Merge branch 'master' into staging

doc/guix.texi

@@ -443,7 +443,8 @@ and rerun the @code{gpg --verify} command.
 @c end authentication part
 
 @item
-As @code{root}, run:
+Now, you need to become the @code{root} user.  Depending on your distribution,
+you may have to run @code{su -} or @code{sudo -i}.  As @code{root}, run:
 
 @example
 # cd /tmp
@@ -11157,6 +11158,23 @@ server.  Alternately, one can specify the @command{sftp-server} command:
            `(("sftp" ,(file-append openssh "/libexec/sftp-server"))))))
 @end example
 
+@item @code{accepted-environment} (default: @code{'()})
+List of strings describing which environment variables may be exported.
+
+Each string gets on its own line.  See the @code{AcceptEnv} option in
+@code{man sshd_config}.
+
+This example allows ssh-clients to export the @code{COLORTERM} variable.
+It is set by terminal emulators, which support colors.  You can use it in
+your shell's ressource file to enable colors for the prompt and commands
+if this variable is set.
+
+@example
+(service openssh-service-type
+         (openssh-configuration
+           (accepted-environment '("COLORTERM"))))
+@end example
+
 @item @code{authorized-keys} (default: @code{'()})
 @cindex authorized keys, SSH
 @cindex SSH authorized keys
@@ -20457,6 +20475,16 @@ of the image size as a function of the size of the system declared in
 Make @var{file} a symlink to the result, and register it as a garbage
 collector root.
 
+@item --skip-checks
+Skip pre-installation safety checks.
+
+By default, @command{guix system init} and @command{guix system
+reconfigure} perform safety checks: they make sure the file systems that
+appear in the @code{operating-system} declaration actually exist
+(@pxref{File Systems}), and that any Linux kernel modules that may be
+needed at boot time are listed in @code{initrd-modules} (@pxref{Initial
+RAM Disk}).  Passing this option skips these tests altogether.
+
 @item --on-error=@var{strategy}
 Apply @var{strategy} when an error occurs when reading @var{file}.
 @var{strategy} may be one of the following:

gnu/build/vm.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
@@ -121,10 +121,8 @@ the #:references-graphs parameter of 'derivation'."
     (format #t "creating ~a image of ~,2f MiB...~%"
             disk-image-format (/ disk-image-size (expt 2 20)))
     (force-output)
-    (unless (zero? (system* "qemu-img" "create" "-f" disk-image-format
+    (invoke "qemu-img" "create" "-f" disk-image-format output
-                            output
              (number->string disk-image-size)))
-      (error "qemu-img failed")))
 
   (mkdir "xchg")
 
@@ -136,8 +134,7 @@ the #:references-graphs parameter of 'derivation'."
           graph-files))
     (_ #f))
 
-  (unless (zero?
+  (apply invoke qemu "-nographic" "-no-reboot"
-           (apply system* qemu "-nographic" "-no-reboot"
          "-m" (number->string memory-size)
          "-object" "rng-random,filename=/dev/urandom,id=guixsd-vm-rng"
          "-device" "virtio-rng-pci,rng=guixsd-vm-rng"
@@ -150,8 +147,6 @@ the #:references-graphs parameter of 'derivation'."
                         ",security_model=none,mount_tag=xchg")
          "-kernel" linux
          "-initrd" initrd
-                  "-append" (string-append "console=ttyS0 --load="
-                                           builder)
          (append
           (if make-disk-image?
               `("-device" "virtio-blk,drive=myhd"
@@ -159,8 +154,7 @@ the #:references-graphs parameter of 'derivation'."
                                          ",format=" disk-image-format
                                          ",id=myhd"))
               '())
-                   arch-specific-flags)))
+          arch-specific-flags))
-    (error "qemu failed" qemu))
 
   ;; When MAKE-DISK-IMAGE? is true, the image is in OUTPUT already.
   (unless make-disk-image?
@@ -240,10 +234,9 @@ actual /dev name based on DEVICE."
                                      partition-size)
                             partitions)
                        ", "))
-  (unless (zero? (apply system* "parted" "--script"
+  (apply invoke "parted" "--script"
          device "mklabel" label-type
-                        (options partitions offset)))
+         (options partitions offset))
-    (error "failed to create partition table"))
 
   ;; Set the 'device' field of each partition.
   (reverse
@@ -265,7 +258,7 @@ actual /dev name based on DEVICE."
   "Create an ext-family file system of TYPE on PARTITION.  If LABEL is true,
 use that as the volume name.  If UUID is true, use it as the partition UUID."
   (format #t "creating ~a partition...\n" type)
-  (unless (zero? (apply system* (string-append "mkfs." type)
+  (apply invoke (string-append "mkfs." type)
          "-F" partition
          `(,@(if label
                  `("-L" ,label)
@@ -273,7 +266,6 @@ use that as the volume name.  If UUID is true, use it as the partition UUID."
            ,@(if uuid
                  `("-U" ,(uuid->string uuid))
                  '()))))
-    (error "failed to create partition")))
 
 (define* (create-fat-file-system partition
                                  #:key label uuid)
@@ -282,11 +274,8 @@ will be determined based on file system size.  If LABEL is true, use that as the
 volume name."
   ;; FIXME: UUID is ignored!
   (format #t "creating FAT partition...\n")
-  (unless (zero? (apply system* "mkfs.fat" partition
+  (apply invoke "mkfs.fat" partition
-                        (if label
+         (if label `("-n" ,label) '())))
-                            `("-n" ,label)
-                            '())))
-    (error "failed to create FAT partition")))
 
 (define* (format-partition partition type
                            #:key label uuid)
@@ -388,12 +377,11 @@ SYSTEM-DIRECTORY is the name of the directory of the 'system' derivation."
     (setenv "TMPDIR" esp)
 
     (mkdir-p efi-directory)
-    (unless (zero? (system* grub-mkstandalone "-O" (car efi-targets)
+    (invoke grub-mkstandalone "-O" (car efi-targets)
             "-o" (string-append efi-directory "/"
                                 (cdr efi-targets))
             ;; Graft the configuration file onto the image.
-                            (string-append "boot/grub/grub.cfg=" config-file)))
+            (string-append "boot/grub/grub.cfg=" config-file))))
-      (error "failed to create GRUB EFI image"))))
 
 (define* (make-iso9660-image grub config-file os-drv target
                              #:key (volume-id "GuixSD_image") (volume-uuid #f)
@@ -416,7 +404,7 @@ GRUB configuration and OS-DRV as the stuff in it."
                    #:deduplicate? #f))
                 closures))
 
-    (unless (zero? (apply system*
+    (apply invoke
            `(,grub-mkrescue "-o" ,target
                             ,(string-append "boot/grub/grub.cfg=" config-file)
                             ,(string-append "gnu/store=" os-drv "/..")
@@ -435,8 +423,7 @@ GRUB configuration and OS-DRV as the stuff in it."
                                                       (not (char=? #\- value)))
                                                     (iso9660-uuid->string
                                                      volume-uuid)))
-                                  `()))))
+                                  `())))))
-      (error "failed to create ISO9660 image"))))
 
 (define* (initialize-hard-disk device
                                #:key

gnu/local.mk

@@ -50,6 +50,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/accessibility.scm		\
   %D%/packages/acct.scm				\
   %D%/packages/acl.scm				\
+  %D%/packages/ada.scm				\
   %D%/packages/admin.scm			\
   %D%/packages/adns.scm				\
   %D%/packages/agda.scm				\
@@ -120,6 +121,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/datastructures.scm		\
   %D%/packages/dav.scm				\
   %D%/packages/dc.scm				\
+  %D%/packages/debian.scm			\
   %D%/packages/debug.scm			\
   %D%/packages/dejagnu.scm			\
   %D%/packages/dico.scm				\
@@ -409,6 +411,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/tcl.scm				\
   %D%/packages/telephony.scm			\
   %D%/packages/terminals.scm			\
+  %D%/packages/terraform.scm			\
   %D%/packages/texinfo.scm			\
   %D%/packages/tex.scm				\
   %D%/packages/textutils.scm			\
@@ -786,7 +789,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/intltool-perl-compatibility.patch	\
   %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\
   %D%/packages/patches/jacal-fix-texinfo.patch			\
+  %D%/packages/patches/java-jeromq-fix-tests.patch		\
   %D%/packages/patches/java-powermock-fix-java-files.patch		\
+  %D%/packages/patches/java-simple-xml-fix-tests.patch		\
   %D%/packages/patches/java-xerces-bootclasspath.patch	\
   %D%/packages/patches/java-xerces-build_dont_unzip.patch	\
   %D%/packages/patches/java-xerces-xjavac_taskdef.patch	\
@@ -886,6 +891,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/llvm-3.5-fix-clang-build-with-gcc5.patch	\
   %D%/packages/patches/llvm-for-extempore.patch			\
   %D%/packages/patches/lm-sensors-hwmon-attrs.patch		\
+  %D%/packages/patches/lrzip-CVE-2017-8842.patch		\
   %D%/packages/patches/lua-CVE-2014-5461.patch                      \
   %D%/packages/patches/lua-pkgconfig.patch                      \
   %D%/packages/patches/lua51-liblua-so.patch                    \
@@ -1080,6 +1086,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/scotch-test-threading.patch		\
   %D%/packages/patches/sdl-libx11-1.6.patch			\
   %D%/packages/patches/seq24-rename-mutex.patch			\
+  %D%/packages/patches/shadow-CVE-2018-7169.patch		\
   %D%/packages/patches/shepherd-close-fds.patch			\
   %D%/packages/patches/shepherd-herd-status-sorted.patch	\
   %D%/packages/patches/shishi-fix-libgcrypt-detection.patch	\
@@ -1132,6 +1139,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/unzip-overflow-long-fsize.patch		\
   %D%/packages/patches/unzip-remove-build-date.patch		\
   %D%/packages/patches/ustr-fix-build-with-gcc-5.patch		\
+  %D%/packages/patches/util-linux-CVE-2018-7738.patch		\
   %D%/packages/patches/util-linux-tests.patch			\
   %D%/packages/patches/upower-builddir.patch			\
   %D%/packages/patches/valgrind-enable-arm.patch		\
@@ -1183,7 +1191,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/xinetd-CVE-2013-4342.patch		\
   %D%/packages/patches/xmodmap-asprintf.patch 			\
   %D%/packages/patches/libyaml-CVE-2014-9130.patch 		\
-  %D%/packages/patches/zathura-plugindir-environment-variable.patch
+  %D%/packages/patches/zathura-plugindir-environment-variable.patch	\
+  %D%/packages/patches/zsh-CVE-2018-7548.patch			\
+  %D%/packages/patches/zsh-CVE-2018-7549.patch
 
