad_bi
+ {
+   register unsigned long value;
+ 
++  if (len == 0)
++    return 0;
++
+   if (bitptr->left == CHAR_BIT)
+     bitptr->cache = *bitptr->byte;
+ 
+Index: libmad-0.15.1b/frame.c
+===================================================================
+--- libmad-0.15.1b.orig/frame.c
++++ libmad-0.15.1b/frame.c
+@@ -120,11 +120,18 @@ static
+ int decode_header(struct mad_header *header, struct mad_stream *stream)
+ {
+   unsigned int index;
++  struct mad_bitptr bufend_ptr;
+ 
+   header->flags        = 0;
+   header->private_bits = 0;
+ 
++  mad_bit_init(&bufend_ptr, stream->bufend);
++
+   /* header() */
++  if (mad_bit_length(&stream->ptr, &bufend_ptr) < 32) {
++    stream->error = MAD_ERROR_BUFLEN;
++    return -1;
++  }
+ 
+   /* syncword */
+   mad_bit_skip(&stream->ptr, 11);
+@@ -225,8 +232,13 @@ int decode_header(struct mad_header *hea
+   /* error_check() */
+ 
+   /* crc_check */
+-  if (header->flags & MAD_FLAG_PROTECTION)
++  if (header->flags & MAD_FLAG_PROTECTION) {
++    if (mad_bit_length(&stream->ptr, &bufend_ptr) < 16) {
++      stream->error = MAD_ERROR_BUFLEN;
++      return -1;
++    }
+     header->crc_target = mad_bit_read(&stream->ptr, 16);
++  }
+ 
+   return 0;
+ }
+@@ -338,7 +350,7 @@ int mad_header_decode(struct mad_header
+       stream->error = MAD_ERROR_BUFLEN;
+       goto fail;
+     }
+-    else if (!(ptr[0] == 0xff && (ptr[1] & 0xe0) == 0xe0)) {
++    else if ((end - ptr >= 2) && !(ptr[0] == 0xff && (ptr[1] & 0xe0) == 0xe0)) {
+       /* mark point where frame sync word was expected */
+       stream->this_frame = ptr;
+       stream->next_frame = ptr + 1;
+@@ -361,6 +373,8 @@ int mad_header_decode(struct mad_header
+     ptr = mad_bit_nextbyte(&stream->ptr);
+   }
+ 
++  stream->error = MAD_ERROR_NONE;
++
+   /* begin processing */
+   stream->this_frame = ptr;
+   stream->next_frame = ptr + 1;  /* possibly bogus sync word */
+@@ -413,7 +427,7 @@ int mad_header_decode(struct mad_header
+     /* check that a valid frame header follows this frame */
+ 
+     ptr = stream->next_frame;
+-    if (!(ptr[0] == 0xff && (ptr[1] & 0xe0) == 0xe0)) {
++    if ((end - ptr >= 2) && !(ptr[0] == 0xff && (ptr[1] & 0xe0) == 0xe0)) {
+       ptr = stream->next_frame = stream->this_frame + 1;
+       goto sync;
+     }
+Index: libmad-0.15.1b/layer12.c
+===================================================================
+--- libmad-0.15.1b.orig/layer12.c
++++ libmad-0.15.1b/layer12.c
+@@ -72,10 +72,18 @@ mad_fixed_t const linear_table[14] = {
+  * DESCRIPTION:	decode one requantized Layer I sample from a bitstream
+  */
+ static
+-mad_fixed_t I_sample(struct mad_bitptr *ptr, unsigned int nb)
++mad_fixed_t I_sample(struct mad_bitptr *ptr, unsigned int nb, struct mad_stream *stream)
+ {
+   mad_fixed_t sample;
++  struct mad_bitptr frameend_ptr;
+ 
++  mad_bit_init(&frameend_ptr, stream->next_frame);
++
++  if (mad_bit_length(ptr, &frameend_ptr) < nb) {
++    stream->error = MAD_ERROR_LOSTSYNC;
++    stream->sync = 0;
++    return 0;
++  }
+   sample = mad_bit_read(ptr, nb);
+ 
+   /* invert most significant bit, extend sign, then scale to fixed format */
+@@ -106,6 +114,10 @@ int mad_layer_I(struct mad_stream *strea
+   struct mad_header *header = &frame->header;
+   unsigned int nch, bound, ch, s, sb, nb;
+   unsigned char allocation[2][32], scalefactor[2][32];
++  struct mad_bitptr bufend_ptr, frameend_ptr;
++
++  mad_bit_init(&bufend_ptr, stream->bufend);
++  mad_bit_init(&frameend_ptr, stream->next_frame);
+ 
+   nch = MAD_NCHANNELS(header);
+ 
+@@ -118,6 +130,11 @@ int mad_layer_I(struct mad_stream *strea
+   /* check CRC word */
+ 
+   if (header->flags & MAD_FLAG_PROTECTION) {
++    if (mad_bit_length(&stream->ptr, &bufend_ptr)
++		< 4 * (bound * nch + (32 - bound))) {
++      stream->error = MAD_ERROR_BADCRC;
++      return -1;
++    }
+     header->crc_check =
+       mad_bit_crc(stream->ptr, 4 * (bound * nch + (32 - bound)),
+ 		  header->crc_check);
+@@ -133,6 +150,11 @@ int mad_layer_I(struct mad_stream *strea
+ 
+   for (sb = 0; sb < bound; ++sb) {
+     for (ch = 0; ch < nch; ++ch) {
++      if (mad_bit_length(&stream->ptr, &frameend_ptr) < 4) {
++	stream->error = MAD_ERROR_LOSTSYNC;
++	stream->sync = 0;
++	return -1;
++      }
+       nb = mad_bit_read(&stream->ptr, 4);
+ 
+       if (nb == 15) {
+@@ -145,6 +167,11 @@ int mad_layer_I(struct mad_stream *strea
+   }
+ 
+   for (sb = bound; sb < 32; ++sb) {
++    if (mad_bit_length(&stream->ptr, &frameend_ptr) < 4) {
++      stream->error = MAD_ERROR_LOSTSYNC;
++      stream->sync = 0;
++      return -1;
++    }
+     nb = mad_bit_read(&stream->ptr, 4);
+ 
+     if (nb == 15) {
+@@ -161,6 +188,11 @@ int mad_layer_I(struct mad_stream *strea
+   for (sb = 0; sb < 32; ++sb) {
+     for (ch = 0; ch < nch; ++ch) {
+       if (allocation[ch][sb]) {
++        if (mad_bit_length(&stream->ptr, &frameend_ptr) < 6) {
++	  stream->error = MAD_ERROR_LOSTSYNC;
++	  stream->sync = 0;
++	  return -1;
++	}
+ 	scalefactor[ch][sb] = mad_bit_read(&stream->ptr, 6);
+ 
+ # if defined(OPT_STRICT)
+@@ -185,8 +217,10 @@ int mad_layer_I(struct mad_stream *strea
+       for (ch = 0; ch < nch; ++ch) {
+ 	nb = allocation[ch][sb];
+ 	frame->sbsample[ch][s][sb] = nb ?
+-	  mad_f_mul(I_sample(&stream->ptr, nb),
++	  mad_f_mul(I_sample(&stream->ptr, nb, stream),
+ 		    sf_table[scalefactor[ch][sb]]) : 0;
++	if (stream->error != 0)
++	  return -1;
+       }
+     }
+ 
+@@ -194,7 +228,14 @@ int mad_layer_I(struct mad_stream *strea
+       if ((nb = allocation[0][sb])) {
+ 	mad_fixed_t sample;
+ 
+-	sample = I_sample(&stream->ptr, nb);
++	if (mad_bit_length(&stream->ptr, &frameend_ptr) < nb) {
++	  stream->error = MAD_ERROR_LOSTSYNC;
++	  stream->sync = 0;
++          return -1;
++	}
++	sample = I_sample(&stream->ptr, nb, stream);
++        if (stream->error != 0)
++	  return -1;
+ 
+ 	for (ch = 0; ch < nch; ++ch) {
+ 	  frame->sbsample[ch][s][sb] =
+@@ -280,13 +321,21 @@ struct quantclass {
+ static
+ void II_samples(struct mad_bitptr *ptr,
+ 		struct quantclass const *quantclass,
+-		mad_fixed_t output[3])
++		mad_fixed_t output[3], struct mad_stream *stream)
+ {
+   unsigned int nb, s, sample[3];
++  struct mad_bitptr frameend_ptr;
++
++  mad_bit_init(&frameend_ptr, stream->next_frame);
+ 
+   if ((nb = quantclass->group)) {
+     unsigned int c, nlevels;
+ 
++    if (mad_bit_length(ptr, &frameend_ptr) < quantclass->bits) {
++      stream->error = MAD_ERROR_LOSTSYNC;
++      stream->sync = 0;
++      return;
++    }
+     /* degrouping */
+     c = mad_bit_read(ptr, quantclass->bits);
+     nlevels = quantclass->nlevels;
+@@ -299,8 +348,14 @@ void II_samples(struct mad_bitptr *ptr,
+   else {
+     nb = quantclass->bits;
+ 
+-    for (s = 0; s < 3; ++s)
++    for (s = 0; s < 3; ++s) {
++      if (mad_bit_length(ptr, &frameend_ptr) < nb) {
++	stream->error = MAD_ERROR_LOSTSYNC;
++	stream->sync = 0;
++	return;
++      }
+       sample[s] = mad_bit_read(ptr, nb);
++    }
+   }
+ 
+   for (s = 0; s < 3; ++s) {
+@@ -336,6 +391,9 @@ int mad_layer_II(struct mad_stream *stre
+   unsigned char const *offsets;
+   unsigned char allocation[2][32], scfsi[2][32], scalefactor[2][32][3];
+   mad_fixed_t samples[3];
++  struct mad_bitptr frameend_ptr;
++
++  mad_bit_init(&frameend_ptr, stream->next_frame);
+ 
+   nch = MAD_NCHANNELS(header);
+ 
+@@ -402,13 +460,24 @@ int mad_layer_II(struct mad_stream *stre
+   for (sb = 0; sb < bound; ++sb) {
+     nbal = bitalloc_table[offsets[sb]].nbal;
+ 
+-    for (ch = 0; ch < nch; ++ch)
++    for (ch = 0; ch < nch; ++ch) {
++      if (mad_bit_length(&stream->ptr, &frameend_ptr) < nbal) {
++	stream->error = MAD_ERROR_LOSTSYNC;
++	stream->sync = 0;
++	return -1;
++      }
+       allocation[ch][sb] = mad_bit_read(&stream->ptr, nbal);
++    }
+   }
+ 
+   for (sb = bound; sb < sblimit; ++sb) {
+     nbal = bitalloc_table[offsets[sb]].nbal;
+ 
++    if (mad_bit_length(&stream->ptr, &frameend_ptr) < nbal) {
++      stream->error = MAD_ERROR_LOSTSYNC;
++      stream->sync = 0;
++      return -1;
++    }
+     allocation[0][sb] =
+     allocation[1][sb] = mad_bit_read(&stream->ptr, nbal);
+   }
+@@ -417,8 +486,14 @@ int mad_layer_II(struct mad_stream *stre
+ 
+   for (sb = 0; sb < sblimit; ++sb) {
+     for (ch = 0; ch < nch; ++ch) {
+-      if (allocation[ch][sb])
++      if (allocation[ch][sb]) {
++	if (mad_bit_length(&stream->ptr, &frameend_ptr) < 2) {
++	  stream->error = MAD_ERROR_LOSTSYNC;
++	  stream->sync = 0;
++	  return -1;
++	}
+ 	scfsi[ch][sb] = mad_bit_read(&stream->ptr, 2);
++      }
+     }
+   }
+ 
+@@ -441,6 +516,11 @@ int mad_layer_II(struct mad_stream *stre
+   for (sb = 0; sb < sblimit; ++sb) {
+     for (ch = 0; ch < nch; ++ch) {
+       if (allocation[ch][sb]) {
++	if (mad_bit_length(&stream->ptr, &frameend_ptr) < 6) {
++	  stream->error = MAD_ERROR_LOSTSYNC;
++	  stream->sync = 0;
++	  return -1;
++	}
+ 	scalefactor[ch][sb][0] = mad_bit_read(&stream->ptr, 6);
+ 
+ 	switch (scfsi[ch][sb]) {
+@@ -451,11 +531,21 @@ int mad_layer_II(struct mad_stream *stre
+ 	  break;
+ 
+ 	case 0:
++	  if (mad_bit_length(&stream->ptr, &frameend_ptr) < 6) {
++	    stream->error = MAD_ERROR_LOSTSYNC;
++	    stream->sync = 0;
++	    return -1;
++	  }
+ 	  scalefactor[ch][sb][1] = mad_bit_read(&stream->ptr, 6);
+ 	  /* fall through */
+ 
+ 	case 1:
+ 	case 3:
++	  if (mad_bit_length(&stream->ptr, &frameend_ptr) < 6) {
++	    stream->error = MAD_ERROR_LOSTSYNC;
++	    stream->sync = 0;
++	    return -1;
++	  }
+ 	  scalefactor[ch][sb][2] = mad_bit_read(&stream->ptr, 6);
+ 	}
+ 
+@@ -487,7 +577,9 @@ int mad_layer_II(struct mad_stream *stre
+ 	if ((index = allocation[ch][sb])) {
+ 	  index = offset_table[bitalloc_table[offsets[sb]].offset][index - 1];
+ 
+-	  II_samples(&stream->ptr, &qc_table[index], samples);
++	  II_samples(&stream->ptr, &qc_table[index], samples, stream);
++	  if (stream->error != 0)
++            return -1;
+ 
+ 	  for (s = 0; s < 3; ++s) {
+ 	    frame->sbsample[ch][3 * gr + s][sb] =
+@@ -505,7 +597,9 @@ int mad_layer_II(struct mad_stream *stre
+       if ((index = allocation[0][sb])) {
+ 	index = offset_table[bitalloc_table[offsets[sb]].offset][index - 1];
+ 
+-	II_samples(&stream->ptr, &qc_table[index], samples);
++	II_samples(&stream->ptr, &qc_table[index], samples, stream);
++	if (stream->error != 0)
++          return -1;
+ 
+ 	for (ch = 0; ch < nch; ++ch) {
+ 	  for (s = 0; s < 3; ++s) {
+Index: libmad-0.15.1b/layer3.c
+===================================================================
+--- libmad-0.15.1b.orig/layer3.c
++++ libmad-0.15.1b/layer3.c
+@@ -598,7 +598,8 @@ enum mad_error III_sideinfo(struct mad_b
+ static
+ unsigned int III_scalefactors_lsf(struct mad_bitptr *ptr,
+ 				  struct channel *channel,
+-				  struct channel *gr1ch, int mode_extension)
++				  struct channel *gr1ch, int mode_extension,
++				  unsigned int bits_left, unsigned int *part2_length)
+ {
+   struct mad_bitptr start;
+   unsigned int scalefac_compress, index, slen[4], part, n, i;
+@@ -644,8 +645,12 @@ unsigned int III_scalefactors_lsf(struct
+ 
+     n = 0;
+     for (part = 0; part < 4; ++part) {
+-      for (i = 0; i < nsfb[part]; ++i)
++      for (i = 0; i < nsfb[part]; ++i) {
++	if (bits_left < slen[part])
++	  return MAD_ERROR_BADSCFSI;
+ 	channel->scalefac[n++] = mad_bit_read(ptr, slen[part]);
++	bits_left -= slen[part];
++      }
+     }
+ 
+     while (n < 39)
+@@ -690,7 +695,10 @@ unsigned int III_scalefactors_lsf(struct
+       max = (1 << slen[part]) - 1;
+ 
+       for (i = 0; i < nsfb[part]; ++i) {
++	if (bits_left < slen[part])
++	  return MAD_ERROR_BADSCFSI;
+ 	is_pos = mad_bit_read(ptr, slen[part]);
++	bits_left -= slen[part];
+ 
+ 	channel->scalefac[n] = is_pos;
+ 	gr1ch->scalefac[n++] = (is_pos == max);
+@@ -703,7 +711,8 @@ unsigned int III_scalefactors_lsf(struct
+     }
+   }
+ 
+-  return mad_bit_length(&start, ptr);
++  *part2_length = mad_bit_length(&start, ptr);
++  return MAD_ERROR_NONE;
+ }
+ 
+ /*
+@@ -712,7 +721,8 @@ unsigned int III_scalefactors_lsf(struct
+  */
+ static
+ unsigned int III_scalefactors(struct mad_bitptr *ptr, struct channel *channel,
+-			      struct channel const *gr0ch, unsigned int scfsi)
++			      struct channel const *gr0ch, unsigned int scfsi,
++			      unsigned int bits_left, unsigned int *part2_length)
+ {
+   struct mad_bitptr start;
+   unsigned int slen1, slen2, sfbi;
+@@ -728,12 +738,20 @@ unsigned int III_scalefactors(struct mad
+     sfbi = 0;
+ 
+     nsfb = (channel->flags & mixed_block_flag) ? 8 + 3 * 3 : 6 * 3;