 MISC_DISTRO_FILES =				\
   %D%/packages/ld-wrapper.in

gnu/packages/ada.scm

@@ -0,0 +1,101 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Danny Milosavljevic <dannym@scratchpost.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages ada)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages python))
+
+(define-public python2-langkit
+  (let ((commit "fe0bc8bf60dbd2937759810df76ac420d99fc15f")
+        (revision "0"))
+    (package
+      (name "python2-langkit")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/AdaCore/langkit.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1abqgw2p8pb1pm54my5kkbbixfhc6l0bwajdv1xlzyrh31xki3wx"))
+                (file-name (string-append name "-" version "-checkout"))))
+      (build-system python-build-system)
+      (propagated-inputs
+       `(("python2-docutils" ,python2-docutils)
+         ("python2-enum34" ,python2-enum34)
+         ("python2-funcy" ,python2-funcy)
+         ("python2-mako" ,python2-mako)))
+      (arguments
+       `(#:python ,python-2
+         #:tests? #f))           ; Tests would requite gprbuild (Ada).
+      (synopsis "Semantic analysis tool generator in Python")
+      (description "@code{Langkit} is a tool whose purpose is to make it easy
+to create syntactic and semantic analysis engines.  Write a language
+specification in our Python DSL and Langkit will generate for you an
+Ada library with bindings for the C and Python programming languages.")
+      (home-page "https://github.com/AdaCore/langkit/")
+      (license license:gpl3+))))   ; and gcc runtime library exception
+
+(define-public python2-libadalang
+  (let ((commit "9b205e9bacdd50a68117727332e16fbef5f6ac49")
+        (revision "0"))
+    (package
+      (name "python2-libadalang")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/AdaCore/libadalang.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "06hsnzj2syqpq2yhg1bb0zil7ydbyqkdmkjbf8j9b5sdgkyh5xrp"))
+                (file-name (string-append name "-" version "-checkout"))))
+      (build-system python-build-system)
+      (native-inputs
+       `(("python2-langkit" ,python2-langkit)
+         ("python2-quex" ,python2-quex-0.67.3)))
+      (arguments
+       `(#:python ,python-2
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'build
+             (lambda _
+               (invoke "python2" "ada/manage.py" "generate")
+               (invoke "python2" "ada/manage.py" "build")))
+           (replace 'check
+             (lambda _
+               (invoke "python2" "ada/manage.py" "test")))
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out")))
+                 (invoke "python2" "ada/manage.py" "install" out)))))))
+      (synopsis "Semantic Analysis for Ada in Python")
+      (description "@code{libadalang} provides a high-performance semantic
+engine for the Ada programming language.")
+      (home-page "https://github.com/AdaCore/libadalang")
+      (license license:gpl3)))) ; and gcc runtime gcc lib exception

gnu/packages/admin.scm

@@ -360,6 +360,7 @@ hostname.")
               (uri (string-append
                     "https://github.com/shadow-maint/shadow/releases/"
                     "download/" version "/shadow-" version ".tar.xz"))
+              (patches (search-patches "shadow-CVE-2018-7169.patch"))
               (sha256
                (base32
                 "0hdpai78n63l3v3fgr3kkiqzhd0awrpfnnzz4mf7lmxdh61qb37w"))))
@@ -1205,7 +1206,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
 (define-public acpica
   (package
     (name "acpica")
-    (version "20180209")
+    (version "20180313")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1213,7 +1214,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
                     version ".tar.gz"))
               (sha256
                (base32
-                "04hyc5s9iiyiznvspx7q73r6ns98d51wrv8zfvqbqv52gqq8hzdh"))))
+                "16galaadmr37q2pvk2gyxrm8d1xldzk31djfxfq9v1c9yq4i425h"))))
     (build-system gnu-build-system)
     (native-inputs `(("flex" ,flex)
                      ("bison" ,bison)))
@@ -2198,7 +2199,7 @@ buffers.")
 (define-public intel-gpu-tools
   (package
     (name "intel-gpu-tools")
-    (version "1.21")
+    (version "1.22")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://cgit.freedesktop.org/xorg/app/"
@@ -2206,7 +2207,7 @@ buffers.")
                                   "intel-gpu-tools-" version ".tar.gz"))
               (sha256
                (base32
-                "1xfy4cgimyyn5qixlrfkadgnl9qwbk30vw8k80g8vjnrcc4hx986"))))
+                "1jx5w5fr6jp67rcrlp5v79cn8kp9n0wgd5pbfgzamlah5cx6j3yd"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; many of the tests try to load kernel modules
@@ -2218,7 +2219,8 @@ buffers.")
              (setenv "NOCONFIGURE" "1")
              (invoke "sh" "autogen.sh"))))))
     (inputs
-     `(("util-macros" ,util-macros)
+     `(("eudev" ,eudev)
+       ("util-macros" ,util-macros)
        ("libdrm" ,libdrm)
        ("libpciaccess" ,libpciaccess)
        ("kmod" ,kmod)
@@ -2242,6 +2244,7 @@ changes, and many require complicated build procedures or specific testing
 environments to get useful results.  Therefore, Intel GPU Tools includes
 low-level tools and tests specifically for development and testing of the
 Intel DRM Driver.")
+    (supported-systems '("i686-linux" "x86_64-linux"))
     (license license:expat)))
 
 (define-public fabric
@@ -2433,7 +2436,7 @@ on systems running the Linux kernel.")
 (define-public masscan
   (package
     (name "masscan")
-    (version "1.0.4")
+    (version "1.0.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/robertdavidgraham/masscan"
@@ -2441,16 +2444,18 @@ on systems running the Linux kernel.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1y9af345g00z83rliv6bmlqg37xwc7xpnx5xqdgmjikzcxgk9pji"))))
+                "0wxddsgyx27z45906icdhdbfsvfj8ij805208qpqjx46i0lnjs50"))))
     (build-system gnu-build-system)
     (inputs
      `(("libpcap" ,libpcap)))
     (arguments
      '(#:test-target "regress"
-       #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:make-flags
+       (list "CC=gcc"
+             (string-append "PREFIX=" (assoc-ref %outputs "out")))
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure) ; There is no ./configure script
+         (delete 'configure)            ; no ./configure script
          (add-after 'unpack 'patch-path
            (lambda* (#:key outputs inputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))

gnu/packages/android.scm

@@ -457,7 +457,7 @@ def _FindRepo():
      ;; TODO: Add git-remote-persistent-https once it is available in guix
      `(("git" ,git)
        ("gnupg" ,gnupg)
-       ("ssh", openssh)))
+       ("ssh" ,openssh)))
     (native-inputs
      `(("nose" ,python2-nose)))
     (home-page "https://code.google.com/p/git-repo/")

gnu/packages/autotools.scm

@@ -7,6 +7,7 @@
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
 ;;; Copyright © 2017 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -124,8 +125,8 @@ know anything about Autoconf or M4.")
                                (string-append "--build=" build)))))))))))
 
 
-(define* (autoconf-wrapper #:optional (autoconf autoconf))
+(define (make-autoconf-wrapper autoconf)
-  "Return an wrapper around AUTOCONF that generates `configure' scripts that
+  "Return a wrapper around AUTOCONF that generates `configure' scripts that
 use our own Bash instead of /bin/sh in shebangs.  For that reason, it should
 only be used internally---users should not end up distributing `configure'
 files with a system-specific shebang."
@@ -191,12 +192,18 @@ exec ~a --no-auto-compile \"$0\" \"$@\"
                        (patch-shebang "configure"))
                      (exit (status:exit-val result))))
                 port)))
-           (chmod (string-append bin "/autoconf") #o555)))))))
+           (chmod (string-append bin "/autoconf") #o555)))))
+
+    ;; Do not show it in the UI since it's meant for internal use.
+    (properties '((hidden? . #t)))))
+
+(define-public autoconf-wrapper
+  (make-autoconf-wrapper autoconf))
 
 (define-public autoconf-archive
   (package
     (name "autoconf-archive")
-    (version "2017.09.28")
+    (version "2018.03.13")
     (source
      (origin
       (method url-fetch)
@@ -204,7 +211,7 @@ exec ~a --no-auto-compile \"$0\" \"$@\"
                           version ".tar.xz"))
       (sha256
        (base32
-        "00gsh9hkrgg291my98plkrwlcpxkfrpq64pglf18kciqbf2bb7sw"))))
+        "0ng1lvpijf3kv7w7nb1shqs23vp0398yicyvkf9lsk56kw6zjxb1"))))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/autoconf-archive/")
     (synopsis "Collection of freely reusable Autoconf macros")
@@ -253,7 +260,7 @@ output is indexed in many ways to simplify browsing.")
               (search-patches "automake-skip-amhello-tests.patch"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("autoconf" ,(autoconf-wrapper))
+     `(("autoconf" ,autoconf-wrapper)
        ("perl" ,perl)))
     (native-search-paths
      (list (search-path-specification
@@ -319,14 +326,14 @@ Makefile, simplifying the entire process for the developer.")
   ;; Make this the default on the next rebuild cycle.
   (package
     (inherit automake)
-    (version "1.16")
+    (version "1.16.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/automake/automake-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "12jvcmkcmd5p14b41w9f7ixd3sca97pymd6lqbkwnl8qn6bjv3zr"))
+                "08g979ficj18i1w6w5219bgmns7czr03iadf20mk3lrzl8wbn1ax"))
               (patches
                (search-patches "automake-skip-amhello-tests.patch"))))))
 
@@ -348,7 +355,7 @@ Makefile, simplifying the entire process for the developer.")
                      ("perl" ,perl)
                      ("help2man" ,help2man) ;because we modify ltmain.sh
                      ("automake" ,automake)      ;some tests rely on 'aclocal'
-                     ("autoconf" ,(autoconf-wrapper)))) ;others on 'autom4te'
+                     ("autoconf" ,autoconf-wrapper))) ;others on 'autom4te'
 
     (arguments
      `(;; Libltdl is provided as a separate package, so don't install it here.

gnu/packages/avahi.scm

@@ -99,10 +99,18 @@ DNS-SD (for \"DNS-Based Service Discovery\") protocols.")
                        (method url-fetch))))))
     (build-system gnu-build-system)
     (arguments
-     ;; The Avahi daemon socket is expected by src/Makefile.am to be at
+     '(#:phases (modify-phases %standard-phases
-     ;; "$(localstatedir)/run/avahi-daemon/socket", so set $(localstatedir)
+                  (add-after 'unpack 'set-avahi-socket-name
-     ;; appropriately.
+                    (lambda _
-     '(#:configure-flags '("--localstatedir=/var")))
+                      ;; The Avahi daemon socket is expected by
+                      ;; src/Makefile.am to be at
+                      ;; "$(localstatedir)/run/avahi-daemon/socket", but
+                      ;; nowadays it lives in /run/avahi-daemon/socket.
+                      ;; Remove the "$(localstatedir)" bit.
+                      (substitute* "src/Makefile.in"
+                        (("\\$\\(localstatedir)/run/avahi-daemon/socket")
+                         "/run/avahi-daemon/socket"))
+                      #t)))))
     (synopsis "Multicast DNS Name Service Switch (@dfn{NSS}) plug-in")
     (description
      "Nss-mdns is a plug-in for the GNU C Library's Name Service Switch

gnu/packages/bioinformatics.scm

@@ -9,6 +9,7 @@
 ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -110,32 +111,6 @@
   #:use-module (srfi srfi-1)
   #:use-module (ice-9 match))
 
-(define-public r-ape
-  (package
-    (name "r-ape")
-    (version "5.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "ape" version))
-       (sha256
-        (base32
-         "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-lattice" ,r-lattice)
-       ("r-nlme" ,r-nlme)
-       ("r-rcpp" ,r-rcpp)))
-    (home-page "http://ape-package.ird.fr/")
-    (synopsis "Analyses of phylogenetics and evolution")
-    (description
-     "This package provides functions for reading, writing, plotting, and
-manipulating phylogenetic trees, analyses of comparative data in a
-phylogenetic framework, ancestral character analyses, analyses of
-diversification and macroevolution, computing distances from DNA sequences,
-and several other tools.")
-    (license license:gpl2+)))
-
 (define-public aragorn
   (package
     (name "aragorn")
@@ -10680,6 +10655,16 @@ block processing.")
                (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
                (rename-file (string-append "hdf5-" ,(package-version hdf5))
                             "hdf5")
+               ;; Remove timestamp and host system information to make
+               ;; the build reproducible.
+               (substitute* "hdf5/src/libhdf5.settings.in"
+                 (("Configured on: @CONFIG_DATE@")
+                  "Configured on: Guix")
+                 (("Uname information:.*")
+                  "Uname information: Linux\n")
+                 ;; Remove unnecessary store reference.
+                 (("C Compiler:.*")
+                  "C Compiler: GCC\n"))
                (rename-file "Makevars.in" "Makevars")
                (substitute* "Makevars"
                  (("HDF5_CXX_LIB=.*")
@@ -10879,6 +10864,34 @@ are optimized per data type and for subsetted calculations such that both
 memory usage and processing time is minimized.")
     (license license:expat)))
 