+-    while (nsfb--)
++    while (nsfb--) {
++      if (bits_left < slen1)
++	return MAD_ERROR_BADSCFSI;
+       channel->scalefac[sfbi++] = mad_bit_read(ptr, slen1);
++      bits_left -= slen1;
++    }
+ 
+     nsfb = 6 * 3;
+-    while (nsfb--)
++    while (nsfb--) {
++      if (bits_left < slen2)
++	return MAD_ERROR_BADSCFSI;
+       channel->scalefac[sfbi++] = mad_bit_read(ptr, slen2);
++      bits_left -= slen2;
++    }
+ 
+     nsfb = 1 * 3;
+     while (nsfb--)
+@@ -745,8 +763,12 @@ unsigned int III_scalefactors(struct mad
+ 	channel->scalefac[sfbi] = gr0ch->scalefac[sfbi];
+     }
+     else {
+-      for (sfbi = 0; sfbi < 6; ++sfbi)
++      for (sfbi = 0; sfbi < 6; ++sfbi) {
++	if (bits_left < slen1)
++	  return MAD_ERROR_BADSCFSI;
+ 	channel->scalefac[sfbi] = mad_bit_read(ptr, slen1);
++	bits_left -= slen1;
++      }
+     }
+ 
+     if (scfsi & 0x4) {
+@@ -754,8 +776,12 @@ unsigned int III_scalefactors(struct mad
+ 	channel->scalefac[sfbi] = gr0ch->scalefac[sfbi];
+     }
+     else {
+-      for (sfbi = 6; sfbi < 11; ++sfbi)
++      for (sfbi = 6; sfbi < 11; ++sfbi) {
++	if (bits_left < slen1)
++	  return MAD_ERROR_BADSCFSI;
+ 	channel->scalefac[sfbi] = mad_bit_read(ptr, slen1);
++	bits_left -= slen1;
++      }
+     }
+ 
+     if (scfsi & 0x2) {
+@@ -763,8 +789,12 @@ unsigned int III_scalefactors(struct mad
+ 	channel->scalefac[sfbi] = gr0ch->scalefac[sfbi];
+     }
+     else {
+-      for (sfbi = 11; sfbi < 16; ++sfbi)
++      for (sfbi = 11; sfbi < 16; ++sfbi) {
++	if (bits_left < slen2)
++	  return MAD_ERROR_BADSCFSI;
+ 	channel->scalefac[sfbi] = mad_bit_read(ptr, slen2);
++	bits_left -= slen2;
++      }
+     }
+ 
+     if (scfsi & 0x1) {
+@@ -772,14 +802,19 @@ unsigned int III_scalefactors(struct mad
+ 	channel->scalefac[sfbi] = gr0ch->scalefac[sfbi];
+     }
+     else {
+-      for (sfbi = 16; sfbi < 21; ++sfbi)
++      for (sfbi = 16; sfbi < 21; ++sfbi) {
++	if (bits_left < slen2)
++	  return MAD_ERROR_BADSCFSI;
+ 	channel->scalefac[sfbi] = mad_bit_read(ptr, slen2);
++	bits_left -= slen2;
++      }
+     }
+ 
+     channel->scalefac[21] = 0;
+   }
+ 
+-  return mad_bit_length(&start, ptr);
++  *part2_length = mad_bit_length(&start, ptr);
++  return MAD_ERROR_NONE;
+ }
+ 
+ /*
+@@ -933,19 +968,17 @@ static
+ enum mad_error III_huffdecode(struct mad_bitptr *ptr, mad_fixed_t xr[576],
+ 			      struct channel *channel,
+ 			      unsigned char const *sfbwidth,
+-			      unsigned int part2_length)
++			      signed int part3_length)
+ {
+   signed int exponents[39], exp;
+   signed int const *expptr;
+   struct mad_bitptr peek;
+-  signed int bits_left, cachesz;
++  signed int bits_left, cachesz, fakebits;
+   register mad_fixed_t *xrptr;
+   mad_fixed_t const *sfbound;
+   register unsigned long bitcache;
+ 
+-  bits_left = (signed) channel->part2_3_length - (signed) part2_length;
+-  if (bits_left < 0)
+-    return MAD_ERROR_BADPART3LEN;
++  bits_left = part3_length;
+ 
+   III_exponents(channel, sfbwidth, exponents);
+ 
+@@ -956,8 +989,12 @@ enum mad_error III_huffdecode(struct mad
+   cachesz  = mad_bit_bitsleft(&peek);
+   cachesz += ((32 - 1 - 24) + (24 - cachesz)) & ~7;
+ 
++  if (bits_left < cachesz) {
++    cachesz = bits_left;
++  }
+   bitcache   = mad_bit_read(&peek, cachesz);
+   bits_left -= cachesz;
++  fakebits = 0;
+ 
+   xrptr = &xr[0];
+ 
+@@ -986,7 +1023,7 @@ enum mad_error III_huffdecode(struct mad
+ 
+     big_values = channel->big_values;
+ 
+-    while (big_values-- && cachesz + bits_left > 0) {
++    while (big_values-- && cachesz + bits_left - fakebits > 0) {
+       union huffpair const *pair;
+       unsigned int clumpsz, value;
+       register mad_fixed_t requantized;
+@@ -1023,10 +1060,19 @@ enum mad_error III_huffdecode(struct mad
+ 	unsigned int bits;
+ 
+ 	bits       = ((32 - 1 - 21) + (21 - cachesz)) & ~7;
++	if (bits_left < bits) {
++	  bits = bits_left;
++	}
+ 	bitcache   = (bitcache << bits) | mad_bit_read(&peek, bits);
+ 	cachesz   += bits;
+ 	bits_left -= bits;
+       }
++      if (cachesz < 21) {
++	unsigned int bits = 21 - cachesz;
++	bitcache <<= bits;
++	cachesz += bits;
++	fakebits += bits;
++      }
+ 
+       /* hcod (0..19) */
+ 
+@@ -1041,6 +1087,8 @@ enum mad_error III_huffdecode(struct mad
+       }
+ 
+       cachesz -= pair->value.hlen;
++      if (cachesz < fakebits)
++	return MAD_ERROR_BADHUFFDATA;
+ 
+       if (linbits) {
+ 	/* x (0..14) */
+@@ -1054,10 +1102,15 @@ enum mad_error III_huffdecode(struct mad
+ 
+ 	case 15:
+ 	  if (cachesz < linbits + 2) {
+-	    bitcache   = (bitcache << 16) | mad_bit_read(&peek, 16);
+-	    cachesz   += 16;
+-	    bits_left -= 16;
++	    unsigned int bits = 16;
++	    if (bits_left < 16)
++	      bits = bits_left;
++	    bitcache   = (bitcache << bits) | mad_bit_read(&peek, bits);
++	    cachesz   += bits;
++	    bits_left -= bits;
+ 	  }
++	  if (cachesz - fakebits < linbits)
++	    return MAD_ERROR_BADHUFFDATA;
+ 
+ 	  value += MASK(bitcache, cachesz, linbits);
+ 	  cachesz -= linbits;
+@@ -1074,6 +1127,8 @@ enum mad_error III_huffdecode(struct mad
+ 	  }
+ 
+ 	x_final:
++	  if (cachesz - fakebits < 1)
++	    return MAD_ERROR_BADHUFFDATA;
+ 	  xrptr[0] = MASK1BIT(bitcache, cachesz--) ?
+ 	    -requantized : requantized;
+ 	}
+@@ -1089,10 +1144,15 @@ enum mad_error III_huffdecode(struct mad
+ 
+ 	case 15:
+ 	  if (cachesz < linbits + 1) {
+-	    bitcache   = (bitcache << 16) | mad_bit_read(&peek, 16);
+-	    cachesz   += 16;
+-	    bits_left -= 16;
++	    unsigned int bits = 16;
++	    if (bits_left < 16)
++	      bits = bits_left;
++	    bitcache   = (bitcache << bits) | mad_bit_read(&peek, bits);
++	    cachesz   += bits;
++	    bits_left -= bits;
+ 	  }
++	  if (cachesz - fakebits < linbits)
++	    return MAD_ERROR_BADHUFFDATA;
+ 
+ 	  value += MASK(bitcache, cachesz, linbits);
+ 	  cachesz -= linbits;
+@@ -1109,6 +1169,8 @@ enum mad_error III_huffdecode(struct mad
+ 	  }
+ 
+ 	y_final:
++	  if (cachesz - fakebits < 1)
++	    return MAD_ERROR_BADHUFFDATA;
+ 	  xrptr[1] = MASK1BIT(bitcache, cachesz--) ?
+ 	    -requantized : requantized;
+ 	}
+@@ -1128,6 +1190,8 @@ enum mad_error III_huffdecode(struct mad
+ 	    requantized = reqcache[value] = III_requantize(value, exp);
+ 	  }
+ 
++	  if (cachesz - fakebits < 1)
++	    return MAD_ERROR_BADHUFFDATA;
+ 	  xrptr[0] = MASK1BIT(bitcache, cachesz--) ?
+ 	    -requantized : requantized;
+ 	}
+@@ -1146,6 +1210,8 @@ enum mad_error III_huffdecode(struct mad
+ 	    requantized = reqcache[value] = III_requantize(value, exp);
+ 	  }
+ 
++	  if (cachesz - fakebits < 1)
++	    return MAD_ERROR_BADHUFFDATA;
+ 	  xrptr[1] = MASK1BIT(bitcache, cachesz--) ?
+ 	    -requantized : requantized;
+ 	}
+@@ -1155,9 +1221,6 @@ enum mad_error III_huffdecode(struct mad
+     }
+   }
+ 
+-  if (cachesz + bits_left < 0)
+-    return MAD_ERROR_BADHUFFDATA;  /* big_values overrun */
+-
+   /* count1 */
+   {
+     union huffquad const *table;
+@@ -1167,15 +1230,24 @@ enum mad_error III_huffdecode(struct mad
+ 
+     requantized = III_requantize(1, exp);
+ 
+-    while (cachesz + bits_left > 0 && xrptr <= &xr[572]) {
++    while (cachesz + bits_left - fakebits > 0 && xrptr <= &xr[572]) {
+       union huffquad const *quad;
+ 
+       /* hcod (1..6) */
+ 
+       if (cachesz < 10) {
+-	bitcache   = (bitcache << 16) | mad_bit_read(&peek, 16);
+-	cachesz   += 16;
+-	bits_left -= 16;
++	unsigned int bits = 16;
++	if (bits_left < 16)
++	  bits = bits_left;
++	bitcache   = (bitcache << bits) | mad_bit_read(&peek, bits);
++	cachesz   += bits;
++	bits_left -= bits;
++      }
++      if (cachesz < 10) {
++	unsigned int bits = 10 - cachesz;
++	bitcache <<= bits;
++	cachesz += bits;
++	fakebits += bits;
+       }
+ 
+       quad = &table[MASK(bitcache, cachesz, 4)];
+@@ -1188,6 +1260,11 @@ enum mad_error III_huffdecode(struct mad
+ 		      MASK(bitcache, cachesz, quad->ptr.bits)];
+       }
+ 
++      if (cachesz - fakebits < quad->value.hlen + quad->value.v
++        + quad->value.w + quad->value.x + quad->value.y)
++	/* We don't have enough bits to read one more entry, consider them
++	 * stuffing bits. */
++	break;
+       cachesz -= quad->value.hlen;
+ 
+       if (xrptr == sfbound) {
+@@ -1236,22 +1313,8 @@ enum mad_error III_huffdecode(struct mad
+ 
+       xrptr += 2;
+     }
+-
+-    if (cachesz + bits_left < 0) {
+-# if 0 && defined(DEBUG)
+-      fprintf(stderr, "huffman count1 overrun (%d bits)\n",
+-	      -(cachesz + bits_left));
+-# endif
+-
+-      /* technically the bitstream is misformatted, but apparently
+-	 some encoders are just a bit sloppy with stuffing bits */
+-
+-      xrptr -= 4;
+-    }
+   }
+ 
+-  assert(-bits_left <= MAD_BUFFER_GUARD * CHAR_BIT);
+-
+ # if 0 && defined(DEBUG)
+   if (bits_left < 0)
+     fprintf(stderr, "read %d bits too many\n", -bits_left);
+@@ -2348,10 +2411,11 @@ void III_freqinver(mad_fixed_t sample[18
+  */
+ static
+ enum mad_error III_decode(struct mad_bitptr *ptr, struct mad_frame *frame,
+-			  struct sideinfo *si, unsigned int nch)
++			  struct sideinfo *si, unsigned int nch, unsigned int md_len)
+ {
+   struct mad_header *header = &frame->header;
+   unsigned int sfreqi, ngr, gr;
++  int bits_left = md_len * CHAR_BIT;
+ 
+   {
+     unsigned int sfreq;
+@@ -2383,6 +2447,7 @@ enum mad_error III_decode(struct mad_bit
+     for (ch = 0; ch < nch; ++ch) {
+       struct channel *channel = &granule->ch[ch];
+       unsigned int part2_length;
++      unsigned int part3_length;
+ 
+       sfbwidth[ch] = sfbwidth_table[sfreqi].l;
+       if (channel->block_type == 2) {
+@@ -2391,18 +2456,30 @@ enum mad_error III_decode(struct mad_bit
+       }
+ 
+       if (header->flags & MAD_FLAG_LSF_EXT) {
+-	part2_length = III_scalefactors_lsf(ptr, channel,
++	error = III_scalefactors_lsf(ptr, channel,
+ 					    ch == 0 ? 0 : &si->gr[1].ch[1],
+-					    header->mode_extension);
++					    header->mode_extension, bits_left, &part2_length);
+       }
+       else {
+-	part2_length = III_scalefactors(ptr, channel, &si->gr[0].ch[ch],
+-					gr == 0 ? 0 : si->scfsi[ch]);
++	error = III_scalefactors(ptr, channel, &si->gr[0].ch[ch],
++					gr == 0 ? 0 : si->scfsi[ch], bits_left, &part2_length);
+       }
++      if (error)
++        return error;
++
++      bits_left -= part2_length;
+ 
+-      error = III_huffdecode(ptr, xr[ch], channel, sfbwidth[ch], part2_length);
++      if (part2_length > channel->part2_3_length)
++        return MAD_ERROR_BADPART3LEN;
++
++      part3_length = channel->part2_3_length - part2_length;
++      if (part3_length > bits_left)
++        return MAD_ERROR_BADPART3LEN;
++
++      error = III_huffdecode(ptr, xr[ch], channel, sfbwidth[ch], part3_length);
+       if (error)
+ 	return error;
++      bits_left -= part3_length;
+     }
+ 
+     /* joint stereo processing */
+@@ -2519,11 +2596,13 @@ int mad_layer_III(struct mad_stream *str
+   unsigned int nch, priv_bitlen, next_md_begin = 0;
+   unsigned int si_len, data_bitlen, md_len;
+   unsigned int frame_space, frame_used, frame_free;
+-  struct mad_bitptr ptr;
++  struct mad_bitptr ptr, bufend_ptr;
+   struct sideinfo si;
+   enum mad_error error;
+   int result = 0;
+ 
++  mad_bit_init(&bufend_ptr, stream->bufend);
++
+   /* allocate Layer III dynamic structures */
+ 
+   if (stream->main_data == 0) {
+@@ -2587,14 +2666,15 @@ int mad_layer_III(struct mad_stream *str
+     unsigned long header;
+ 
+     mad_bit_init(&peek, stream->next_frame);
++    if (mad_bit_length(&peek, &bufend_ptr) >= 57) {
++      header = mad_bit_read(&peek, 32);
++      if ((header & 0xffe60000L) /* syncword | layer */ == 0xffe20000L) {
++        if (!(header & 0x00010000L))  /* protection_bit */
++	  mad_bit_skip(&peek, 16);  /* crc_check */
+ 
+-    header = mad_bit_read(&peek, 32);
+-    if ((header & 0xffe60000L) /* syncword | layer */ == 0xffe20000L) {
+-      if (!(header & 0x00010000L))  /* protection_bit */
+-	mad_bit_skip(&peek, 16);  /* crc_check */
+-
+-      next_md_begin =
+-	mad_bit_read(&peek, (header & 0x00080000L) /* ID */ ? 9 : 8);
++        next_md_begin =
++	  mad_bit_read(&peek, (header & 0x00080000L) /* ID */ ? 9 : 8);
++      }
+     }
+ 
+     mad_bit_finish(&peek);
+@@ -2653,7 +2733,7 @@ int mad_layer_III(struct mad_stream *str
+   /* decode main_data */
+ 
+   if (result == 0) {
+-    error = III_decode(&ptr, frame, &si, nch);
++    error = III_decode(&ptr, frame, &si, nch, md_len);
+     if (error) {
+       stream->error = error;
+       result = -1;