+(define-public r-phangorn
+  (package
+    (name "r-phangorn")
+    (version "2.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "phangorn" version))
+       (sha256
+        (base32
+         "0xc8k552nxczy19jr0xjjagrzc8x6lafasgk2c099ls8bc1yml1i"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-fastmatch" ,r-fastmatch)
+       ("r-igraph" ,r-igraph)
+       ("r-magrittr" ,r-magrittr)
+       ("r-matrix" ,r-matrix)
+       ("r-quadprog" ,r-quadprog)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/KlausVigo/phangorn")
+    (synopsis "Phylogenetic analysis in R")
+    (description
+     "Phangorn is a package for phylogenetic analysis in R.  It supports
+estimation of phylogenetic trees and networks using Maximum Likelihood,
+Maximum Parsimony, distance methods and Hadamard conjugation.")
+    (license license:gpl2+)))
+
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
@@ -11407,7 +11420,7 @@ models.  TADbit is complemented by TADkit for visualizing 3D models.")
        ("tcsh" ,tcsh)
        ("perl" ,perl)
        ("libpng" ,libpng)
-       ("mysql" ,mysql)
+       ("mariadb" ,mariadb)
        ("openssl" ,openssl)))
     (home-page "http://genome.cse.ucsc.edu/index.html")
     (synopsis "Assorted bioinformatics utilities")
@@ -12664,6 +12677,13 @@ once.  This package provides tools to perform Drop-seq analyses.")
      `(#:parallel-tests? #f             ; not supported
        #:phases
        (modify-phases %standard-phases
+         ;; "test.sh" runs STAR, which requires excessive amounts of memory.
+         (add-after 'unpack 'disable-resource-intensive-test
+           (lambda _
+             (substitute* "Makefile.in"
+               (("(^  tests/test_trim_galore/test.sh).*" _ m) m)
+               (("^  test.sh") ""))
+             #t))
          (add-after 'install 'wrap-executable
            ;; Make sure the executable finds all R modules.
            (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -12713,3 +12733,277 @@ and a configuration file which describes the experiment.  In addition to
 quality control of the experiment, the pipeline produces a differential
 expression report comparing samples in an easily configurable manner.")
     (license license:gpl3+)))
+
+(define-public pigx-chipseq
+  (package
+    (name "pigx-chipseq")
+    (version "0.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
+                                  "releases/download/v" version
+                                  "/pigx_chipseq-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1jliwhifnjgl9x0z730bzpxswi2s84fyg5y8cagbyzpw509452f5"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'wrap-executable
+           ;; Make sure the executable finds all R modules.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/pigx-chipseq")
+                 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+                 `("PYTHONPATH"  ":" = (,(getenv "PYTHONPATH")))))
+             #t)))))
+    (inputs
+     `(("r-minimal" ,r-minimal)
+       ("r-argparser" ,r-argparser)
+       ("r-chipseq" ,r-chipseq)
+       ("r-data-table" ,r-data-table)
+       ("r-genomation" ,r-genomation)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-rcas" ,r-rcas)
+       ("r-stringr" ,r-stringr)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-heatmaply" ,r-heatmaply)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-plotly" ,r-plotly)
+       ("python-wrapper" ,python-wrapper)
+       ("python-pyyaml" ,python-pyyaml)
+       ("snakemake" ,snakemake)
+       ("macs" ,macs)
+       ("multiqc" ,multiqc)
+       ("perl" ,perl)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+       ("fastqc" ,fastqc)
+       ("bowtie" ,bowtie)
+       ("idr" ,idr)
+       ("snakemake" ,snakemake)
+       ("samtools" ,samtools)
+       ("bedtools" ,bedtools)
+       ("kentutils" ,kentutils)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+    (synopsis "Analysis pipeline for ChIP sequencing experiments")
+    (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
+calling and reporting for ChIP sequencing experiments.  It is easy to use and
+produces high quality reports.  The inputs are reads files from the sequencing
+experiment, and a configuration file which describes the experiment.  In
+addition to quality control of the experiment, the pipeline enables to set up
+multiple peak calling analysis and allows the generation of a UCSC track hub
+in an easily configurable manner.")
+    (license license:gpl3+)))
+
+(define-public pigx-bsseq
+  (package
+    (name "pigx-bsseq")
+    (version "0.0.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
+                                  "releases/download/v" version
+                                  "/pigx_bsseq-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1h8ma99vi7hs83nafvjpq8jmaq9977j3n11c4zd95hai0cf7zxmp"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'set-timezone
+           ;; The readr package is picky about timezones.
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "TZ" "UTC+1")
+             (setenv "TZDIR"
+                     (string-append (assoc-ref inputs "tzdata")
+                                    "/share/zoneinfo"))
+             #t))
+         (add-after 'install 'wrap-executable
+           ;; Make sure the executable finds all R modules.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/pigx-bsseq")
+                 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+                 `("PYTHONPATH"  ":" = (,(getenv "PYTHONPATH")))))
+             #t)))))
+    (native-inputs
+     `(("tzdata" ,tzdata)))
+    (inputs
+     `(("r-minimal" ,r-minimal)
+       ("r-annotationhub" ,r-annotationhub)
+       ("r-dt" ,r-dt)
+       ("r-genomation" ,r-genomation)
+       ("r-methylkit" ,r-methylkit)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-bookdown" ,r-bookdown)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggbio" ,r-ggbio)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+       ("python-wrapper" ,python-wrapper)
+       ("python-pyyaml" ,python-pyyaml)
+       ("snakemake" ,snakemake)
+       ("bismark" ,bismark)
+       ("fastqc" ,fastqc)
+       ("bowtie" ,bowtie)
+       ("trim-galore" ,trim-galore)
+       ("cutadapt" ,cutadapt)
+       ("samtools" ,samtools)))
+    (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+    (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
+    (description "PiGx BSseq is a data processing pipeline for raw fastq read
+data of bisulfite experiments; it produces reports on aggregate methylation
+and coverage and can be used to produce information on differential
+methylation and segmentation.")
+    (license license:gpl3+)))
+
+(define-public pigx-scrnaseq
+  (package
+    (name "pigx-scrnaseq")
+    (version "0.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
+                                  "releases/download/v" version
+                                  "/pigx_scrnaseq-" version ".tar.gz"))
+              (sha256
+               (base32
+                "03gwp83823ji59y6nvyz89i4yd3faaqpc3791qia71i91470vfsg"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard")
+			    "/share/java/picard.jar")
+	     (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools")
+			    "/share/java/dropseq.jar"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'wrap-executable
+           ;; Make sure the executable finds all R modules.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/pigx-scrnaseq")
+                 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+                 `("PYTHONPATH"  ":" = (,(getenv "PYTHONPATH")))))
+             #t)))))
+    (inputs
+     `(("dropseq-tools" ,dropseq-tools)
+       ("fastqc" ,fastqc)
+       ("java-picard" ,java-picard)
+       ("java" ,icedtea-8)
+       ("python-wrapper" ,python-wrapper)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-pandas" ,python-pandas)
+       ("python-numpy" ,python-numpy)
+       ("python-loompy" ,python-loompy)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+       ("snakemake" ,snakemake)
+       ("star" ,star)
+       ("r-minimal" ,r-minimal)
+       ("r-argparser" ,r-argparser)
+       ("r-cowplot" ,r-cowplot)
+       ("r-data-table" ,r-data-table)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+       ("r-dplyr" ,r-dplyr)
+       ("r-dropbead" ,r-dropbead)
+       ("r-dt" ,r-dt)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-hdf5array" ,r-hdf5array)
+       ("r-pheatmap" ,r-pheatmap)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-rtsne" ,r-rtsne)
+       ("r-scater" ,r-scater)
+       ("r-scran" ,r-scran)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-stringr" ,r-stringr)
+       ("r-yaml" ,r-yaml)))
+    (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+    (synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
+    (description "PiGX scRNAseq is an analysis pipeline for preprocessing and
+quality control for single cell RNA sequencing experiments.  The inputs are
+read files from the sequencing experiment, and a configuration file which
+describes the experiment.  It produces processed files for downstream analysis
+and interactive quality reports.  The pipeline is designed to work with UMI
+based methods.")
+    (license license:gpl3+)))
+
+(define-public pigx
+  (package
+    (name "pigx")
+    (version "0.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx/"
+                                  "releases/download/v" version
+                                  "/pigx-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1nxb2hbp40yg3j7n56k4dhsd2fl1j8g0wpiiln56prqzljwnlgmf"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("python" ,python)
+       ("pigx-bsseq" ,pigx-bsseq)
+       ("pigx-chipseq" ,pigx-chipseq)
+       ("pigx-rnaseq" ,pigx-rnaseq)
+       ("pigx-scrnaseq" ,pigx-scrnaseq)))
+    (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+    (synopsis "Analysis pipelines for genomics")
+    (description "PiGx is a collection of genomics pipelines.  It includes the
+following pipelines:
+
+@itemize
+@item PiGx BSseq for raw fastq read data of bisulfite experiments
+@item PiGx RNAseq for RNAseq samples
+@item PiGx scRNAseq for single cell dropseq analysis
+@item PiGx ChIPseq for reads from ChIPseq experiments
+@end itemize
+
+All pipelines are easily configured with a simple sample sheet and a
+descriptive settings file.  The result is a set of comprehensive, interactive
+HTML reports with interesting findings about your samples.")
+    (license license:gpl3+)))
+
+(define-public r-diversitree
+  (package
+    (name "r-diversitree")
+    (version "0.9-10")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "diversitree" version))
+        (sha256
+         (base32
+          "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-desolve" ,r-desolve)
+       ("r-rcpp" ,r-rcpp)
+       ("r-suplex" ,r-subplex)))
+    (home-page "https://www.zoology.ubc.ca/prog/diversitree")
+    (synopsis "Comparative 'phylogenetic' analyses of diversification")
+    (description "This package contains a number of comparative \"phylogenetic\"
+methods, mostly focusing on analysing diversification and character evolution.
+Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
+and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
+Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
+include Markov models of discrete and continuous trait evolution and constant
+rate speciation and extinction.")
+    (license license:gpl2+)))

gnu/packages/bootloaders.scm

@@ -181,7 +181,7 @@ menu to select one of the installed operating systems.")
     (synopsis "GRand Unified Boot loader (UEFI version)")
     (inputs
      `(("efibootmgr" ,efibootmgr)
-       ("mtools", mtools)
+       ("mtools" ,mtools)
        ,@(package-inputs grub)))
     (arguments
      `(;; TODO: Tests need a UEFI firmware for qemu. There is one at

gnu/packages/build-tools.scm

@@ -90,7 +90,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
                   ;; Meson calls the various executables in out/bin through the
                   ;; Python interpreter, so we cannot use the shell wrapper.
                   (delete 'wrap))))
-    (inputs `(("ninja", ninja)))
+    (inputs `(("ninja" ,ninja)))
     (propagated-inputs `(("python" ,python)))
     (home-page "https://mesonbuild.com/")
     (synopsis "Build system designed to be fast and user-friendly")

gnu/packages/calcurse.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,7 +30,7 @@
 (define-public calcurse
   (package
     (name "calcurse")
-    (version "4.2.2")
+    (version "4.3.0")
     (source
      (origin
       (method url-fetch)
@@ -37,7 +38,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "0il0y06akdqgy0f9p40m4x6arn66nh7sr1w1i41bszycs7div266"))))
+        "16jzg0nasnxdlz23i121x41pq5kbxmjzk52c5d863rg117fc7v1i"))))
     (build-system gnu-build-system)
     (inputs `(("ncurses" ,ncurses)))
     (native-inputs `(("tzdata" ,tzdata-for-tests)))

gnu/packages/cdrom.scm

@@ -698,14 +698,14 @@ laid out on the image.")
 (define-public libburn
   (package
     (name "libburn")
-    (version "1.4.6")
+    (version "1.4.8")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://files.libburnia-project.org/releases/"
                                  "libburn-" version ".tar.gz"))
              (sha256
               (base32
-               "0wbh49s3az3sfpai09z1zdgynq7wnwrk31v5589033274nmzldlx"))))
+               "19lxnzn8bz70glrrrn2hs43gf5g7gfbcka9rcbckhv1pb7is509y"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -720,14 +720,14 @@ DVD-RW, DVD-R, DVD-R/DL, BD-R, and BD-RE.")
 (define-public libisofs
   (package
     (name "libisofs")
-    (version "1.4.6")
+    (version "1.4.8")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://files.libburnia-project.org/releases/"
                                  "libisofs-" version ".tar.gz"))
              (sha256
               (base32
-               "02m5g6lbmmkh2xc5xzq5zaf3ma6v31gls66aj886b3cq9qw0paql"))))
+               "0scvqb72qq24wcg814p1iw1dknldl21hr1hxsc1wy9vc6vgyk7fw"))))
     (build-system gnu-build-system)
     (inputs
      `(("zlib" ,zlib)
@@ -737,11 +737,11 @@ DVD-RW, DVD-R, DVD-R/DL, BD-R, and BD-RE.")
     (home-page "https://dev.lovelyhq.com/libburnia/libisofs")
     (synopsis "Library to create ISO 9660 images")
     (description
-     "Libisofs creates ISO 9660 (also known as ECMA-119) filesystem images
+     "Libisofs creates ISO 9660 (also known as ECMA-119) file system images
 which can either be written to POSIX file objects or handed over to
 libburn for being written directly to optical media.
 It can read metadata of ISO 9660 filesystems, manipulate them, and use them
-to produce new complete filesystem images or add-on images to be appended
+to produce new complete file system images or add-on images to be appended
-to the read filesystem image.
+to the read file system image.
 Supported extensions to ISO 9660 are Rock Ridge, Joliet, AAIP, zisofs.")
     (license gpl2+)))

gnu/packages/chemistry.scm

@@ -73,8 +73,8 @@ only with Python 2 and NumPy < 1.9.")
     (build-system python-build-system)
     (inputs
      `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
-       ("python-scientific", python2-scientific)
+       ("python-scientific" ,python2-scientific)
-       ("netcdf", netcdf)
+       ("netcdf" ,netcdf)
        ("gv" ,gv)))
     (propagated-inputs
      `(("python-mmtk" ,python2-mmtk)))

gnu/packages/code.scm

@@ -37,6 +37,7 @@
   #:use-module (gnu packages databases)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages graphviz)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages perl)
@@ -419,9 +420,9 @@ functionality such as HTML output.")
          "0scjbp1z201q8njvrxqz7lk2m9b6k2rxd5q1shrng6532r7ndif2"))))
     (build-system cmake-build-system)
     (arguments
-     '(#:configure-flags
+     '(#:build-type "RelWithDebInfo"
+       #:configure-flags
        '("-DRTAGS_NO_ELISP_FILES=1"
-         "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
          "-DCMAKE_CXX_FLAGS=-std=c++11"
          "-DBUILD_TESTING=FALSE")
        #:tests? #f))
@@ -497,3 +498,32 @@ importantly we give you proper follow-symbol and find-references support.")
     (description "This package provides a wrapper around @command{make} to
 produce colored output.")
     (license license:gpl2+)))
+
+(define-public makefile2graph
+  (package
+    (name "makefile2graph")
+    (version "1.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/lindenb/" name
+                                  "/archive/v" version ".tar.gz"))
+              (sha256
+               (base32
+                "0h1vchkpmm9h6s87p5nf0ksjxcmsxpx8k62a508w428n570wcr4l"))
+              (file-name (string-append name "-" version ".tar.gz"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:test-target "test"
+       #:make-flags (list "CC=gcc" (string-append "prefix=" %output))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))))
+    (native-inputs
+     `(("graphviz" ,graphviz)))
+    (home-page "https://github.com/lindenb/makefile2graph")
+    (synopsis "Creates a graph of dependencies from GNU Make")
+    (description
+     "@code{make2graph} creates a graph of dependencies from GNU Make.  The
+output is a graphviz-dot file, a Gexf-XML file or a list of the deepest
+independent targets.")
+    (license license:expat)))

gnu/packages/compression.scm

@@ -21,6 +21,7 @@
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1017,7 +1018,8 @@ human-readable output.")
              "http://ck.kolivas.org/apps/lrzip/lrzip-" version ".tar.bz2"))
        (sha256
         (base32
-         "0mb449vmmwpkalq732jdyginvql57nxyd31sszb108yps1lf448d"))))
+         "0mb449vmmwpkalq732jdyginvql57nxyd31sszb108yps1lf448d"))
+       (patches (search-patches "lrzip-CVE-2017-8842.patch"))))
     (build-system gnu-build-system)
     (native-inputs
      `(;; nasm is only required when building for 32-bit x86 platforms
@@ -1655,7 +1657,7 @@ speed.")
     (source (package-source zstd))
     (build-system gnu-build-system)
     (native-inputs
-     `(("googletest", googletest)))
+     `(("googletest" ,googletest)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -2110,3 +2112,46 @@ single-member files which can't be decompressed in parallel.")
    (description "innoextract allows extracting Inno Setup installers under
 non-Windows systems without running the actual installer using wine.")
    (license license:zlib)))
+
+(define-public google-brotli
+  (package
+    (name "google-brotli")
+    (version "1.0.2")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/google/brotli/archive/v"
+                                 version ".tar.gz"))
+             (sha256
+              (base32
+               "08kl9gww2058p1p7j9xqmcmrabcfihhj3fq984d7fi3bchb2mky2"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'rename-static-libraries
+           ;; The build tools put a 'static' suffix on the static libraries, but
+           ;; other applications don't know how to find these.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((lib (string-append (assoc-ref %outputs "out") "/lib/")))
+               (rename-file (string-append lib "libbrotlicommon-static.a")
+                            (string-append lib "libbrotlicommon.a"))
+               (rename-file (string-append lib "libbrotlidec-static.a")
+                            (string-append lib "libbrotlidec.a"))
+               (rename-file (string-append lib "libbrotlienc-static.a")
+                            (string-append lib "libbrotlienc.a"))
+               #t))))
+       #:configure-flags
+       (list ;; Defaults to "lib64" on 64-bit archs.
+             (string-append "-DCMAKE_INSTALL_LIBDIR="
+                            (assoc-ref %outputs "out") "/lib"))))
+    (home-page "https://github.com/google/brotli")
+    (synopsis "General-purpose lossless compression")
+    (description "This package provides the reference implementation of Brotli,
+a generic-purpose lossless compression algorithm that compresses data using a
+combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd
+order context modeling, with a compression ratio comparable to the best
+currently available general-purpose compression methods.  It is similar in speed
+with @code{deflate} but offers more dense compression.
+
+The specification of the Brotli Compressed Data Format is defined in RFC 7932.")
+    (license license:expat)))

gnu/packages/connman.scm

@@ -70,7 +70,7 @@
              (string-append
               "--with-dbusdatadir=" (assoc-ref %outputs "out") "/share"))))
     (native-inputs
-     `(("pkg-config", pkg-config)
+     `(("pkg-config" ,pkg-config)
        ("python" ,python-2)))
     (inputs
      `(("dbus" ,dbus)
@@ -84,7 +84,7 @@
        ;; TODO: add neard, ofono
        ("openconnect" ,openconnect)
        ("openvpn" ,openvpn)
-       ("ppp", ppp)
+       ("ppp" ,ppp)
        ("vpnc" ,vpnc)
        ("wpa-supplicant" ,wpa-supplicant)))
     (home-page "https://01.org/connman")

gnu/packages/cran.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,6 +33,32 @@
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web))
 