gnu/packages/patches/libmad-md_size.patch

@@ -0,0 +1,60 @@
+Copied from Debian.
+
+From: Kurt Roeckx <kurt@roeckx.be>
+Date: Sun, 28 Jan 2018 15:44:08 +0100
+Subject: Check the size of the main data
+
+The main data to decode a frame can come from the current frame and part of the
+previous frame, the so called bit reservoir. si.main_data_begin is the part of
+the previous frame we need for this frame. frame_space is the amount of main
+data that can be in this frame, and next_md_begin is the part of this frame that
+is going to be used for the next frame.
+
+The maximum amount of data from a previous frame that the format allows is 511
+bytes. The maximum frame size for the defined bitrates is at MPEG 2.5 layer 2
+at 320 kbit/s and 8 kHz sample rate which gives 72 * (320000 / 8000) + 1 = 2881.
+So those defines are not large enough:
+ # define MAD_BUFFER_GUARD      8
+ # define MAD_BUFFER_MDLEN      (511 + 2048 + MAD_BUFFER_GUARD)
+
+There is also support for a "free" bitrate which allows you to create any frame
+size, which can be larger than the buffer.
+
+Changing the defines is not an option since it's part of the ABI, so we check
+that the main data fits in the bufer.
+
+The previous frame data is stored in *stream->main_data and contains
+stream->md_len bytes. If stream->md_len is larger than the data we
+need from the previous frame (si.main_data_begin) it still wouldn't fit
+in the buffer, so just keep the data that we need.
+
+Index: libmad-0.15.1b/layer3.c
+===================================================================
+--- libmad-0.15.1b.orig/layer3.c
++++ libmad-0.15.1b/layer3.c
+@@ -2608,6 +2608,11 @@ int mad_layer_III(struct mad_stream *str
+     next_md_begin = 0;
+ 
+   md_len = si.main_data_begin + frame_space - next_md_begin;
++  if (md_len + MAD_BUFFER_GUARD > MAD_BUFFER_MDLEN) {
++    stream->error = MAD_ERROR_LOSTSYNC;
++    stream->sync = 0;
++    return -1;
++  }
+ 
+   frame_used = 0;
+ 
+@@ -2625,8 +2630,11 @@ int mad_layer_III(struct mad_stream *str
+       }
+     }
+     else {
+-      mad_bit_init(&ptr,
+-		   *stream->main_data + stream->md_len - si.main_data_begin);
++      memmove(stream->main_data,
++	*stream->main_data + stream->md_len - si.main_data_begin,
++	si.main_data_begin);
++      stream->md_len = si.main_data_begin;
++      mad_bit_init(&ptr, *stream->main_data);
+ 
+       if (md_len > si.main_data_begin) {
+ 	assert(stream->md_len + md_len -

gnu/packages/patches/libvirt-remove-ATTRIBUTE_UNUSED.patch

@@ -1,34 +0,0 @@
-From: Tobias Geerinckx-Rice <me@tobias.gr>
-Date: Thu, 25 Jul 2019 21:48:25 +0200
-Subject: [PATCH]: libvirt: remove ATTRIBUTE_UNUSED
-
-This should fix the error reported here[0].  Patch taken verbatim from
-upstream[1].
-
-[0]: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36634#28
-[1]: https://github.com/libvirt/libvirt/commit/759bf903a6c24a8efa25c7cf4b099d952eda9bd3
-
-From 759bf903a6c24a8efa25c7cf4b099d952eda9bd3 Mon Sep 17 00:00:00 2001
-From: Pavel Hrdina <phrdina@redhat.com>
-Date: Mon, 22 Jul 2019 14:46:34 +0200
-Subject: [PATCH] vircgroupv2: remove ATTRIBUTE_UNUSED for used attribute
-
-Signed-off-by: Pavel Hrdina <phrdina@redhat.com>
-Acked-by: Peter Krempa <pkrempa@redhat.com>
----
- src/util/vircgroupv2.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/util/vircgroupv2.c b/src/util/vircgroupv2.c
-index af3192c99c..e36c36685b 100644
---- a/src/util/vircgroupv2.c
-+++ b/src/util/vircgroupv2.c
-@@ -399,7 +399,7 @@ virCgroupV2EnableController(virCgroupPtr group,
- 
- 
- static int
--virCgroupV2MakeGroup(virCgroupPtr parent ATTRIBUTE_UNUSED,
-+virCgroupV2MakeGroup(virCgroupPtr parent,
-                      virCgroupPtr group,
-                      bool create,
-                      unsigned int flags)

gnu/packages/patches/mame-rapidjson-fix.patch

@@ -0,0 +1,37 @@
+From 0b5b13cf1e28550b49c387dec93f9801f029e313 Mon Sep 17 00:00:00 2001
+From: Julian Sikorski <belegdol+github@gmail.com>
+Date: Mon, 5 Aug 2019 21:16:54 +0200
+Subject: [PATCH] Fix building using system rapidjson
+
+---
+ scripts/target/mame/arcade.lua | 1 +
+ src/mame/video/midtunit.cpp    | 4 ++--
+ 2 files changed, 3 insertions(+), 2 deletions(-)
+
+diff --git a/scripts/target/mame/arcade.lua b/scripts/target/mame/arcade.lua
+index 964daa3572f..ef30ae3c2c2 100644
+--- a/scripts/target/mame/arcade.lua
++++ b/scripts/target/mame/arcade.lua
+@@ -930,6 +930,7 @@ function createMAMEProjects(_target, _subtarget, _name)
+ 		ext_includedir("flac"),
+ 		ext_includedir("glm"),
+ 		ext_includedir("jpeg"),
++		ext_includedir("rapidjson"),
+ 	}
+ 
+ end
+diff --git a/src/mame/video/midtunit.cpp b/src/mame/video/midtunit.cpp
+index b4cb98abacf..b307f3f722b 100644
+--- a/src/mame/video/midtunit.cpp
++++ b/src/mame/video/midtunit.cpp
+@@ -20,8 +20,8 @@
+ #include "emuopts.h" // Used by PNG logging
+ #include "png.h" // Used by PNG logging
+ 
+-#include "rapidjson/include/rapidjson/prettywriter.h" // Used by JSON logging
+-#include "rapidjson/include/rapidjson/stringbuffer.h" // Used by JSON logging
++#include <rapidjson/prettywriter.h> // Used by JSON logging
++#include <rapidjson/stringbuffer.h> // Used by JSON logging
+ 
+ DEFINE_DEVICE_TYPE(MIDTUNIT_VIDEO, midtunit_video_device, "tunitvid", "Midway T-Unit Video")
+ DEFINE_DEVICE_TYPE(MIDWUNIT_VIDEO, midwunit_video_device, "wunitvid", "Midway W-Unit Video")

gnu/packages/patches/nss-freebl-stubs.patch

@@ -0,0 +1,20 @@
+This patch is required for Makefile-based builds of NSS 3.45 on armhf-linux.
+
+Taken from upstream bug tracker:
+https://bugzilla.mozilla.org/show_bug.cgi?id=1571316
+
+diff --git a/nss/lib/freebl/ecl/curve25519_32.c b/nss/lib/freebl/ecl/curve25519_32.c
+--- a/nss/lib/freebl/ecl/curve25519_32.c
++++ b/nss/lib/freebl/ecl/curve25519_32.c
+@@ -29,6 +29,10 @@
+  *  1. Convert custom integer types to stdint.h types
+  */
+ 
++#ifdef FREEBL_NO_DEPEND
++#include "../stubs.h"
++#endif
++
+ #include "ecl-priv.h"
+ 
+ /* fe means field element. Here the field is \Z/(2^255-19). An element t,
+

gnu/packages/patches/pcre2-fix-jit_match-crash.patch

@@ -0,0 +1,25 @@
+From: Tobias Geerinckx-Rice <me@tobias.gr>
+Date: Thu, 01 Aug 2019 21:12:52 +0200
+Subject: [PATCH] gnu: pcre2: Fix jit_match crash.
+
+Fixes <https://bugs.exim.org/show_bug.cgi?id=2421>, reported as a ‘secrity
+problem’.
+
+Copied verbatim from upstream[0].
+
+[0]: https://vcs.pcre.org/pcre2/code/trunk/src/pcre2_jit_compile.c?view=patch&r1=1089&r2=1092&pathrev=1092
+
+--- trunk/src/pcre2_jit_compile.c	2019/05/10 13:15:20	1089
++++ trunk/src/pcre2_jit_compile.c	2019/05/13 16:38:18	1092
+@@ -8571,7 +8571,10 @@
+ PCRE2_SPTR bptr;
+ uint32_t c;
+ 
+-GETCHARINC(c, cc);
++/* Patch by PH */
++/* GETCHARINC(c, cc); */
++
++c = *cc++;
+ #if PCRE2_CODE_UNIT_WIDTH == 32
+ if (c >= 0x110000)
+   return NULL;

gnu/packages/patches/scribus-poppler.patch

@@ -1,72 +0,0 @@
-Fix build with recent Poppler.
-
-From d867ec3c386baaed1b8e076dd70b278863411480 Mon Sep 17 00:00:00 2001
-From: Jean Ghali <jghali@libertysurf.fr>
-Date: Mon, 30 Apr 2018 09:19:33 +0000
-Subject: [PATCH] =?UTF-8?q?#15289:=20FTBFS=201.5.4=20with=20error:=20inval?=
- =?UTF-8?q?id=20conversion=20from=20=E2=80=98const=20GooString*=E2=80=99?=
- =?UTF-8?q?=20to=20=E2=80=98GooString*=E2=80=99?=
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-git-svn-id: svn://scribus.net/trunk/Scribus@22498 11d20701-8431-0410-a711-e3c959e3b870
----
- scribus/plugins/import/pdf/importpdf.cpp | 2 +-
- scribus/plugins/import/pdf/importpdf.h   | 2 +-
- scribus/plugins/import/pdf/slaoutput.cpp | 2 +-
- scribus/plugins/import/pdf/slaoutput.h   | 2 +-
- 4 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/scribus/plugins/import/pdf/importpdf.cpp b/scribus/plugins/import/pdf/importpdf.cpp
-index c1802861aa..d4c5a9ba49 100644
---- a/scribus/plugins/import/pdf/importpdf.cpp
-+++ b/scribus/plugins/import/pdf/importpdf.cpp
-@@ -1081,7 +1081,7 @@ QRectF PdfPlug::getCBox(int box, int pgNum)
- 	return cRect;
- }
- 
--QString PdfPlug::UnicodeParsedString(GooString *s1)
-+QString PdfPlug::UnicodeParsedString(const GooString *s1)
- {
- 	if ( !s1 || s1->getLength() == 0 )
- 		return QString();
-diff --git a/scribus/plugins/import/pdf/importpdf.h b/scribus/plugins/import/pdf/importpdf.h
-index c8c5efcd0d..5249562692 100644
---- a/scribus/plugins/import/pdf/importpdf.h
-+++ b/scribus/plugins/import/pdf/importpdf.h
-@@ -81,7 +81,7 @@ class PdfPlug : public QObject
- private:
- 	bool convert(const QString& fn);
- 	QRectF getCBox(int box, int pgNum);
--	QString UnicodeParsedString(GooString *s1);
-+	QString UnicodeParsedString(const GooString *s1);
- 	
- 	QList<PageItem*> Elements;
- 	double baseX, baseY;
-diff --git a/scribus/plugins/import/pdf/slaoutput.cpp b/scribus/plugins/import/pdf/slaoutput.cpp
-index be1815dc29..17b6357246 100644
---- a/scribus/plugins/import/pdf/slaoutput.cpp
-+++ b/scribus/plugins/import/pdf/slaoutput.cpp
-@@ -4252,7 +4252,7 @@ void SlaOutputDev::pushGroup(QString maskName, GBool forSoftMask, GBool alpha, b
- 	m_groupStack.push(gElements);
- }
- 
--QString SlaOutputDev::UnicodeParsedString(GooString *s1)
-+QString SlaOutputDev::UnicodeParsedString(const GooString *s1)
- {
- 	if ( !s1 || s1->getLength() == 0 )
- 		return QString();
-diff --git a/scribus/plugins/import/pdf/slaoutput.h b/scribus/plugins/import/pdf/slaoutput.h
-index 20e8b2d311..6698c030e0 100644
---- a/scribus/plugins/import/pdf/slaoutput.h
-+++ b/scribus/plugins/import/pdf/slaoutput.h
-@@ -266,7 +266,7 @@ class SlaOutputDev : public OutputDev
- 	int getBlendMode(GfxState *state);
- 	void applyMask(PageItem *ite);
- 	void pushGroup(QString maskName = "", GBool forSoftMask = gFalse, GBool alpha = gFalse, bool inverted = false);
--	QString UnicodeParsedString(GooString *s1);
-+	QString UnicodeParsedString(const GooString *s1);
- 	bool checkClip();
- 	bool pathIsClosed;
- 	QString CurrColorFill;