+(define-public r-ape
+  (package
+    (name "r-ape")
+    (version "5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ape" version))
+       (sha256
+        (base32
+         "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lattice" ,r-lattice)
+       ("r-nlme" ,r-nlme)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "http://ape-package.ird.fr/")
+    (synopsis "Analyses of phylogenetics and evolution")
+    (description
+     "This package provides functions for reading, writing, plotting, and
+manipulating phylogenetic trees, analyses of comparative data in a
+phylogenetic framework, ancestral character analyses, analyses of
+diversification and macroevolution, computing distances from DNA sequences,
+and several other tools.")
+    (license license:gpl2+)))
+
 (define-public r-colorspace
   (package
     (name "r-colorspace")
@@ -1652,7 +1679,7 @@ simplifying cross-class interoperability.")
      `(("r-quadprog" ,r-quadprog)
        ("r-xts" ,r-xts)
        ("r-zoo" ,r-zoo)))
-    (home-page "http://r-forge.r-project.org/projects/returnanalytics/")
+    (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
     (synopsis "Econometric tools for performance and risk analysis")
     (description "This is a collection of econometric functions for
 performance and risk analysis.  This package aims to aid practitioners and
@@ -1782,14 +1809,14 @@ statistics, etc.")
 (define-public r-scatterplot3d
   (package
     (name "r-scatterplot3d")
-    (version "0.3-40")
+    (version "0.3-41")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scatterplot3d" version))
        (sha256
         (base32
-         "0ababcj87kx7860mica9y2ydlhskxmgj9n46crx036cila512jc2"))))
+         "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
     (synopsis "3D scatter plot")
@@ -1969,7 +1996,7 @@ traveling salesman problem).")
          "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/qap/")
+    (home-page "https://cran.r-project.org/web/packages/qap/")
     (synopsis "Heuristics for the quadratic assignment problem (QAP)")
     (description "This package implements heuristics for the @dfn{quadratic
 assignment problem} (QAP).  Currently only a simulated annealing heuristic is
@@ -1989,7 +2016,7 @@ available.")
          "02ba6zj9bjwrzykamjp40ajynx9xjx9h2i85n0ym0r5lcki4x6fn"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-cluster" ,r-cluster)))
-    (home-page "http://cran.r-project.org/web/packages/gclus/")
+    (home-page "https://cran.r-project.org/web/packages/gclus/")
     (synopsis "Clustering graphics")
     (description "This package orders panels in scatterplot matrices and
 parallel coordinate displays by some merit index.  It contains various indices
@@ -2328,7 +2355,7 @@ rules with R.")
          "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/leaps/")
+    (home-page "https://cran.r-project.org/web/packages/leaps/")
     (synopsis "Regression subset selection")
     (description
      "This package provides tools for regression subset selection, including
@@ -2349,7 +2376,7 @@ exhaustive search.")
     (properties `((upstream-name . "splus2R")))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/splus2R/")
+    (home-page "https://cran.r-project.org/web/packages/splus2R/")
     (synopsis "Supplemental S-PLUS functionality in R")
     (description
      "Currently there are many functions in S-PLUS that are missing in R.  To
@@ -2372,7 +2399,7 @@ provides some missing S-PLUS functionality in R.")
     (propagated-inputs
      `(("r-mass" ,r-mass)
        ("r-splus2r" ,r-splus2r)))
-    (home-page "http://cran.r-project.org/web/packages/ifultools/")
+    (home-page "https://cran.r-project.org/web/packages/ifultools/")
     (synopsis "Insightful research tools")
     (description "This package provides C code used by the wmtsa, fractal, and
 sapa R packages.")
@@ -2393,7 +2420,7 @@ sapa R packages.")
     (propagated-inputs
      `(("r-ifultools" ,r-ifultools)
        ("r-splus2r" ,r-splus2r)))
-    (home-page "http://cran.r-project.org/web/packages/sapa/")
+    (home-page "https://cran.r-project.org/web/packages/sapa/")
     (synopsis "Spectral analysis for physical applications")
     (description "This package provides software for the book Spectral
 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
@@ -2417,7 +2444,7 @@ Cambridge University Press, 1993.")
        ("r-ttr" ,r-ttr)
        ("r-xts" ,r-xts)
        ("r-zoo" ,r-zoo)))
-    (home-page "http://cran.r-project.org/web/packages/quantmod/")
+    (home-page "https://cran.r-project.org/web/packages/quantmod/")
     (synopsis "Quantitative financial modelling framework")
     (description "This package provides a quantitative financial modelling
 framework to allow users to specify, build, trade, and analyse quantitative
@@ -2442,7 +2469,7 @@ financial trading strategies.")
        ("r-zoo" ,r-zoo)))
     (native-inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/tseries/")
+    (home-page "https://cran.r-project.org/web/packages/tseries/")
     (synopsis "Time series analysis and computational finance")
     (description
      "This package provides functions relating to time series analysis and
@@ -2465,7 +2492,7 @@ computational finance.")
      `(("r-ifultools" ,r-ifultools)
        ("r-mass" ,r-mass)
        ("r-splus2r" ,r-splus2r)))
-    (home-page "http://cran.r-project.org/web/packages/wmtsa/")
+    (home-page "https://cran.r-project.org/web/packages/wmtsa/")
     (synopsis "Wavelet methods for time series analysis")
     (description
      "This package provides software to accompany the book \"Wavelet Methods
@@ -2541,7 +2568,7 @@ multivariate distributions.")
        ("r-scatterplot3d" ,r-scatterplot3d)
        ("r-splus2r" ,r-splus2r)
        ("r-wmtsa" ,r-wmtsa)))
-    (home-page "http://cran.r-project.org/web/packages/fractal/")
+    (home-page "https://cran.r-project.org/web/packages/fractal/")
     (synopsis "Fractal time series modeling and analysis")
     (description
      "This package provides tools for stochastic fractal and deterministic
@@ -2562,7 +2589,7 @@ chaotic time series analysis.")
     (build-system r-build-system)
     (propagated-inputs `(("r-nlme" ,r-nlme)))
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/urca/")
+    (home-page "https://cran.r-project.org/web/packages/urca/")
     (synopsis "Unit root and cointegration tests for time series data")
     (description
      "This package provides unit root and cointegration tests encountered in
@@ -2610,7 +2637,7 @@ interface.")
      `(("r-extradistr" ,r-extradistr)))
     (native-inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/trend/")
+    (home-page "https://cran.r-project.org/web/packages/trend/")
     (synopsis "Non-parametric trend tests and change-point detection")
     (description
      "The analysis of environmental data often requires the detection of
@@ -2639,7 +2666,7 @@ sample Robust Rank-Order Distributional Test.")
     (build-system r-build-system)
     (propagated-inputs `(("r-matrix" ,r-matrix)))
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://r-forge.r-project.org/projects/expm/")
+    (home-page "https://r-forge.r-project.org/projects/expm/")
     (synopsis "Tools for matrix exponentials and related quantities")
     (description
      "This package provides tools for the computation of the matrix
@@ -2661,7 +2688,7 @@ exponential, logarithm, square root, and related quantities.")
     (propagated-inputs
      `(("r-expm" ,r-expm)
        ("r-matrix" ,r-matrix)))
-    (home-page "http://cran.r-project.org/web/packages/complexplus/")
+    (home-page "https://cran.r-project.org/web/packages/complexplus/")
     (synopsis "Functions of complex or real variables")
     (description
      "This package extends several functions to the complex domain, including
@@ -2732,7 +2759,7 @@ ordered factor data types.")
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)
        ("r-phontools" ,r-phontools)))
-    (home-page "http://cran.r-project.org/web/packages/powerplus/")
+    (home-page "https://cran.r-project.org/web/packages/powerplus/")
     (synopsis "Exponentiation operations")
     (description
      "This package provides tools for the computation of matrix and scalar
@@ -2924,3 +2951,266 @@ created.  Experimental designs may be blocked or blocked designs created from
 a candidate list, using several criteria.  The blocking can be done when whole
 and within plot factors interact.")
     (license license:gpl2+)))
+
+(define-public r-signal
+  (package
+    (name "r-signal")
+    (version "0.7-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "signal" version))
+       (sha256
+        (base32
+         "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mass" ,r-mass)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/signal/")
+    (synopsis "Signal processing")
+    (description
+     "This package provides a set of signal processing functions originally
+written for Matlab and GNU Octave.  It includes filter generation utilities,
+filtering functions, resampling routines, and visualization of filter models.
+It also includes interpolation functions.")
+    (license license:gpl2)))
+
+(define-public r-psych
+  (package
+    (name "r-psych")
+    (version "1.7.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "psych" version))
+       (sha256
+        (base32
+         "0daismb8pdk392vdy304hqx0m3jx62gx3a0hygjygc125rhfla7k"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-foreign" ,r-foreign)
+       ("r-lattice" ,r-lattice)
+       ("r-mnormt" ,r-mnormt)
+       ("r-nlme" ,r-nlme)))
+    (home-page "http://cran.r-project.org/web/packages/psych")
+    (synopsis "Procedures for psychological, psychometric, and personality research")
+    (description
+     "This package provides a general purpose toolbox for personality,
+psychometric theory and experimental psychology.  The functions are primarily
+for multivariate analysis and scale construction using factor analysis,
+principal component analysis, cluster analysis and reliability analysis,
+although others provide basic descriptive statistics.  It provides functions
+for analyzing data at multiple levels within and between group statistics,
+including correlations and factor analysis; functions for simulating and
+testing particular item and test structures are included.  Several functions
+serve as a useful front end for structural equation modeling.")
+    (license license:gpl2+)))
+
+(define-public r-gsubfn
+  (package
+    (name "r-gsubfn")
+    (version "0.6-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gsubfn" version))
+       (sha256
+        (base32
+         "196x4c3ihf4q3i0v7b1xa6jm8jjld2rsx00qz03n90wfnjdx5idv"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-proto" ,r-proto)))
+    (home-page "http://gsubfn.googlecode.com")
+    (synopsis "Utilities for strings and function arguments.")
+    (description
+     "This package provides @code{gsubfn} which is like @code{gsub} but can
+take a replacement function or certain other objects instead of the
+replacement string.  Matches and back references are input to the replacement
+function and replaced by the function output.  @code{gsubfn} can be used to
+split strings based on content rather than delimiters and for quasi-perl-style
+string interpolation.  The package also has facilities for translating
+formulas to functions and allowing such formulas in function calls instead of
+functions.")
+    (license license:gpl2+)))
+
+(define-public r-sqldf
+  (package
+    (name "r-sqldf")
+    (version "0.4-11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sqldf" version))
+       (sha256
+        (base32
+         "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-chron" ,r-chron)
+       ("r-dbi" ,r-dbi)
+       ("r-gsubfn" ,r-gsubfn)
+       ("r-proto" ,r-proto)
+       ("r-rsqlite" ,r-rsqlite)))
+    (home-page "https://github.com/ggrothendieck/sqldf")
+    (synopsis "Manipulate R data frames using SQL")
+    (description
+     "The @code{sqldf} function is typically passed a single argument which is
+an SQL select statement where the table names are ordinary R data frame names.
+@code{sqldf} transparently sets up a database, imports the data frames into
+that database, performs the SQL statement and returns the result using a
+heuristic to determine which class to assign to each column of the returned
+data frame.  The @code{sqldf} or @code{read.csv.sql} functions can also be
+used to read filtered files into R even if the original files are larger than
+R itself can handle.")
+    (license license:gpl2)))
+
+(define-public r-abind
+  (package
+    (name "r-abind")
+    (version "1.4-5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abind" version))
+       (sha256
+        (base32
+         "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/abind/")
+    (synopsis "Combine multidimensional arrays")
+    (description
+     "This package provides tools to combine multidimensional arrays into a
+single array.  This is a generalization of @code{cbind} and @code{rbind}.  It
+works with vectors, matrices, and higher-dimensional arrays.  It also provides
+the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
+extracting and replacing data in arrays.")
+    (license license:lgpl2.0+)))
+
+(define-public r-prroc
+  (package
+    (name "r-prroc")
+    (version "1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "PRROC" version))
+       (sha256
+        (base32
+         "03hvh92lq4i4w4mla9bvwrwb4626f4hvlxgdn57hamp70960vjyc"))))
+    (properties `((upstream-name . "PRROC")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/PRROC/")
+    (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
+    (description
+     "This package computes the areas under the @dfn{precision-recall} (PR)
+and ROC curve for weighted (e.g. soft-labeled) and unweighted data.  In
+contrast to other implementations, the interpolation between points of the PR
+curve is done by a non-linear piecewise function.  In addition to the areas
+under the curves, the curves themselves can also be computed and plotted by a
+specific S3-method.")
+    (license license:gpl3)))
+
+(define-public r-vim
+  (package
+    (name "r-vim")
+    (version "4.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "VIM" version))
+       (sha256
+        (base32
+         "1vjcs5wvjv94ln01d94h9rs4j50d3ky4n26mm3prgh13raylrmnd"))))
+    (properties `((upstream-name . "VIM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-car" ,r-car)
+       ("r-colorspace" ,r-colorspace)
+       ("r-data-table" ,r-data-table)
+       ("r-e1071" ,r-e1071)
+       ("r-laeken" ,r-laeken)
+       ("r-mass" ,r-mass)
+       ("r-nnet" ,r-nnet)
+       ("r-rcpp" ,r-rcpp)
+       ("r-robustbase" ,r-robustbase)
+       ("r-sp" ,r-sp)
+       ("r-vcd" ,r-vcd)))
+    (home-page "https://github.com/alexkowa/VIM")
+    (synopsis "Visualization and imputation of missing values")
+    (description
+     "This package provides tools for the visualization of missing and/or
+imputed values are introduced, which can be used for exploring the data and
+the structure of the missing and/or imputed values.  Depending on this
+structure of the missing values, the corresponding methods may help to
+identify the mechanism generating the missing values and allows to explore the
+data including missing values.  In addition, the quality of imputation can be
+visually explored using various univariate, bivariate, multiple and
+multivariate plot methods.")
+    (license license:gpl2+)))
+
+(define-public r-fnn
+  (package
+    (name "r-fnn")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "FNN" version))
+       (sha256
+        (base32
+         "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
+    (properties `((upstream-name . "FNN")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/FNN")
+    (synopsis "Fast nearest neighbor search algorithms and applications")
+    (description
+     "This package provides cover-tree and kd-tree fast k-nearest neighbor
+search algorithms.  Related applications including KNN classification,
+regression and information measures are implemented.")
+    ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
+    ;; later can be used.
+    (license license:gpl2+)))
+
+(define-public r-smoother
+  (package
+    (name "r-smoother")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "smoother" version))
+       (sha256
+        (base32
+         "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ttr" ,r-ttr)))
+    (home-page "http://cran.r-project.org/web/packages/smoother")
+    (synopsis "Functions relating to the smoothing of numerical data")
+    (description
+     "This package provides a collection of methods for smoothing numerical
+data, commencing with a port of the Matlab gaussian window smoothing function.
+In addition, several functions typically used in smoothing of financial data
+are included.")
+    (license license:gpl2)))
+
+(define-public r-riverplot
+  (package
+    (name "r-riverplot")
+    (version "0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "riverplot" version))
+       (sha256
+        (base32
+         "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
+    (build-system r-build-system)
+    (home-page "https://logfc.wordpress.com")
+    (synopsis "Sankey or ribbon plots")
+    (description
+     "Sankey plots are a type of diagram that is convenient to illustrate how
+flow of information, resources etc. separates and joins, much like observing
+how rivers split and merge.  For example, they can be used to compare
+different clusterings.  This package provides an implementation of Sankey
+plots for R.")
+    (license license:gpl2+)))