gnu/packages/patches/strace-ipc-tests.patch

@@ -0,0 +1,30 @@
+Fix a test failure on some systems.
+
+Taken from upstream:
+https://github.com/strace/strace/commit/4377e3a1535a0ec3a42da8a1366ad6943f4efa0e
+
+diff --git a/tests/gen_tests.in b/tests/gen_tests.in
+index 4a506b94c..4fdf4722c 100644
+--- a/tests/gen_tests.in
++++ b/tests/gen_tests.in
+@@ -168,16 +168,16 @@ ipc_msg-Xabbrev	+ipc.sh -Xabbrev -a26
+ ipc_msg-Xraw	+ipc.sh -Xraw -a16
+ ipc_msg-Xverbose	+ipc.sh -Xverbose -a34
+ ipc_msgbuf-Xabbrev	+ipc_msgbuf.test -Xabbrev
+-ipc_msgbuf-Xraw	+ipc_msgbuf.test -Xraw -a22
++ipc_msgbuf-Xraw	+ipc_msgbuf.test -Xraw -a20
+ ipc_msgbuf-Xverbose	+ipc_msgbuf.test -Xverbose
+ ipc_sem	+ipc.sh -a29
+ ipc_sem-Xabbrev	+ipc.sh -Xabbrev -a29
+ ipc_sem-Xraw	+ipc.sh -Xraw -a19
+ ipc_sem-Xverbose	+ipc.sh -Xverbose -a36
+-ipc_shm	+ipc.sh -a29
+-ipc_shm-Xabbrev	+ipc.sh -Xabbrev -a29
++ipc_shm	+ipc.sh -a26
++ipc_shm-Xabbrev	+ipc.sh -Xabbrev -a26
+ ipc_shm-Xraw	+ipc.sh -Xraw -a19
+-ipc_shm-Xverbose	+ipc.sh -Xverbose -a36
++ipc_shm-Xverbose	+ipc.sh -Xverbose -a34
+ kcmp	-a22
+ kcmp-y	-a22 -y -e trace=kcmp
+ kern_features -a16

gnu/packages/pcre.scm

@@ -94,7 +94,7 @@ POSIX regular expression API.")
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/pcre/pcre2/"
                                   version "/pcre2-" version ".tar.bz2"))
-
+              (patches (search-patches "pcre2-fix-jit_match-crash.patch"))
               (sha256
                (base32
                 "1anqi7vpbfzag7imccrc6di1zl5rl63ab7rfpmajpw6d1kzlsl9m"))))

gnu/packages/pdf.scm

@@ -419,7 +419,7 @@ using the DjVuLibre library.")
 (define-public zathura-pdf-mupdf
   (package
     (name "zathura-pdf-mupdf")
-    (version "0.3.4")
+    (version "0.3.5")
     (source (origin
               (method url-fetch)
               (uri
@@ -427,7 +427,7 @@ using the DjVuLibre library.")
                               "/download/zathura-pdf-mupdf-" version ".tar.xz"))
               (sha256
                (base32
-                "166d5nz47ixzwj4pixsd5fd9qvjf5v34cdqi3p72vr23pswk2hyn"))))
+                "1pjwsb7zwclxsvz229fl7y2saf1pv3ifwv3ay8viqxgrp9x3z9hq"))))
     (native-inputs `(("pkg-config" ,pkg-config)))
     (inputs
      `(("jbig2dec" ,jbig2dec)
@@ -604,7 +604,7 @@ extracting content or merging files.")
 (define-public mupdf
   (package
     (name "mupdf")
-    (version "1.15.0")
+    (version "1.16.1")
     (source
       (origin
         (method url-fetch)
@@ -612,7 +612,7 @@ extracting content or merging files.")
                             name "-" version "-source.tar.xz"))
         (sha256
          (base32
-          "0kmcz3ivxmqmks8vg50ri1zar18q5svk829z0g1kj08lgz7kcl2n"))
+          "1npmy92lkj41nnc14b4fpq7z62pminy94zsdbrczj22jpn283rvg"))
         (modules '((guix build utils)))
         (snippet
          ;; We keep lcms2 since it is different than our lcms.

gnu/packages/perl.scm

@@ -4082,7 +4082,7 @@ relic support.")
         (base32
          "0h3wfnpv5d4d3f9xzmwkchay6251nhzngdv3f6xia56mj4hxabs0"))))
     (build-system perl-build-system)
-    (inputs
+    (propagated-inputs
      `(("perl-clone-choose" ,perl-clone-choose)))
     (home-page "https://metacpan.org/release/Hash-Merge")
     (synopsis "Merge arbitrarily deep hashes into a single hash")
@@ -9010,15 +9010,15 @@ Tree::Simple::Visitor::* objects.")
 (define-public perl-try-tiny
   (package
     (name "perl-try-tiny")
-    (version "0.22")
+    (version "0.30")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/D/DO/DOY/"
+       (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/"
                            "Try-Tiny-" version ".tar.gz"))
        (sha256
         (base32
-         "068vdbpacfawc3lkfs0b82xxl27h3l0gj14iada3vlwk8rps9yv0"))))
+         "0szgvlz19yz3mq1lbzmwh8w5dh6agg5s16xv22zrnl83r7ax0nys"))))
     (build-system perl-build-system)
     (home-page "https://metacpan.org/release/Try-Tiny")
     (synopsis "Minimal try/catch with proper preservation of $@@")

gnu/packages/photo.scm

@@ -70,14 +70,14 @@
 (define-public libraw
   (package
     (name "libraw")
-    (version "0.19.3")
+    (version "0.19.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.libraw.org/data/LibRaw-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0xs1qb6pcvc4c43fy5xi3nkqxcif77gakkw99irf0fc5iccdd5px"))))
+                "07wnzw9k3mwdq9dmpmg94al3ksc065kskfbxkknnmhvrsv2iri8k"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

gnu/packages/php.scm

@@ -58,15 +58,15 @@
 (define-public php
   (package
     (name "php")
-    (version "7.3.6")
+    (version "7.3.8")
     (home-page "https://secure.php.net/")
     (source (origin
               (method url-fetch)
               (uri (string-append home-page "distributions/"
-                                  name "-" version ".tar.xz"))
+                                  "php-" version ".tar.xz"))
               (sha256
                (base32
-                "0r51aiff2abbr3d2swhvja0wm56sjxzqbciabcvvq3m3v9kqkz7y"))
+                "19fm990yl97fq538lkp0m1imbp30qrx7785x211w1n15wqm6n17n"))
               (modules '((guix build utils)))
               (snippet
                '(with-directory-excursion "ext"
@@ -76,7 +76,7 @@
                             ;;"mbstring/libmbfl"
                             ;;"date/lib"
                             ;;"bcmath/libbcmath"
-                            ;;"fileinfo/libmagic" ; This is a patched version of libmagic.
+                            ;;"fileinfo/libmagic" ; a patched version of libmagic
                             '("gd/libgd"
                               "mbstring/oniguruma"
                               "pcre/pcre2lib"
@@ -378,7 +378,7 @@
      `(("pkg-config" ,pkg-config)
        ("bison" ,bison)
        ("intltool" ,intltool)
-       ("procps" ,procps)))         ; For tests.
+       ("procps" ,procps)))             ; for tests
     (synopsis "PHP programming language")
     (description
       "PHP (PHP Hypertext Processor) is a server-side (CGI) scripting

gnu/packages/plotutils.scm

@@ -198,8 +198,7 @@ colors, styles, options and details.")
        ("perl" ,perl)
        ("texinfo" ,texinfo)           ;For generating documentation
        ;; For the manual and the tests.
-       ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
+       ("texlive" ,(texlive-union (list texlive-amsfonts
-                                        texlive-latex-amsfonts
                                         texlive-latex-geometry
                                         texlive-latex-graphics
                                         texlive-latex-oberdiek ; for ifluatex

gnu/packages/python-xyz.scm

@@ -3211,14 +3211,14 @@ provides additional functionality on the produced Mallard documents.")
 (define-public python-cython
   (package
     (name "python-cython")
-    (version "0.29.11")
+    (version "0.29.13")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Cython" version))
        (sha256
         (base32
-         "1866m01ggl2h3rky4hac3m5p048gg4a0jb09ljkknryiqln54fkn"))))
+         "13k37lrcgagwwnzr5bzririsscb793vndj234d475x1h9ad0d7f2"))))
     (build-system python-build-system)
     ;; we need the full python package and not just the python-wrapper
     ;; because we need libpython3.3m.so
@@ -3548,12 +3548,11 @@ color scales, and color space conversion easy.  It has support for:
        ("pkg-config" ,pkg-config)
        ("python-sphinx" ,python-sphinx)
        ("python-numpydoc" ,python-numpydoc)
-       ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
+       ("texlive" ,(texlive-union (list texlive-fonts-cm-super
-                                        texlive-fonts-cm-super
                                         texlive-fonts-ec
                                         texlive-generic-ifxetex
                                         texlive-generic-pdftex
-                                        texlive-latex-amsfonts
+                                        texlive-amsfonts
                                         texlive-latex-capt-of
                                         texlive-latex-cmap
                                         texlive-latex-environ
@@ -3952,7 +3951,7 @@ toolkits.")
        ("python-ipykernel" ,python-ipykernel)
        ("python-mock" ,python-mock)
        ("graphviz" ,graphviz)
-       ("texlive" ,(texlive-union (list texlive-latex-amsfonts
+       ("texlive" ,(texlive-union (list texlive-amsfonts
                                         texlive-latex-amsmath
                                         texlive-latex-enumitem
                                         texlive-latex-expdlist
@@ -3963,7 +3962,6 @@ toolkits.")
 
                                         texlive-generic-pdftex
 
-                                        texlive-fonts-amsfonts
                                         texlive-fonts-ec
                                         texlive-fonts-adobe-times
                                         texlive-fonts-txfonts)))
@@ -5520,11 +5518,10 @@ computing.")
      `(("python-sphinx" ,python-sphinx)
        ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme)
        ;; FIXME: It's possible that a smaller union would work just as well.
-       ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
+       ("texlive" ,(texlive-union (list texlive-amsfonts
                                         texlive-fonts-ec
                                         texlive-generic-ifxetex
                                         texlive-generic-pdftex
-                                        texlive-latex-amsfonts
                                         texlive-latex-capt-of
                                         texlive-latex-cmap
                                         texlive-latex-environ
@@ -8805,20 +8802,24 @@ python-xdo for newer bindings.)")
 (define-public python-mako
   (package
     (name "python-mako")
-    (version "1.0.13")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Mako" version))
        (sha256
         (base32
-         "0h95n0g0k1jwxiqarr09navpfajarvbmpm8mhmw66c25qc675vlm"))))
+         "0jqa3qfpykyn4fmkn0kh6043sfls7br8i2bsdbccazcvk9cijsd3"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda _
+                      (invoke "pytest" "-vv"))))))
     (propagated-inputs
      `(("python-markupsafe" ,python-markupsafe)))
     (native-inputs
      `(("python-mock" ,python-mock)
-       ("python-nose" ,python-nose)
        ("python-pytest" ,python-pytest)))
     (home-page "https://www.makotemplates.org/")
     (synopsis "Templating language for Python")

gnu/packages/regex.scm

@@ -30,7 +30,7 @@
 (define-public re2
    (package
      (name "re2")
-     (version "2019-07-01")
+     (version "2019-08-01")
      (home-page "https://github.com/google/re2")
      (source (origin
                (method git-fetch)
@@ -38,7 +38,7 @@
                (file-name (git-file-name name version))
                (sha256
                 (base32
-                 "1ric6gdnf5mqj5iy5f81al49mr3mmjqj3nqi3mw2hjdbbgwkdn71"))))
+                 "11w9x16y26nfgliis28ivrh9b1x6pxawdwxfwxfjh34h57c0dkzg"))))
      (build-system gnu-build-system)
      (arguments
       `(#:modules ((guix build gnu-build-system)

gnu/packages/ruby.scm

@@ -4849,14 +4849,14 @@ alternative to Marshal for Object serialization. ")
 (define-public ruby-pg
   (package
     (name "ruby-pg")
-    (version "1.1.3")
+    (version "1.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (rubygems-uri "pg" version))
        (sha256
         (base32
-         "1pnjw3rspdfjssxyf42jnbsdlgri8ylysimp0s28wxb93k6ff2qb"))))
+         "0fmnyxcyrvgdbgq7m09whgn9i8rwfybk0w8aii1nc4g5kqw0k2jy"))))
     (build-system ruby-build-system)
     (arguments
      '(#:test-target "spec"))
@@ -4865,7 +4865,7 @@ alternative to Marshal for Object serialization. ")
        ("ruby-hoe" ,ruby-hoe)
        ("ruby-rspec" ,ruby-rspec)))
     (inputs
-     `(("postgresql" ,postgresql-9.6)))
+     `(("postgresql" ,postgresql)))
     (synopsis "Ruby interface to PostgreSQL")
     (description "Pg is the Ruby interface to the PostgreSQL RDBMS.  It works
 with PostgreSQL 9.0 and later.")

gnu/packages/samba.scm

@@ -154,14 +154,14 @@ anywhere.")
 (define-public samba
   (package
     (name "samba")
-    (version "4.10.5")
+    (version "4.10.6")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://download.samba.org/pub/samba/stable/"
                                  "samba-" version ".tar.gz"))
              (sha256
               (base32
-               "0xb3mz38hcayqxchk0ws9mxn10vswsn97jbxl4gcwi4cbrnjc43c"))))
+               "0hpgdqlyczj98pkh2ldglvvnkrb1q541r3qikdvxq0qjvd9fpywy"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/scanner.scm