gnu/packages/curl.scm

@@ -6,6 +6,7 @@
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -47,7 +48,7 @@
   (package
    (name "curl")
    (version "7.57.0")
-   (replacement curl-7.58.0)
+   (replacement curl-7.59.0)
    (source (origin
             (method url-fetch)
             (uri (string-append "https://curl.haxx.se/download/curl-"
@@ -136,10 +137,10 @@ tunneling, and so on.")
                                   "See COPYING in the distribution."))
    (home-page "https://curl.haxx.se/")))
 
-(define-public curl-7.58.0
+(define-public curl-7.59.0
   (package
     (inherit curl)
-    (version "7.58.0")
+    (version "7.59.0")
     (source
       (origin
         (method url-fetch)
@@ -147,12 +148,12 @@ tunneling, and so on.")
                             version ".tar.xz"))
         (sha256
          (base32
-          "1qz303lagxidmkyym90mxiaqnqddwi2219vzydsyn29n4iski0ba"))))))
+          "1z310hrjm2vmbcpkyp81dcmj9rk127zkjyawpy2pah0nz6yslkp4"))))))
 
 (define-public kurly
   (package
     (name "kurly")
-    (version "1.1.0")
+    (version "1.2.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -161,19 +162,24 @@ tunneling, and so on.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1q192f457sjypgvwq7grrf8gq8w272p3zf1d5ppc20mriqm0mbc3"))))
+                "01kp33gvzxmk6ipz7323wqwmbc90q2mwzsjig8rzpqsm4kji5hi6"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/davidjpeacock/kurly"
        #:install-source? #f
        #:phases
        (modify-phases %standard-phases
-         (add-after 'install 'install-readme
+         (add-after 'install 'install-documentation
-           (lambda* (#:key outputs import-path #:allow-other-keys)
+           (lambda* (#:key import-path outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
+             (let* ((source (string-append "src/" import-path))
-                    (readme (string-append "src/" import-path "/README.md"))
+                    (out (assoc-ref outputs "out"))
-                    (misc (string-append out "/share/kurly/misc/")))
+                    (doc (string-append out "/share/doc/" ,name "-" ,version))
-               (install-file readme misc)
+                    (man (string-append out "/share/man/man1")))
+               (with-directory-excursion source
+                 (install-file "README.md" doc)
+                 (mkdir-p man)
+                 (copy-file "meta/kurly.man"
+                            (string-append man "/kurly.1")))
                #t))))))
     (inputs
      `(("go-github-com-alsm-ioprogress" ,go-github-com-alsm-ioprogress)

gnu/packages/databases.scm

@@ -31,6 +31,7 @@
 ;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Kristofer Buffington <kristoferbuffington@gmail.com>
 ;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -58,6 +59,7 @@
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages curl)
@@ -92,6 +94,7 @@
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages valgrind)
+  #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
@@ -1356,7 +1359,7 @@ module, and nothing else.")
 (define-public perl-sql-abstract
   (package
     (name "perl-sql-abstract")
-    (version "1.84")
+    (version "1.85")
     (source
      (origin
        (method url-fetch)
@@ -1364,7 +1367,7 @@ module, and nothing else.")
                            "SQL-Abstract-" version ".tar.gz"))
        (sha256
         (base32
-         "0xayvgv6nic61jm3nhg41rzwgm8h83wfyazvpaks0z7asjillpv5"))))
+         "1aycggrvppy2zgkwwn85jkdz93n5gsx4dambrjk67k5067hayi4z"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-module-install" ,perl-module-install)
@@ -2738,3 +2741,120 @@ Replay oplog entries between MongoDB servers
 Monitor read/write activity on a mongo server
 @end table")
     (license license:asl2.0)))
+
+(define-public apache-arrow
+  (package
+    (name "apache-arrow")
+    (version "0.7.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/apache/arrow")
+               (commit (string-append "apache-arrow-" version))))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32
+            "1x7sdd8lbs3nfqjql1pcgbkjc19bls56zmgjayshkmablvlc4dy3"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'enter-source-directory
+           (lambda _ (chdir "cpp") #t))
+         (add-after 'unpack 'set-env
+           (lambda _
+             (setenv "BOOST_ROOT" (assoc-ref %build-inputs "boost"))
+             (setenv "BROTLI_HOME" (assoc-ref %build-inputs "brotli"))
+             (setenv "FLATBUFFERS_HOME" (assoc-ref %build-inputs "flatbuffers"))
+             (setenv "JEMALLOC_HOME" (assoc-ref %build-inputs "jemalloc"))
+             (setenv "RAPIDJSON_HOME" (assoc-ref %build-inputs "rapidjson"))
+             #t)))
+       #:build-type "Release"
+       #:configure-flags
+       (list "-DARROW_PYTHON=ON"
+
+             ;; Install to PREFIX/lib (the default is
+             ;; PREFIX/lib64).
+             (string-append "-DCMAKE_INSTALL_LIBDIR="
+                            (assoc-ref %outputs "out")
+                            "/lib")
+
+             ;; XXX These Guix package offer static
+             ;; libraries that are not position independent,
+             ;; and ld fails to link them into the arrow .so
+             "-DARROW_WITH_SNAPPY=OFF"
+             "-DARROW_WITH_ZLIB=OFF"
+             "-DARROW_WITH_ZSTD=OFF"
+             "-DARROW_WITH_LZ4=OFF"
+
+             ;; Building the tests forces on all the
+             ;; optional features and the use of static
+             ;; libraries.
+             "-DARROW_BUILD_TESTS=OFF"
+             "-DARROW_BUILD_STATIC=OFF")))
+    (inputs
+     `(("boost" ,boost)
+       ("rapidjson" ,rapidjson)
+       ("brotli" ,google-brotli)
+       ("flatbuffers" ,flatbuffers)
+       ;; Arrow is not yet compatible with jemalloc >= 5:
+       ;; https://issues.apache.org/jira/browse/ARROW-1141
+       ("jemalloc" ,jemalloc-4.5.0)
+       ("python-3" ,python)
+       ("python-numpy" ,python-numpy)))
+    (home-page "https://arrow.apache.org/")
+    (synopsis "Columnar in-memory analytics")
+    (description "Apache Arrow is a columnar in-memory analytics layer
+designed to accelerate big data. It houses a set of canonical in-memory
+representations of flat and hierarchical data along with multiple
+language-bindings for structure manipulation. It also provides IPC and common
+algorithm implementations.")
+    (license license:asl2.0)))
+
+(define-public python-pyarrow
+  (package
+    (name "python-pyarrow")
+    (version "0.7.0")
+    (source
+      (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/apache/arrow")
+             (commit (string-append "apache-arrow-" version))))
+       (file-name (git-file-name name version))
+       (sha256
+         (base32
+           "1x7sdd8lbs3nfqjql1pcgbkjc19bls56zmgjayshkmablvlc4dy3"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:tests? #f ; XXX Test failures related to missing libhdfs, libhdfs3,
+                   ; and "Unsupported numpy type 22".
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'enter-source-directory
+           (lambda _ (chdir "python") #t))
+         (add-after 'unpack 'set-env
+           (lambda _
+             (setenv "ARROW_HOME" (assoc-ref %build-inputs "apache-arrow"))
+             #t)))))
+    (propagated-inputs
+     `(("apache-arrow" ,apache-arrow)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-six" ,python-six)))
+    (native-inputs
+     `(("cmake" ,cmake)
+       ("python-cython" ,python-cython)
+       ("python-pytest" ,python-pytest)
+       ("python-setuptools-scm" ,python-setuptools-scm)))
+    (home-page "https://arrow.apache.org/docs/python/")
+    (synopsis "Python bindings for Apache Arrow")
+    (description "This library provides a Pythonic API wrapper for the reference
+Arrow C++ implementation, along with tools for interoperability with pandas,
+NumPy, and other traditional Python scientific computing packages.")
+    (license license:asl2.0)))
+
+(define-public python2-pyarrow
+  (package-with-python2 python-pyarrow))