@@ -34,15 +34,16 @@
 (define-public sane-backends-minimal
   (package
     (name "sane-backends-minimal")
-    (version "1.0.27")
+    (version "1.0.28")
     (source (origin
              (method url-fetch)
              (uri (string-append
-                   "https://alioth.debian.org/frs/download.php/latestfile/176/"
+                   "https://gitlab.com/sane-project/backends/uploads/"
+                   "9e718daff347826f4cfe21126c8d5091/"
                    "sane-backends-" version ".tar.gz"))
              (sha256
               (base32
-               "1j9nbqspaj0rlgalafb5z6r606k0i22kz0rcpd744p176yzlfdr9"))
+               "00yy8q9hqdf0zjxxl4d8njr9zf0hhi3a9ib23ikc2anqf8zhy9ii"))
              (modules '((guix build utils)))
              (snippet
               ;; Generated HTML files and udev rules normally embed a
@@ -63,6 +64,10 @@
          (add-before 'configure 'disable-backends
            (lambda _
              (setenv "BACKENDS" " ")
+
+             ;; Disable tests that may require back ends to be built.
+             (substitute* "testsuite/Makefile.in"
+               ((" backend ") " "))
              #t))
          (add-after 'unpack 'disable-failing-tests
            (lambda _
@@ -113,6 +118,7 @@ package contains the library, but no drivers.")
     (name "sane-backends")
     (inputs
      `(("hplip" ,(@ (gnu packages cups) hplip-minimal))
+       ("libjpeg" ,libjpeg)             ; wanted by pixma, epsonds, others
        ("libpng" ,libpng)               ; support ‘scanimage --format=png’
        ,@(package-inputs sane-backends-minimal)))
     (arguments

gnu/packages/scribus.scm

@@ -48,7 +48,7 @@
 (define-public scribus
   (package
     (name "scribus")
-    (version "1.5.4")
+    (version "1.5.5")
     (source
      (origin
        (method url-fetch)
@@ -56,86 +56,7 @@
                            version "/scribus-" version ".tar.xz"))
        (sha256
         (base32
-         "00ys0p6h3iq77kh72dkl0qrf7qvznq18qdrgiq10gfxja1995034"))
+         "0w9zzsiaq3f7vpxybk01c9z2b4qqg67mzpyfb2gjchz8dhdb423r"))))
-       (patches (append
-                 ;; Scribus relies heavily on Poppler internals, which have
-                 ;; changed a lot since the latest Scribus release (2018-04).
-                 ;; Thus, we require a bunch of patches to stay compatible.
-                 (search-patches "scribus-poppler.patch")
-                 (list (origin
-                         (method url-fetch)
-                         (uri (string-append
-                               "https://github.com/scribusproject/scribus/commit/"
-                               "7d4ceeb5cac32287769e3c0238699e0b3e56c24d.patch"))
-                         (file-name "scribus-poppler-0.64.patch")
-                         (sha256
-                          (base32
-                           "1kr27bfzkpabrh42nsrrvlqyycdg9isbavpaa5spgmrhidcg02xj")))
-                       (origin
-                         (method url-fetch)
-                         (uri (string-append
-                               "https://github.com/scribusproject/scribus/commit/"
-                               "76561c1a55cd07c268f8f2b2fea888532933700b.patch"))
-                         (file-name "scribus-poppler-config.patch")
-                         (sha256
-                          (base32
-                           "01k18xjj82c3ndzp89dlpfhhdccc8z0acf8b04r592jyr5y9rc19")))
-                       (origin
-                         (method url-fetch)
-                         (uri (string-append
-                               "https://github.com/scribusproject/scribus/commit/"
-                               "8e05d26c19097ac2ad5b4ebbf40a3771ee6faf9c.patch"))
-                         (file-name "scribus-poppler-0.69.patch")
-                         (sha256
-                          (base32
-                           "1avdmsj5l543j0irq18nxgiw99n395jj56ih5dsal59fn0wbqk42")))
-                       (origin
-                         (method url-fetch)
-                         (uri (string-append "https://git.archlinux.org/svntogit/"
-                                             "community.git/plain/trunk/scribus-"
-                                             "poppler-0.70.patch?h=packages/scribus&id="
-                                             "8ef43ee2fceb0753ed5a76bb0a11c84775898ffc"))
-                         (file-name "scribus-poppler-0.70.patch")
-                         (sha256
-                          (base32
-                           "0dw7ix3jaj0y1q97cmmqwb2qgdx760yhxx86wa8rnx0xhfi5x6qr")))
-                       ;; This and the preceding patch are taken from Arch Linux
-                       ;; because they are adjusted for the Scribus release tarball
-                       ;; rather than the upstream master branch.
-                       (origin
-                         (method url-fetch)
-                         (uri (string-append "https://git.archlinux.org/svntogit/"
-                                             "community.git/plain/trunk/scribus-"
-                                             "poppler-0.75.patch?h=packages/scribus&id="
-                                             "4d35c4ad4869c1dcce9243c4786ff303bdd5c601"))
-                         (file-name "scribus-poppler-0.75.patch")
-                         (sha256
-                          (base32
-                           "1lhf2srp7iv44zzdbr3kqa0lfjmm77nalxnx80jqaixhr5yq2s8f")))
-                       (origin
-                         (method url-fetch)
-                         (uri (string-append
-                               "https://github.com/scribusproject/scribus/commit/"
-                               "9449265592a5195153d72c2a511d2010b0cf5b0b.patch"))
-                         (file-name "scribus-poppler-0.76.patch")
-                         (sha256
-                          (base32
-                           "0zghiqra9s6f6v06fdr97gdhiw41zr8r6vqh4ar4yw7rqn2771jd"))))
-                 (search-patches "scribus-poppler-0.73.patch")))
-       ;; The --binary flag is required for 'scribus-poppler-0.75.patch', because
-       ;; we need to retain the CRLF line endings.
-       (patch-flags '("-p1" "--binary"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           (for-each (lambda (file)
-                       (substitute* file
-                         ;; These are required for compatibility with Poppler 0.71.
-                         (("GBool") "bool") (("gTrue") "true") (("gFalse") "false")
-                         ;; ...and this for Poppler 0.72.
-                         (("getCString") "c_str")))
-                     (find-files "scribus/plugins/import/pdf"))
-           #t))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ;no test target
@@ -145,9 +66,9 @@
        (modify-phases %standard-phases
          (add-after 'install 'wrap-program
            (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Fix "ImportError: No module named _sysconfigdata_nd" where
+             ;; Fix "ImportError: No module named _sysconfigdata_nd"
-             ;; Scribus checks PATH and eventually runs system's Python
+             ;; runtime error where Scribus checks PATH and eventually
-             ;; instead of package's.
+             ;; runs system's Python instead of package's.
              (let* ((out (assoc-ref outputs "out"))
                     (py2 (assoc-ref inputs "python")))
                (wrap-program (string-append out "/bin/scribus")
@@ -188,12 +109,13 @@
     (home-page "https://www.scribus.net")
     (synopsis "Desktop publishing and page layout program")
     (description
-     "Scribus is a @dfn{desktop publishing} (DTP) application and can be used
+     "Scribus is a @dfn{desktop publishing} (DTP) application and can
-for many tasks; from brochure design to newspapers, magazines, newsletters and
+be used for many tasks; from brochure design to newspapers, magazines,
-posters to technical documentation.  Scribus supports professional DTP
+newsletters and posters to technical documentation.  Scribus supports
-features, such as CMYK color and a color management system to soft proof
+professional DTP features, such as CMYK color and a color management
-images for high quality color printing, flexible PDF creation options,
+system to soft proof images for high quality color printing, flexible
-Encapsulated PostScript import/export and creation of four color separations,
+PDF creation options, Encapsulated PostScript import/export and
-import of EPS/PS and SVG as native vector graphics, Unicode text including
+creation of four color separations, import of EPS/PS and SVG as native
-right to left scripts such as Arabic and Hebrew via freetype.")
+vector graphics, Unicode text including right to left scripts such as
+Arabic and Hebrew via FreeType.")
     (license license:gpl2+)))

gnu/packages/search.scm

@@ -49,14 +49,14 @@
 (define-public xapian
   (package
     (name "xapian")
-    (version "1.4.11")
+    (version "1.4.12")
     ;; Note: When updating Xapian, remember to update xapian-bindings below.
     (source (origin
               (method url-fetch)
               (uri (string-append "https://oligarchy.co.uk/xapian/" version
                                   "/xapian-core-" version ".tar.xz"))
               (sha256
-               (base32 "01xwqljnp5afjf9097lyfbqc6x5bcqszfdkn9l1j86imwbrv45lz"))))
+               (base32 "0z5c1y9vp519h2x2igjq39v6j615nppry0wasd0xn4hphgd3d2jg"))))
     (build-system gnu-build-system)
     (inputs `(("zlib" ,zlib)
               ("util-linux" ,util-linux)))
@@ -94,7 +94,7 @@ rich set of boolean query operators.")
                                   "/xapian-bindings-" version ".tar.xz"))
               (sha256
                (base32
-                "13bi2vr5d39ys49nlwmsv64ik5pdwkz28bh08hyylrhanb45d8wx"))))
+                "0j9awiiw9zf97r60m848absq43k37gghpyw7acxqjazfzd71fxvm"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-python3")

gnu/packages/security-token.scm

@@ -64,7 +64,7 @@
 (define-public ccid
   (package
     (name "ccid")
-    (version "1.4.30")
+    (version "1.4.31")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -72,7 +72,7 @@
                     name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "0z7zafdg75fr1adlv2x0zz34s07gljcjg2lsz76s1048w1xhh5xc"))))
+                "1xz8ikr6vk73w3xnwb931yq8lqc1zrj8c3v34n6h63irwjvdfj3b"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags (list (string-append "--enable-usbdropdir=" %output

gnu/packages/shells.scm

@@ -709,18 +709,17 @@ interactive POSIX shell targeted at resource-constrained systems.")
 (define-public mksh
   (package
     (name "mksh")
-    (version "56")
+    (version "57")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.mirbsd.org/MirOS/dist/mir/mksh/mksh-R"
                            version ".tgz"))
        (sha256
-        (base32
+        (base32 "0xdykm1z710wriwd6nc8s8lwk2dwjl63dq96xxaawlid31a1241x"))))
-         "1x4zjj9259ijpf8jw0nyh1fnr1pbm5fwvylclpvcrlb45xrglf5d"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ; tests require access to /dev/tty
+     `(#:tests? #f                      ; tests require access to /dev/tty
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
@@ -744,7 +743,7 @@ interactive POSIX shell targeted at resource-constrained systems.")
 Korn Shell programming language and a successor to the Public Domain Korn
 Shell (pdksh).")
     (license (list miros
-                   isc)))) ; strlcpy.c
+                   isc))))              ; strlcpy.c
 
 (define-public oil-shell
   (package

gnu/packages/statistics.scm

@@ -75,6 +75,7 @@
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
@@ -180,7 +181,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "3.6.0")
+    (version "3.6.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -188,7 +189,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "02bmylmzrm9sdidirmwy233lghmd2346z725ca71ari68lzarz1n"))))
+                "128kifbq0w25y8aq77w289ddax5i5w2djcfsqgffrb3i7syrxajv"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -319,9 +320,8 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("texinfo" ,texinfo) ; for building HTML manuals
-       ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
+       ("texlive" ,(texlive-union (list texlive-fonts-ec
-                                        texlive-fonts-ec
+                                        texlive-amsfonts
-                                        texlive-latex-amsfonts
                                         texlive-latex-base
                                         texlive-latex-fancyvrb
                                         texlive-latex-graphics
@@ -397,14 +397,14 @@ available, greatly increasing its breadth and scope.")
 (define-public r-boot
   (package
     (name "r-boot")
-    (version "1.3-22")
+    (version "1.3-23")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "boot" version))
        (sha256
         (base32
-         "1z2dig1mi76b3b9ck6qlkh07l3hs478gaf70db5nv8x7w2qhq7yg"))))
+         "0bx07zbb5nfz2xfgnzbspg7r5vxz4bjdz1ry4d1vk434vlcrxj1h"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/boot")
     (synopsis "Bootstrap functions for R")
@@ -502,14 +502,14 @@ code for possible problems.")
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-71")
+    (version "0.8-72")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
+         "124c9229is44p2rv7xyh2q86nsfi7vzyyh5n3c5ihziqrp4ig723"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")
@@ -588,14 +588,14 @@ and operations on them using LAPACK and SuiteSparse.")
 (define-public r-nlme
   (package
     (name "r-nlme")
-    (version "3.1-140")
+    (version "3.1-141")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nlme" version))
        (sha256
         (base32
-         "0k9x5j34fx093a023da9ny3b3101lbwpmfm27mkvfj950l22z88x"))))
+         "0ml00g79bimjcl0sgn6h55l5b4gfmnsnc1vvmivggn0318k4c04i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -804,13 +804,13 @@ effects of different types of color-blindness.")
 (define-public r-digest
   (package
     (name "r-digest")
-    (version "0.6.19")
+    (version "0.6.20")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "digest" version))
        (sha256
-        (base32 "1x6cbj9qvkk7pxv9xdqibazw3x8psjp6x0m0ildx1jwyb2ymkl98"))))
+        (base32 "1irhk2jaj9cg57cxprgyn1if06x121xwcxh1fzzn3148bl5lnrq5"))))
     (build-system r-build-system)
     ;; Vignettes require r-knitr, which requires r-digest, so we have to
     ;; disable them and the tests.
@@ -1138,13 +1138,13 @@ legends.")
 (define-public r-ggplot2
   (package
     (name "r-ggplot2")
-    (version "3.2.0")
+    (version "3.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggplot2" version))
        (sha256
-        (base32 "1cvk9pw59kxx19kamqwa15h26rbznp0vvqpn7y8kgjssnrzqkdii"))))
+        (base32 "0mjswqiqcwm0aqxll16bx2kwa6c9km3aql87bdj4347n1ali94g3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -1404,13 +1404,13 @@ data derived from /etc/mime.types in UNIX-type systems.")
 (define-public r-markdown
   (package
     (name "r-markdown")
-    (version "1.0")
+    (version "1.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "markdown" version))
               (sha256
                (base32
-                "19nrz0ba1yd5kicd65crkkz2r3kialm2hm6zdkp495l2s5r80b8p"))))
+                "06zwbrp14bri3470anadd7dvgmw06xf8df6v2pk64wx3f9sd934d"))))
     (build-system r-build-system)
     ;; Skip check phase because the tests require the r-knitr package to be
     ;; installed. This prevents installation failures. Knitr normally
@@ -1418,7 +1418,8 @@ data derived from /etc/mime.types in UNIX-type systems.")
     ;; package.
     (arguments `(#:tests? #f))
     (propagated-inputs
-     `(("r-mime" ,r-mime)))
+     `(("r-mime" ,r-mime)
+       ("r-xfun" ,r-xfun)))
     (home-page "https://github.com/rstudio/markdown")
     (synopsis "Markdown rendering for R")
     (description
@@ -1448,13 +1449,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
 (define-public r-knitr
   (package
     (name "r-knitr")
-    (version "1.23")
+    (version "1.24")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "knitr" version))
               (sha256
                (base32
-                "16ba4258c915xydhniw4cw7fvv1vp4cnwd1w49ykx7zw00rznfq6"))))
+                "12bvs9fd61m7k7bq321qzrh2ccl9rq653s1anrvfb9s5ni1j0378"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-evaluate" ,r-evaluate)
@@ -1603,18 +1604,19 @@ R packages that praise their users.")
 (define-public r-testthat
   (package
     (name "r-testthat")
-    (version "2.1.1")
+    (version "2.2.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "testthat" version))
               (sha256
                (base32
-                "03jgr0hlr77yp0aib4v30yjyjrjsa8dczr02yk21m93vl25vqvkp"))))
+                "0y0bvggm4pzkzp6xn7b8cf3ybqp9ijxkhhyp3z49a9iipc90bvk7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
        ("r-crayon" ,r-crayon)
        ("r-digest" ,r-digest)
+       ("r-evaluate" ,r-evaluate)
        ("r-magrittr" ,r-magrittr)
        ("r-praise" ,r-praise)
        ("r-r6" ,r-r6)
@@ -1696,13 +1698,13 @@ and printing capabilities than traditional data frames.")
 (define-public r-dplyr
   (package
     (name "r-dplyr")
-    (version "0.8.1")
+    (version "0.8.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "dplyr" version))
               (sha256
                (base32
-                "1nw12hzk1jcac5879nfmf1yp98jpb3i59qkb8sfpk2cd6zqgfgjz"))))
+                "032c89wa04g9rih9shyvwl3il0bsrv3xk489x6867sk9bb3amd38"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -1979,13 +1981,13 @@ inference for statistical models.")
 (define-public r-coda
   (package
     (name "r-coda")
-    (version "0.19-2")
+    (version "0.19-3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "coda" version))
               (sha256
                (base32
-                "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7"))))
+                "1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -2021,14 +2023,14 @@ and environmental data in the framework of Euclidean exploratory methods.")
 (define-public r-xml2
   (package
     (name "r-xml2")
-    (version "1.2.0")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xml2" version))
        (sha256
         (base32
-         "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
+         "1x3q3a0xv8j0nx3hs4d3pfjm5g9nvaxmfrapba9f4nrkqi3z2l1h"))))
     (build-system r-build-system)
     (inputs
      `(("libxml2" ,libxml2)
@@ -2136,14 +2138,14 @@ R version.")
 (define-public r-checkmate
   (package
     (name "r-checkmate")
-    (version "1.9.3")
+    (version "1.9.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "checkmate" version))
        (sha256
         (base32
-         "15ccwvmw73c2zz1k10k5zdn8px0rrbnvs1b4nzvlb0iwj7cimhp4"))))
+         "08ddpgs4mv5d5y4j054pm8drmxkn7yvhfpbghwxlizjpnxa5g8ps"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)))
@@ -2333,14 +2335,14 @@ collation, and NAMESPACE files.")
 (define-public r-openssl
   (package
     (name "r-openssl")
-    (version "1.4")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openssl" version))
        (sha256
         (base32
-         "0mh4xwb9wnn5j2n1zzmjldqjqv2nn4wdidiixxciaqrqsi0l9834"))))
+         "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
     (build-system r-build-system)
     (inputs
      `(("libressl" ,libressl)))
@@ -2366,13 +2368,13 @@ integers.")
 (define-public r-httr
   (package
     (name "r-httr")
-    (version "1.4.0")
+    (version "1.4.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httr" version))
               (sha256
                (base32
-                "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn"))))
+                "0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-curl" ,r-curl)
@@ -2392,20 +2394,16 @@ functions make it easy to control additional request components.")
 (define-public r-git2r
   (package
     (name "r-git2r")
-    (version "0.25.2")
+    (version "0.26.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "git2r" version))
               (sha256
                (base32
-                "15kpvz6ry2r8ii5hzinjwkggc5kgmkbcpsdwzahsf8gha52w80p0"))))
+                "0dbl845sahv2i641ncaf06w06djravwc5wknp9syzx0ad8l0kmhk"))))
     (build-system r-build-system)
-    ;; This R package contains modified sources of libgit2.  This modified
-    ;; version of libgit2 is built as the package is built.  Hence libgit2 is
-    ;; not among the inputs of this package.
     (inputs
-     `(("libssh2" ,libssh2) ; for SSH transport
+     `(("libgit2" ,libgit2)
-       ("openssl" ,openssl)
        ("zlib" ,zlib)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -2438,13 +2436,13 @@ informative error messages when it's not available.")
 (define-public r-devtools
   (package
     (name "r-devtools")
-    (version "2.0.2")
+    (version "2.1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "devtools" version))
               (sha256
                (base32
-                "028pppj39ng7q17k27531s8k00lmw982vz5krn74n9b8f2azm8lr"))))
+                "0393v7nr22gr5g9afgrhq4ab3lwbqy6fd3shnmlhdpqam5357xy1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -2457,9 +2455,11 @@ informative error messages when it's not available.")
        ("r-pkgbuild" ,r-pkgbuild)
        ("r-pkgload" ,r-pkgload)
        ("r-rcmdcheck" ,r-rcmdcheck)
+       ("r-roxygen2" ,r-roxygen2)
        ("r-remotes" ,r-remotes)
        ("r-rstudioapi" ,r-rstudioapi)
        ("r-sessioninfo" ,r-sessioninfo)
+       ("r-testthat" ,r-testthat)
        ("r-usethis" ,r-usethis)
        ("r-withr" ,r-withr)))
     (home-page "https://github.com/hadley/devtools")
@@ -2490,18 +2490,19 @@ were originally a part of the r-devtools package.")
 (define-public r-hms
   (package
     (name "r-hms")
-    (version "0.4.2")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hms" version))
        (sha256
         (base32
-         "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
+         "06snfqdczr0x0nbp7qnvwhlp2pw0wx9c2y3xb4gr1wrvbik74y58"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rlang" ,r-rlang)
-       ("r-pkgconfig" ,r-pkgconfig)))
+       ("r-pkgconfig" ,r-pkgconfig)
+       ("r-vctrs" ,r-vctrs)))
     (home-page "https://github.com/rstats-db/hms")
     (synopsis "Pretty time of day")
     (description
@@ -2597,13 +2598,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.500.2.0")
+    (version "0.9.600.4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1lyvpb7n54ijlqns29qiixqr39334knf67cnixvlic58945glrhv"))))
+                "07jg2667xyhmp1fbcdi5nnhmkk81da76s9rlswfq4k2sjsmbfmr0"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     ;; All needed for vignettes
@@ -2695,14 +2696,14 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "1.13")
+    (version "1.14")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
           (base32
-            "1vv3b8nlw8ra19492rjg3na42lwh3xr5a2jy2ia81fvvs846pywn"))))
+            "0qfw5rkvwqpgix32g6qy9xrr50awmm146aqbm836xravih2b2dpn"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2788,17 +2789,18 @@ that package, other packages are unaffected.")
 (define-public r-blob
   (package
     (name "r-blob")
-    (version "1.1.1")
+    (version "1.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "blob" version))
               (sha256
                (base32
-                "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
+                "08z071jzac4gasgfgab0y5g3ilfmlw08ln813wphxg07hsiczw8s"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-prettyunits" ,r-prettyunits)
-       ("r-tibble" ,r-tibble)))
+       ("r-rlang" ,r-rlang)
+       ("r-vctrs" ,r-vctrs)))
     (home-page "https://github.com/hadley/blob")
     (synopsis "Simple S3 Class for representing vectors of binary data")
     (description "Raw vectors in R are useful for storing a single binary
@@ -2810,13 +2812,13 @@ a column in data frame.")
 (define-public r-rsqlite
   (package
     (name "r-rsqlite")
-    (version "2.1.1")
+    (version "2.1.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RSQLite" version))
               (sha256
                (base32
-                "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
+                "1inrhap5cs0wry2jbw42fx9wwxb3qdzlpy0ba4f6a29bs8jx9nk6"))))
     (properties `((upstream-name . "RSQLite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3069,14 +3071,14 @@ standard R subsetting and Kronecker products.")
 (define-public r-iterators
   (package
     (name "r-iterators")
-    (version "1.0.10")
+    (version "1.0.12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "iterators" version))
        (sha256
         (base32
-         "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
+         "0jwzxaa3jm1xzgfv5pn0xqkk7rhm0xwvgn85w7xaw8xx1vb33gwn"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/iterators")
     (synopsis "Iterator construct for R")
@@ -3089,14 +3091,14 @@ data.")
 (define-public r-foreach
   (package
     (name "r-foreach")
-    (version "1.4.4")
+    (version "1.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreach" version))
        (sha256
         (base32
-         "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
+         "0q7iyniw5iri4hl57bhil3r69s5wnaijzn0q0x4h3z42245jqqwm"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-codetools" ,r-codetools)
@@ -3117,14 +3119,14 @@ parallel.")
 (define-public r-doparallel
   (package
     (name "r-doparallel")
-    (version "1.0.14")
+    (version "1.0.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doParallel" version))
        (sha256
         (base32
-         "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb"))))
+         "0vnqbha3gig3awbfvsfx3ni5jir398md1n7xmsb8jihnjsk7xbbi"))))
     (properties `((upstream-name . "doParallel")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3140,14 +3142,14 @@ using the parallel package.")
 (define-public r-domc
   (package
     (name "r-domc")
-    (version "1.3.5")
+    (version "1.3.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doMC" version))
        (sha256
         (base32
-         "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
+         "1cn9gxavhvjswip8pwvkpi7q6wpzdllcsdjabga8akf55nggqxr9"))))
     (properties `((upstream-name . "doMC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3163,13 +3165,13 @@ using the multicore functionality of the parallel package.")
 (define-public r-dt
   (package
     (name "r-dt")
-    (version "0.7")
+    (version "0.8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DT" version))
               (sha256
                (base32
-                "0b6ywgzk9b35y5f69zwfz3vv7qwqqj3xsmy0xymf7nfcvrqg3qqx"))))
+                "08cfmv3d5awvd9h8648bvidcg2ak5pvl2p6vqwqwy1l82ia506ch"))))
     (properties
      `((upstream-name . "DT")))
     (build-system r-build-system)
@@ -3177,6 +3179,7 @@ using the multicore functionality of the parallel package.")
      `(("r-crosstalk" ,r-crosstalk)
        ("r-htmltools" ,r-htmltools)
        ("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-jsonlite" ,r-jsonlite)
        ("r-magrittr" ,r-magrittr)
        ("r-promises" ,r-promises)))
     (home-page "http://rstudio.github.io/DT")
@@ -3315,14 +3318,14 @@ package registries.")
 (define-public r-rngtools
   (package
     (name "r-rngtools")
-    (version "1.3.1.1")
+    (version "1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rngtools" version))
        (sha256
         (base32
-         "0k1nlcxggflq0043m15dfclnqnzchkpw2ik7jk82h4dqwvysiqcr"))))
+         "1kivj594bn774lbn29ws2rmzy2km99sza0j3jqvhal6hwmk27a9s"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -4566,19 +4569,19 @@ Farebrother's algorithm or Liu et al.'s algorithm.")
 (define-public r-cowplot
   (package
     (name "r-cowplot")
-    (version "0.9.4")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cowplot" version))
        (sha256
         (base32
-         "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv"))))
+         "19cqdhgfyr1wj0fz0c5ly8f0aiy9sfgzq6lzb78hkx0hdp2agybh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
        ("r-gtable" ,r-gtable)
-       ("r-plyr" ,r-plyr)
+       ("r-rlang" ,r-rlang)
        ("r-scales" ,r-scales)))
     (home-page "https://github.com/wilkelab/cowplot")
     (synopsis "Streamlined plot theme and plot annotations for ggplot2")
@@ -4640,14 +4643,14 @@ regression.")
 (define-public r-fastica
   (package
     (name "r-fastica")
-    (version "1.2-1")
+    (version "1.2-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fastICA" version))
        (sha256
         (base32
-         "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
+         "1zpijqcipm0aa3rxj0mys06lskqy4dbppjpxr1aby0j16y9ka8ij"))))
     (properties `((upstream-name . "fastICA")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/fastICA")
@@ -4749,14 +4752,14 @@ models, generalized linear models and model-based clustering.")
 (define-public r-mclust
   (package
     (name "r-mclust")
-    (version "5.4.4")
+    (version "5.4.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mclust" version))
        (sha256
         (base32
-         "039ymr57bq5327gypizw0v2qb81j6bkqhjdh8yj23qa5sh51phyc"))))
+         "0whandnda1fnjn5k3hgxdbp3b0xr7nlzy1j37saqb536h8q9dwkm"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -4919,14 +4922,14 @@ generally.")
 (define-public r-robust
   (package
     (name "r-robust")
-    (version "0.4-18")
+    (version "0.4-18.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "robust" version))
        (sha256
         (base32
-         "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
+         "0xs098pfw5zdcdk3rsxkylfl6d2pyp566s5v92bzhgl7h8c90cfy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-fit-models" ,r-fit-models)
@@ -5025,14 +5028,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.")
 (define-public r-pbapply
   (package
     (name "r-pbapply")
-    (version "1.4-0")
+    (version "1.4-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pbapply" version))
        (sha256
         (base32
-         "0bn7a9ni36xy5acnrl9ky3gd1k8jr5kxgazzh3pzd1q6bri1nx7k"))))
+         "1bbws9n90cqnnp5k58hp852jwmm6513jnhn4vzhl9f8x314k6qxk"))))
     (build-system r-build-system)
     (home-page "https://github.com/psolymos/pbapply")
     (synopsis "Adding progress bar to apply functions")
@@ -5138,14 +5141,14 @@ using modular prediction and response module classes.")
 (define-public r-quantreg
   (package
     (name "r-quantreg")
-    (version "5.41")
+    (version "5.51")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "quantreg" version))
        (sha256
         (base32
-         "110ax3ngn6i94h7iw7ha67kfsmj94hycp7lk62nmyvkp34vpfykh"))))
+         "1cdx51a9g6fjq2g9arr6wp6ghkyl2m6bs2dj4kcycvpn8p9304yz"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))

gnu/packages/syncthing.scm

@@ -30,7 +30,7 @@
 (define-public syncthing
   (package
     (name "syncthing")
-    (version "1.2.0")
+    (version "1.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/syncthing/syncthing"
@@ -38,7 +38,7 @@
                                   "/syncthing-source-v" version ".tar.gz"))
               (sha256
                (base32
-                "1l7crhggg2vq4y7pgzsj8wp7k4l9hw5yblflly5bzwywzxz8ff83"))
+                "1b6fidpkwfa2bm6hlv4p0bzxa1ha6s88vajczhryhqi5vjfxafri"))
               (modules '((guix build utils)))
               ;; Delete bundled ("vendored") free software source code.
               (snippet '(begin
@@ -422,7 +422,7 @@ address of the default LAN gateway.")
 (define-public go-github-com-lib-pq
   (package
     (name "go-github-com-lib-pq")
-    (version "1.1.1")
+    (version "1.2.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -431,7 +431,7 @@ address of the default LAN gateway.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0g64wlg1l1ybq4x44idksl4pgm055s58jxc6r6x4qhqm5q76h0km"))))
+                "08j1smm6rassdssdks4yh9aspa1dv1g5nvwimmknspvhx8a7waqz"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/lib/pq"
@@ -793,8 +793,8 @@ using sh's word-splitting rules.")
       (license expat))))
 
 (define-public go-github-com-syncthing-notify
-  (let ((commit "4e389ea6c0d84e6195eb585ffaf62c8c143306ae")
+  (let ((commit "69c7a957d3e261f9744f46b3dd4d608d8480ad90")
-        (revision "4"))
+        (revision "5"))
     (package
       (name "go-github-com-syncthing-notify")
       (version (git-version "0.0.0" revision commit))
@@ -806,7 +806,7 @@ using sh's word-splitting rules.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "19gvl14s1l9m82f8c2xsjcr8lmbqrvw1mxkayvfcpimvxfz0j61i"))))
+                  "1mmdzyfnmjabyhbipl4bggw4w5nlxyyjp0d93qd824kj07kmsr1f"))))
       (build-system go-build-system)
       (arguments
        '(#:import-path "github.com/syncthing/notify"))

gnu/packages/terminals.scm

@@ -57,6 +57,7 @@
   #:use-module (gnu packages golang)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages libcanberra)
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages ncurses)
@@ -954,7 +955,7 @@ tmux.")
 (define-public kitty
   (package
     (name "kitty")
-    (version "0.14.2")
+    (version "0.14.3")
     (home-page "https://sw.kovidgoyal.net/kitty/")
     (source
      (origin
@@ -965,7 +966,7 @@ tmux.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "15iv3k7iryf10n8n67d37x24pzcarq97a3dr42lbld00k1lx19az"))
+         "0wi6b6b1nyp16rcpcghk6by62wy6qsamv1xdymyn0zbqgd8h9n6b"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -984,6 +985,7 @@ tmux.")
      `(("python" ,python)
        ("harfbuzz" ,harfbuzz)
        ("zlib" ,zlib)
+       ("libcanberra" ,libcanberra)
        ("libpng" ,libpng)
        ("freetype" ,freetype)
        ("fontconfig" ,fontconfig)

gnu/packages/text-editors.scm

@@ -400,15 +400,14 @@ editors.")
 (define-public texmacs
   (package
     (name "texmacs")
-    (version "1.99.9")
+    (version "1.99.11")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.texmacs.org/Download/ftp/tmftp/"
                            "source/TeXmacs-" version "-src.tar.gz"))
        (sha256
-        (base32
+        (base32 "12bp0f34izzqimz49lfpgf4lyz3h45s9xbmk8v6zsawdjki76alg"))
-         "0i95sf9y8qpgxd8f39cprbp3s200nm9lml0xdpyn46n838acvw19"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -424,7 +423,7 @@ editors.")
        ("python" ,python-wrapper)
        ("qt" ,qt-4)))
     (arguments
-     `(#:tests? #f ;no check target
+     `(#:tests? #f                      ; no check target
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'gzip-flags

gnu/packages/version-control.scm

@@ -146,14 +146,14 @@ as well as the classic centralized workflow.")
    (name "git")
    ;; XXX When updating Git, check if the special 'git-source' input to cgit
    ;; needs to be updated as well.
-   (version "2.22.0")
+   (version "2.22.1")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://kernel.org/software/scm/git/git-"
                                 version ".tar.xz"))
             (sha256
              (base32
-              "17zj6jwx3s6bybd290f1mj5iym1r64560rmnf0p63x4akxclp7hm"))))
+              "093qjgagha937w96izkpsjkhxf5drsa7rvk5snlyjivqnwxgkqac"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("native-perl" ,perl)
@@ -166,7 +166,7 @@ as well as the classic centralized workflow.")
                 version ".tar.xz"))
           (sha256
            (base32
-            "0fpfqw0h4g4v478fscic8z714i0ls5w7946vzhmq31lf7nizsb2f"))))
+            "17vpqv9g8li58njx7z5124b3c2zb2n63z4dalh5gw9iys7qb8446"))))
       ;; For subtree documentation.
       ("asciidoc" ,asciidoc)
       ("docbook-xsl" ,docbook-xsl)
@@ -1301,7 +1301,7 @@ following features:
 (define-public subversion
   (package
     (name "subversion")
-    (version "1.10.4")
+    (version "1.10.6")
     (source (origin
              (method url-fetch)
              (uri
@@ -1312,7 +1312,7 @@ following features:
                                 "subversion-" version ".tar.bz2")))
              (sha256
               (base32
-               "18c1vdq32nil76w678lxmp73jsbqha3dmzgmfrj76nc0xjmywql2"))))
+               "19zc215mhpnm92mlyl5jbv57r5zqp6cavr3s2g9yglp6j4kfgj0q"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases

gnu/packages/video.scm

@@ -473,16 +473,18 @@ and creating Matroska files from other media files (@code{mkvmerge}).")
 (define-public x265
   (package
     (name "x265")
-    (version "3.1.1")
+    (version "3.1.2")
     (outputs '("out" "static"))
     (source
       (origin
         (method url-fetch)
-        (uri (string-append "https://download.videolan.org/videolan/x265/"
+        (uri (list (string-append "https://bitbucket.org/multicoreware/x265"
-                            "x265_" version ".tar.gz"))
+                                  "/downloads/x265_" version ".tar.gz")
+                   (string-append "https://download.videolan.org/videolan/x265/"
+                                  "x265_" version ".tar.gz")))
         (sha256
          (base32
-          "1l68lgdbsi4wjz5vad98ggx7mf92rnvzlq34m6w0a08ark3h0yc2"))
+          "1ajr59gjj47gnczfb2qhmzclj746pdiq9a1d81b0mq22k8f5yy3g"))
         (patches (search-patches "x265-arm-flags.patch"))
         (modules '((guix build utils)))
         (snippet '(begin
@@ -700,7 +702,7 @@ libebml is a C++ library to read and write EBML files.")
 (define-public libva
   (package
     (name "libva")
-    (version "2.4.1")
+    (version "2.5.0")
     (source
      (origin
        (method url-fetch)
@@ -712,7 +714,7 @@ libebml is a C++ library to read and write EBML files.")
              (string-append "https://www.freedesktop.org/software/vaapi/releases/"
                             "libva/libva-" version "/libva-" version ".tar.bz2")))
        (sha256
-        (base32 "0w7fkkrnfizzglviybxiyhxcvd3mfsiqlpda7rwj3ccihn857q79"))))
+        (base32 "0y38mw1ggxm15zq06r4qpwhd5wx4bppw1rsxpr6sq1m5d79rra1s"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -790,17 +792,18 @@ operate properly.")
 (define-public ffmpeg
   (package
     (name "ffmpeg")
-    (version "4.1.4")
+    (version "4.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "1qd7a10gs12ifcp31gramcgqjl77swskjfp7cijibgyg5yl4kw7i"))))
+               "1mgcxm7sqkajx35px05szsmn9mawwm03cfpmk3br7bcp3a1i0gq2"))))
     (build-system gnu-build-system)
     (inputs
-     `(("fontconfig" ,fontconfig)
+     `(("dav1d" ,dav1d)
+       ("fontconfig" ,fontconfig)
        ("freetype" ,freetype)
        ("frei0r-plugins" ,frei0r-plugins)
        ("gnutls" ,gnutls)
@@ -899,6 +902,7 @@ operate properly.")
          "--enable-libbluray"
          "--enable-libcaca"
          "--enable-libcdio"
+         "--enable-libdav1d"
          "--enable-libfreetype"
          "--enable-libmp3lame"
          "--enable-libopus"
@@ -981,9 +985,10 @@ audio/video codec library.")
     (arguments
      (substitute-keyword-arguments (package-arguments ffmpeg)
        ((#:configure-flags flags)
-        `(delete "--enable-libaom" ,flags))))
+        `(delete "--enable-libdav1d" (delete "--enable-libaom"
-    (inputs (alist-delete "libaom"
+                 ,flags)))))
-                          (package-inputs ffmpeg)))))
+    (inputs (alist-delete "dav1d" (alist-delete "libaom"
+                          (package-inputs ffmpeg))))))
 
 (define-public ffmpeg-for-stepmania
   (hidden-package
@@ -1480,7 +1485,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2019.07.30")
+    (version "2019.08.02")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/rg3/youtube-dl/releases/"
@@ -1488,7 +1493,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0nb5xvq4aq0az8y5wb54zp5q4qzfhs7rcb39yp6j5q8jyjp9kzwy"))))
+                "101b6jrf6ckbxrn76ppvgdyrb25p7d247kn8qgq7n476sfnkfg2p"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
@@ -1619,7 +1624,7 @@ other site that youtube-dl supports.")
 (define-public you-get
   (package
     (name "you-get")
-    (version "0.4.1302")
+    (version "0.4.1328")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1628,7 +1633,7 @@ other site that youtube-dl supports.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1fwwzslv1vpjr8q0fq10dbngr8zai1n3d6na700cgpky4j9y0y99"))))
+                "1r9qffwvxmp74byva12h2jsn3n33vyim052sx9lykv5dygibbp65"))))
     (build-system python-build-system)
     (inputs
      `(("ffmpeg" ,ffmpeg)))             ; for multi-part and >=1080p videos
@@ -2061,12 +2066,6 @@ capabilities.")
        ("libass" ,libass)
        ("tesseract-ocr" ,tesseract-ocr)
        ("zimg" ,zimg)))
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     (home-page "http://www.vapoursynth.com/")
     (synopsis "Video processing framework")
     (description "VapourSynth is a C++ library and Python module for video
@@ -2509,12 +2508,6 @@ Other features include a live preview and live streaming.")
                (base32
                 "18yfkr70lr1x1hc8snn2ldnbzdcc7b64xmkqrfk8w59gpg7sl1xn"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen.sh
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)))
@@ -2766,6 +2759,7 @@ of modern, widely supported codecs.")
      (list (search-path-specification
             (variable "LIBVA_DRIVERS_PATH")
             (files '("lib/dri")))))
+    (supported-systems '("i686-linux" "x86_64-linux"))
     (home-page "https://01.org/linuxmedia/vaapi")
     (synopsis "VA-API video acceleration driver for Intel GEN Graphics devices")
     (description
@@ -2898,10 +2892,7 @@ practically any type of media.")
          (add-after 'unpack 'change-to-build-dir
            (lambda _
              (chdir "Project/GNU/Library")
-             #t))
+             #t)))))
-         (add-after 'change-to-build-dir 'autogen
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     (home-page "https://mediaarea.net/en/MediaInfo")
     (synopsis "Library for retrieving media metadata")
     (description "MediaInfo is a library used for retrieving technical
@@ -3538,7 +3529,7 @@ transitions, and effects and then export your film to many common formats.")
 (define-public dav1d
   (package
     (name "dav1d")
-    (version "0.2.2")
+    (version "0.4.0")
     (source
       (origin
         (method url-fetch)
@@ -3550,7 +3541,8 @@ transitions, and effects and then export your film to many common formats.")
                    (string-append "https://code.videolan.org/videolan/dav1d/-/"
                                   "archive/" version "/dav1d-" version ".tar.bz2")))
         (sha256
-         (base32 "1llf4v486avj83d31670vdd5nshbq10qrx9vwrm1j078dh4ax4q0"))))
+         (base32
+          "08yqml01lbcpflrshdpvn88jv3xd8gm559qikiwyrh41a3kb4lr5"))))
     (build-system meson-build-system)
     (native-inputs `(("nasm" ,nasm)))
     (home-page "https://code.videolan.org/videolan/dav1d")

gnu/packages/vim.scm

@@ -814,7 +814,7 @@ refactor Vim in order to:
 (define-public vifm
   (package
     (name "vifm")
-    (version "0.10")
+    (version "0.10.1")
     (source
       (origin
         (method url-fetch)
@@ -825,35 +825,35 @@ refactor Vim in order to:
                               "vifm-" version ".tar.bz2")))
         (sha256
          (base32
-          "1f380xcyjnm4xmcdazs6dj064bwddhywvn3mgm36k7r7b2gnjnp0"))))
+          "0fyhxh7ndjn8fyjhj14ymkr3pjcs3k1xbs43g7xvvq85vdb6y04r"))))
     (build-system gnu-build-system)
     (arguments
-    '(#:configure-flags '("--disable-build-timestamp")
+     '(#:configure-flags '("--disable-build-timestamp")
-      #:phases
+       #:phases
-      (modify-phases %standard-phases
+       (modify-phases %standard-phases
-        (add-after 'patch-source-shebangs 'patch-test-shebangs
+         (add-after 'patch-source-shebangs 'patch-test-shebangs
-          (lambda _
+           (lambda _
-            (substitute* (cons* "src/background.c"
+             (substitute* (cons* "src/background.c"
-                                "src/cfg/config.c"
+                                 "src/cfg/config.c"
-                                (find-files "tests" "\\.c$"))
+                                 (find-files "tests" "\\.c$"))
-              (("/bin/sh") (which "sh"))
+               (("/bin/sh") (which "sh"))
-              (("/bin/bash") (which "bash")))
+               (("/bin/bash") (which "bash")))
-            ;; This test segfaults
+             ;; This test segfaults
-            (substitute* "tests/Makefile"
+             (substitute* "tests/Makefile"
-              (("misc") ""))
+               (("misc") ""))
-            #t))
+             #t))
-         (add-after 'install 'install-vim-plugin-files
+          (add-after 'install 'install-vim-plugin-files
-           (lambda* (#:key outputs #:allow-other-keys)
+            (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
+              (let* ((out (assoc-ref outputs "out"))
-                    (vifm (string-append out "/share/vifm"))
+                     (vifm (string-append out "/share/vifm"))
-                    (vimfiles (string-append out "/share/vim/vimfiles")))
+                     (vimfiles (string-append out "/share/vim/vimfiles")))
-               (copy-recursively (string-append vifm "/colors")
+                (copy-recursively (string-append vifm "/colors")
-                                 (string-append vimfiles "/colors"))
+                                  (string-append vimfiles "/colors"))
-               (copy-recursively (string-append vifm "/vim")
+                (copy-recursively (string-append vifm "/vim")
-                                 vimfiles)
+                                  vimfiles)
-               (delete-file-recursively (string-append vifm "/colors"))
+                (delete-file-recursively (string-append vifm "/colors"))
-               (delete-file-recursively (string-append vifm "/vim")))
+                (delete-file-recursively (string-append vifm "/vim")))
-             #t)))))
+              #t)))))
     (native-inputs
      `(("groff" ,groff))) ; for the documentation
     (inputs

gnu/packages/virtualization.scm

@@ -391,16 +391,14 @@ manage system or application containers.")
 (define-public libvirt
   (package
     (name "libvirt")
-    (version "5.5.0")
+    (version "5.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://libvirt.org/sources/libvirt-"
                            version ".tar.xz"))
        (sha256
-        (base32 "1s1mzw4cmkcfivs1kphpgy4lpddx0w1qnjysr4ggk5558w4yy1i3"))
+        (base32 "1d5rmcx5fgb024hw8chbiv886n3jal5wp2yajjk5l4qh9s9gkx35"))))
-       (patches
-        (search-patches "libvirt-remove-ATTRIBUTE_UNUSED.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -534,15 +532,15 @@ three libraries:
 (define-public python-libvirt
   (package
     (name "python-libvirt")
-    (version "5.5.0")
+    (version "5.6.0")
     (source
      (origin
        (method url-fetch)
-       ;; The latest version hosted on PyPI at 5.5.0 release time was 5.3.0.
+       ;; The latest version hosted on PyPI at 5.6.0 release time was 5.5.0.
        (uri (string-append "https://libvirt.org/sources/python/libvirt-python-"
                            version ".tar.gz"))
        (sha256
-        (base32 "00x6idyw9xrrr21vrnsyw37q2sd8yh4n6pwh0l28hh9yp3nsy72n"))))
+        (base32 "11i440aibykxw22fzyavmrvn67s8rmnijw5bag0yx9r8jpnkzwad"))))
     (build-system python-build-system)
     (arguments
      `(#:phases

gnu/packages/vpn.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2013, 2016, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
@@ -227,11 +227,6 @@ the entire VPN in a network namespace accessible only through SSH.")
        ("automake" ,automake)))
     (inputs
      `(("libevent" ,libevent)))
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _ (invoke "sh" "autogen.sh"))))))
     (home-page "https://github.com/cernekee/ocproxy")
     (synopsis "OpenConnect proxy")
     (description
@@ -244,19 +239,20 @@ the user specifically asks to proxy, so the @dfn{VPN} interface no longer
 (define-public openconnect
   (package
    (name "openconnect")
-   (version "8.03")
+   (version "8.04")
    (source (origin
             (method url-fetch)
             (uri (string-append "ftp://ftp.infradead.org/pub/openconnect/"
                                 "openconnect-" version ".tar.gz"))
-            (sha256 (base32
+            (sha256
-                     "1wlypi68kqqg2mdck8wvf6aanhrmf9i7z6lngyxvcrp23jdzz34h"))))
+             (base32 "07zqcl2ykdc4mgix9sbv4jgpg7cybifxfgrycvf99ckq7xp9r5wq"))))
    (build-system gnu-build-system)
-   (inputs
+   (propagated-inputs
     `(("libxml2" ,libxml2)
       ("gnutls" ,gnutls)
-      ("vpnc-scripts" ,vpnc-scripts)
       ("zlib" ,zlib)))
+   (inputs
+    `(("vpnc-scripts" ,vpnc-scripts)))
    (native-inputs
     `(("gettext" ,gettext-minimal)
       ("pkg-config" ,pkg-config)))

gnu/packages/vulkan.scm

@@ -150,7 +150,7 @@ interpretation of the specifications for these languages.")
 (define-public vulkan-headers
   (package
     (name "vulkan-headers")
-    (version "1.1.112")
+    (version "1.1.114")
     (source
      (origin
        (method git-fetch)
@@ -160,7 +160,7 @@ interpretation of the specifications for these languages.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0iia2wlq38hvxwip6r3k5946ylrlk42fw50mhf0pdjxjh02p8zn5"))))
+         "0fdvh26nxibylh32lj8b62d9nf9j25xa0il9zg362wmr2zgm8gka"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))                    ; No tests.
@@ -184,7 +184,7 @@ interpretation of the specifications for these languages.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1819bgmpjlikcc25bkmwwb7mp1rlyrq2v74wybg1g40ix70v0m0d"))))
+         "1rkm6dzdzxva62shscipz3kpp66x4kgmwvp1ski2fvf4jzzcbv7h"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ;FIXME: 23/39 tests fail.  Try "tests/run_all_tests.sh".
@@ -257,7 +257,7 @@ and the ICD.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0an9hqvvpfmfld2pkszzwi7ccb9g2ijjqqzlj24dqg9kqnmcr3x4"))))
+         "1lz06mpni8ghf1xcxi4g6ck306lfaqwfi6f1w64kp9hczmvapfhf"))))
     (build-system cmake-build-system)
     (inputs
      `(("glslang" ,glslang)

gnu/packages/web.scm

@@ -2231,7 +2231,7 @@ development server with Starman.")
 (define-public perl-cgi
   (package
     (name "perl-cgi")
-    (version "4.38")
+    (version "4.44")
     (source
      (origin
        (method url-fetch)
@@ -2239,7 +2239,7 @@ development server with Starman.")
                            "CGI-" version ".tar.gz"))
        (sha256
         (base32
-         "1m779315rzj4mpgscw209a2wk18iwg2n8zibn8aak4mv56jz8n4c"))))
+         "020jrygslqixrxd2nzc2l8ac39ynqzsy83nnnr3mqn6kxfvmyhqj"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-test-deep" ,perl-test-deep)
@@ -2874,7 +2874,7 @@ used by the HTTP protocol (and then some more).")
 (define-public perl-http-message
   (package
     (name "perl-http-message")
-    (version "6.15")
+    (version "6.18")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -2882,7 +2882,7 @@ used by the HTTP protocol (and then some more).")
                    version ".tar.gz"))
              (sha256
               (base32
-               "11fbvisyvi6bw8z9iq9fm9mraf69qyds09fblhl9gyvg7ccll93v"))))
+               "04lih0fn89jpyk74c4aq1rzq18h8v4zd3x0lik2r9dl8sdqd2q6h"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-try-tiny" ,perl-try-tiny)))

gnu/packages/wine.scm

@@ -164,10 +164,14 @@
                       (copy-file (string-append (assoc-ref inputs "mesa")
                                  "/share/vulkan/icd.d/radeon_icd.i686.json")
                                  (string-append icd "/radeon_icd.i686.json"))
+                      (copy-file (string-append (assoc-ref inputs "mesa")
+                                 "/share/vulkan/icd.d/intel_icd.i686.json")
+                                 (string-append icd "/intel_icd.i686.json"))
                       (wrap-program (string-append out "/bin/wine-preloader")
                                     `("VK_ICD_FILENAMES" ":" =
                                       (,(string-append icd
-                                        "/radeon_icd.i686.json"))))
+                                        "/radeon_icd.i686.json" ":"
+                                        icd "/intel_icd.i686.json"))))
                       #t)))))
              (_
               `())
@@ -224,7 +228,9 @@ integrate Windows applications into your desktop.")
                                      (assoc-ref inputs "mesa")
                                      "/share/vulkan/icd.d/intel_icd.x86_64.json" ":"
                                      (assoc-ref inputs "wine")
-                                     "/share/vulkan/icd.d/radeon_icd.i686.json"))))
+                                     "/share/vulkan/icd.d/radeon_icd.i686.json" ":"
+                                     (assoc-ref inputs "wine")
+                                     "/share/vulkan/icd.d/intel_icd.i686.json"))))
                    (wrap-program (string-append out "/bin/wine64-preloader")
                                  `("VK_ICD_FILENAMES" ":" =
                                    (,(string-append (assoc-ref inputs "mesa")
@@ -232,7 +238,9 @@ integrate Windows applications into your desktop.")
                                      ":" (assoc-ref inputs "mesa")
                                      "/share/vulkan/icd.d/intel_icd.x86_64.json"
                                      ":" (assoc-ref inputs "wine")
-                                     "/share/vulkan/icd.d/radeon_icd.i686.json"))))
+                                     "/share/vulkan/icd.d/radeon_icd.i686.json"
+                                     ":" (assoc-ref inputs "wine")
+                                     "/share/vulkan/icd.d/intel_icd.i686.json"))))
                    #t)))))
            (_
             `())
@@ -310,7 +318,7 @@ integrate Windows applications into your desktop.")
 (define-public wine-staging-patchset-data
   (package
     (name "wine-staging-patchset-data")
-    (version "4.12.1")
+    (version "4.13")
     (source
      (origin
        (method git-fetch)
@@ -320,7 +328,7 @@ integrate Windows applications into your desktop.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1bvpvj6vcw2p6vcjm6mw5maarbs4lfw1ix3pj020w4n3kg4nmmc4"))))
+         "0bbwsd2qpjilxpjscqbp78p0gl0awj1yj62g0wvybh4x89fzy8zj"))))
     (build-system trivial-build-system)
     (native-inputs
      `(("bash" ,bash)
@@ -366,7 +374,7 @@ integrate Windows applications into your desktop.")
               (file-name (string-append name "-" version ".tar.xz"))
               (sha256
                (base32
-                "09yjfb2k14y11k19lm8dqmb8qwxyhh67d5q1gqv480y64mljvkx0"))))
+                "0rqx8g394aj5q913cd18zsi60sldvxarrp178w6ja0y4rd8l25vr"))))
     (inputs `(("autoconf" ,autoconf) ; for autoreconf
               ("faudio" ,faudio)
               ("ffmpeg" ,ffmpeg)
@@ -393,10 +401,14 @@ integrate Windows applications into your desktop.")
                       (copy-file (string-append (assoc-ref inputs "mesa")
                                  "/share/vulkan/icd.d/radeon_icd.i686.json")
                                  (string-append icd "/radeon_icd.i686.json"))
+                      (copy-file (string-append (assoc-ref inputs "mesa")
+                                 "/share/vulkan/icd.d/intel_icd.i686.json")
+                                 (string-append icd "/intel_icd.i686.json"))
                       (wrap-program (string-append out "/bin/wine-preloader")
                                     `("VK_ICD_FILENAMES" ":" =
                                       (,(string-append icd
-                                        "/radeon_icd.i686.json"))))
+                                        "/radeon_icd.i686.json" ":"
+                                        icd "/intel_icd.i686.json"))))
                       #t)))))
              (_
               `())
@@ -407,10 +419,7 @@ integrate Windows applications into your desktop.")
                     (script (string-append (assoc-ref %build-inputs
                             "wine-staging-patchset-data")
                             "/share/wine-staging/patches/patchinstall.sh")))
-               ;; Exclude specific patches that conflict with FAudio.
+               (invoke script (string-append "DESTDIR=" ".") "--all")
-               (invoke script (string-append "DESTDIR=" ".") "--all" "-W"
-                       "xaudio2-revert" "-W" "xaudio2_CommitChanges" "-W"
-                       "xaudio2_7-WMA_support" "-W" "xaudio2_7-CreateFX-FXEcho")
                #t)))
          (add-after 'configure 'patch-dlopen-paths
            ;; Hardcode dlopened sonames to absolute paths.
@@ -467,7 +476,9 @@ integrated into the main branch.")
                                      (assoc-ref inputs "mesa")
                                      "/share/vulkan/icd.d/intel_icd.x86_64.json" ":"
                                      (assoc-ref inputs "wine-staging")
-                                     "/share/vulkan/icd.d/radeon_icd.i686.json"))))
+                                     "/share/vulkan/icd.d/radeon_icd.i686.json" ":"
+                                     (assoc-ref inputs "wine-staging")
+                                     "/share/vulkan/icd.d/intel_icd.i686.json"))))
                    (wrap-program (string-append out "/bin/wine64-preloader")
                                  `("VK_ICD_FILENAMES" ":" =
                                    (,(string-append (assoc-ref inputs "mesa")
@@ -475,7 +486,9 @@ integrated into the main branch.")
                                      ":" (assoc-ref inputs "mesa")
                                      "/share/vulkan/icd.d/intel_icd.x86_64.json"
                                      ":" (assoc-ref inputs "wine-staging")
-                                     "/share/vulkan/icd.d/radeon_icd.i686.json"))))
+                                     "/share/vulkan/icd.d/radeon_icd.i686.json"
+                                     ":" (assoc-ref inputs "wine-staging")
+                                     "/share/vulkan/icd.d/intel_icd.i686.json"))))
                    #t)))))
            (_
             `())
@@ -487,9 +500,7 @@ integrated into the main branch.")
                             "wine-staging-patchset-data")
                             "/share/wine-staging/patches/patchinstall.sh")))
                ;; Exclude specific patches that conflict with FAudio.
-               (invoke script (string-append "DESTDIR=" ".") "--all" "-W"
+               (invoke script (string-append "DESTDIR=" ".") "--all")
-                       "xaudio2-revert" "-W" "xaudio2_CommitChanges" "-W"
-                       "xaudio2_7-WMA_support" "-W" "xaudio2_7-CreateFX-FXEcho")
                #t)))
          (add-after 'install 'copy-wine32-binaries
            (lambda* (#:key outputs #:allow-other-keys)

gnu/packages/wm.scm

@@ -130,20 +130,19 @@ the leaves of a full binary tree.")
 (define-public i3status
   (package
     (name "i3status")
-    (version "2.12")
+    (version "2.13")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://i3wm.org/i3status/i3status-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "06krpbijv4yi33nypg6qcn4hilcrdyarsdpd9fmr2cq46qaqiikg"))))
+                "0rhlzb96mw64z2jnhwz9nibc7pxg549626lz5642xxk5hpzwk2ff"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:make-flags (list "CC=gcc" (string-append "PREFIX=" %output))
+     `(;; XXX: Do an "out of source" build to work around
-       #:phases
+       ;; <https://github.com/i3/i3status/issues/339>.
-       (modify-phases %standard-phases
+       #:out-of-source? #t
-         (delete 'configure))
        #:tests? #f)) ; no test suite
     (inputs
      `(("openlibm" ,openlibm)
@@ -155,7 +154,10 @@ the leaves of a full binary tree.")
        ("libcap" ,libcap)
        ("asciidoc" ,asciidoc)))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("pkg-config" ,pkg-config)
+       ("docbook-xsl" ,docbook-xsl)
+       ("libxml2" ,libxml2)             ;for XML_CATALOG_FILES
+       ("xmlto" ,xmlto)))
     (home-page "https://i3wm.org/i3status/")
     (synopsis "Status bar for i3bar, dzen2, xmobar or similar programs")
     (description "i3status is a small program for generating a status bar for
@@ -170,14 +172,14 @@ commands would.")
 (define-public i3-wm
   (package
     (name "i3-wm")
-    (version "4.16.1")
+    (version "4.17")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://i3wm.org/downloads/i3-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "0xl56y196vxv001gvx35xwfr25zah8m3xwizp9ycdgdc0rfc4rdb"))))
+                "1z8qmkkq9dhqmqy8sjw3rnpnmnb8v7lr456bs0qzp23bgpj17gjf"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -287,8 +289,6 @@ Despite the name it should work with any X11 window manager.")
       (arguments
        `(#:make-flags (list "CC=gcc" (string-append "PREFIX=" %output))
          #:phases (modify-phases %standard-phases
-                    (add-after 'unpack 'autogen
-                      (lambda _ (invoke "sh" "autogen.sh")))
                     (add-after 'install 'install-doc
                       (lambda* (#:key outputs #:allow-other-keys)
                         (let* ((out (assoc-ref outputs "out"))

gnu/packages/xiph.scm

@@ -235,15 +235,14 @@ It currently supports:
 (define flac
   (package
    (name "flac")
-   (version "1.3.2")
+   (version "1.3.3")
    (source (origin
             (method url-fetch)
             (uri (string-append "https://downloads.xiph.org/releases/flac/flac-"
                                 version ".tar.xz"))
             (sha256
              (base32
-              "0gymm2j3276kr9nz6vmgfwsdfrq6c449n40a0mzz8h6wc7nw7kwi"))
+              "0j0p9sf56a2fm2hkjnf7x3py5ir49jyavg4q5zdyd7bcf6yq4gi1"))))
-            (patches (search-patches "flac-CVE-2017-6888.patch"))))
    (build-system gnu-build-system)
    (arguments
     `(#:parallel-tests? #f))

gnu/packages/xorg.scm

@@ -1136,7 +1136,7 @@ themselves.")
 (define-public libpciaccess
   (package
     (name "libpciaccess")
-    (version "0.14")
+    (version "0.16")
     (source
       (origin
         (method url-fetch)
@@ -1146,7 +1146,7 @@ themselves.")
                ".tar.bz2"))
         (sha256
           (base32
-            "197jbcpvp4z4x6j705mq2y4fsnnypy6f85y8xalgwhgx5bhl7x9x"))))
+            "12glp4w1kgvmqn89lk19cgr6jccd3awxra4dxisp7pagi06rsk11"))))
     (build-system gnu-build-system)
     (arguments
      '(;; Make sure libpciaccess can read compressed 'pci.ids' files as
@@ -2921,8 +2921,8 @@ X server.")
 
 
 (define-public xf86-video-intel
-  (let ((commit "6afed33b2d673d88674f0c76efe500ae414e8e1b")
+  (let ((commit "6f4972d5c368c30e971a23c1dc370d3e43761282")
-        (revision "13"))
+        (revision "14"))
     (package
       (name "xf86-video-intel")
       (version (git-version "2.99.917" revision commit))
@@ -2935,7 +2935,7 @@ X server.")
                (commit commit)))
          (sha256
           (base32
-           "1s3fqlqzmql7s15m7qy21vai93n6q9f0ccpv0p353rwfx16mmf35"))
+           "0bc46qqglzfm4g9q4c2vgynvps2ng0xvlxnjpm9d6z4q6scdhz59"))
          (file-name (git-file-name name version))))
       (build-system gnu-build-system)
       (inputs `(("mesa" ,mesa)