gnu/packages/datamash.scm

@@ -28,7 +28,7 @@
 (define-public datamash
   (package
     (name "datamash")
-    (version "1.2")
+    (version "1.3")
     (source
      (origin
       (method url-fetch)
@@ -36,7 +36,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "15jrv3ly0vgvwwi2qjmhi39n7wrklwifdk961wwfaxyc5jr6zm78"))))
+        "19jpcv4ryvbz0476d6dgpxpbjkpmih4q84wj06nslls338bm5fzf"))))
     (native-inputs
      `(("which" ,which)                 ;for tests
        ("perl" ,perl)))                 ;for help2man

gnu/packages/debian.scm

@@ -0,0 +1,170 @@
+;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
+;;;
+;;; 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 debian)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix download)
+  #:use-module (guix packages)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system trivial)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages wget))
+
+(define-public debian-archive-keyring
+  (package
+    (name "debian-archive-keyring")
+    (version "2017.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "mirror://debian/pool/main/d/" name "/"
+                            name "_" version ".tar.xz"))
+        (sha256
+         (base32
+          "1pdwgipfi0y4svhxlw8arhq792f1g3vlmw4raphizy7sa65vd4ca"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:test-target "verify-results"
+       #:parallel-build? #f ; has race conditions
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; no configure script
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (apt (string-append out "/etc/apt/trusted.gpg.d/"))
+                    (key (string-append out "/share/keyrings/")))
+               (install-file "keyrings/debian-archive-keyring.gpg" key)
+               (install-file "keyrings/debian-archive-removed-keys.gpg" key)
+               (for-each (lambda (file)
+                           (install-file file apt))
+                         (find-files "trusted.gpg" "\\.gpg$")))
+             #t)))))
+    (native-inputs
+     `(("gnupg" ,gnupg)
+       ("jetring" ,jetring)))
+    (home-page "https://packages.qa.debian.org/d/debian-archive-keyring.html")
+    (synopsis "GnuPG archive keys of the Debian archive")
+    (description
+     "The Debian project digitally signs its Release files.  This package
+contains the archive keys used for that.")
+    (license (list license:public-domain ; the keys
+                   license:gpl2+)))) ; see debian/copyright
+
+(define-public ubuntu-keyring
+  (package
+    (name "ubuntu-keyring")
+    (version "2018.02.28")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://launchpad.net/ubuntu/+archive/primary/"
+                            "+files/" name "_" version ".tar.gz"))
+        (sha256
+         (base32
+          "1zj3012cz7rlx9pm39wnwa0lmi1h38n6bkgbz81vnmcsvqsc9a3a"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder (begin
+                   (use-modules (guix build utils))
+                   (let* ((out (assoc-ref %outputs "out"))
+                          (apt (string-append out "/etc/apt/trusted.gpg.d/"))
+                          (key (string-append out "/share/keyrings/")))
+                     (setenv "PATH" (string-append
+                                      (assoc-ref %build-inputs "gzip") "/bin:"
+                                      (assoc-ref %build-inputs "tar") "/bin"))
+                     (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
+                     (for-each (lambda (file)
+                                 (install-file file apt))
+                               (find-files "." "ubuntu-[^am].*\\.gpg$"))
+                     (for-each (lambda (file)
+                                 (install-file file key))
+                               (find-files "." "ubuntu-[am].*\\.gpg$")))
+                   #t)))
+    (native-inputs
+     `(("tar" ,tar)
+       ("gzip" ,gzip)))
+    (home-page "https://launchpad.net/ubuntu/+source/ubuntu-keyring")
+    (synopsis "GnuPG keys of the Ubuntu archive")
+    (description
+     "The Ubuntu project digitally signs its Release files.  This package
+contains the archive keys used for that.")
+    (license (list license:public-domain ; the keys
+                   license:gpl2+)))) ; see debian/copyright
+
+(define-public debootstrap
+  (package
+    (name "debootstrap")
+    (version "1.0.93")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "mirror://debian/pool/main/d/" name "/"
+                            name "_" version ".tar.gz"))
+        (sha256
+         (base32
+          "1nyp9fwb7xrk1vin81dmgx2g9rb52yg4gwz4rcx97gamw4mlvbfd"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-after 'unpack 'patch-source
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out    (assoc-ref outputs "out"))
+                   (wget   (assoc-ref inputs "wget"))
+                   (debian (assoc-ref inputs "debian-keyring"))
+                   (ubuntu (assoc-ref inputs "ubuntu-keyring")))
+               (substitute* "Makefile"
+                 (("/usr") "")
+                 (("-o root -g root") "")
+                 (("chown root.*") "\n"))
+               (substitute* "scripts/sid"
+                 (("/usr") debian))
+               (substitute* "scripts/gutsy"
+                 (("/usr") ubuntu))
+               (substitute* "debootstrap"
+                 (("=/usr") (string-append "=" out)))
+               (substitute* "functions"
+                 (("wget ") (string-append wget "/bin/wget ")))
+               #t)))
+         (add-after 'install 'install-man-file
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (install-file "debootstrap.8"
+                             (string-append out "/share/man/man8"))
+               #t))))
+       #:make-flags (list (string-append "DESTDIR=" (assoc-ref %outputs "out")))
+       #:tests? #f)) ; no tests
+    (inputs
+     `(("debian-keyring" ,debian-archive-keyring)
+       ("ubuntu-keyring" ,ubuntu-keyring)
+       ("wget" ,wget)))
+    ;; The following are required for debootstrap to work correctly
+    (propagated-inputs
+     `(("binutils" ,binutils)
+       ("gnupg" ,gnupg)
+       ("perl" ,perl)))
+    (home-page "https://anonscm.debian.org/cgit/d-i/debootstrap.git")
+    (synopsis "Bootstrap a basic Debian system")
+    (description "Debootstrap is used to create a Debian base system from
+scratch, without requiring the availability of @code{dpkg} or @code{apt}.
+It does this by downloading .deb files from a mirror site, and carefully
+unpacking them into a directory which can eventually be chrooted into.")
+    (license license:gpl2)))

gnu/packages/django.scm

@@ -75,7 +75,7 @@
              (zero? (system* "python" "tests/runtests.py")))))))
     ;; TODO: Install extras/django_bash_completion.
     (native-inputs
-     `(("tzdata", tzdata-for-tests)
+     `(("tzdata" ,tzdata-for-tests)
        ;; bcrypt and argon2-cffi are extra requirements not yet in guix
        ;;("python-argon2-cffi" ,python-argon2-cffi) ; >= 16.1.0
        ;;("python-bcrypt" ,python-bcrypt) ; not py-bcrypt!
@@ -182,13 +182,13 @@ useful tools for testing Django applications and projects.")
 (define-public python-django-filter
   (package
     (name "python-django-filter")
-    (version "0.14.0")
+    (version "1.1.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "django-filter" version))
               (sha256
                (base32
-                "0f78hmk8c903zwfzlsiw7ivgag81ymmb5hi73rzxbhnlg2v0l3fx"))))
+                "0slpfqfhnjrzlrb6vmswyhrzn01p84s16j2x1xib35gg4fxg23pc"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
@@ -198,6 +198,8 @@ useful tools for testing Django applications and projects.")
              (zero? (system* "python" "runtests.py")))))))
     (native-inputs
      `(("python-django" ,python-django)
+       ("python-djangorestframework" ,python-djangorestframework)
+       ("python-django-crispy-forms" ,python-django-crispy-forms)
        ("python-mock" ,python-mock)))
     (home-page "https://django-filter.readthedocs.io/en/latest/")
     (synopsis "Reusable Django application to filter querysets dynamically")
@@ -265,15 +267,18 @@ account authentication.")
 (define-public python-django-gravatar2
   (package
     (name "python-django-gravatar2")
-    (version "1.4.0")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "django-gravatar2" version))
        (sha256
         (base32
-         "1v4qyj6kms321yw0z2g1kch6b2dskmv6fjd6sfxzwr4xshq9mccl"))))
+         "1qsv40xywbqsf4mkrmsswrpzqd7nfljxpfiim9an2z3dykn5rka6"))))
     (build-system python-build-system)
+    (arguments
+     '(;; TODO: The django project for the tests is missing from the release.
+       #:tests? #f))
     (inputs
      `(("python-django" ,python-django)))
     (home-page "https://github.com/twaddington/django-gravatar")
@@ -755,3 +760,52 @@ Django projects, which allows association of a number of tags with any
 
 (define-public python2-django-tagging
   (package-with-python2 python-django-tagging))
+
+(define-public python-djangorestframework
+  (package
+    (name "python-djangorestframework")
+    (version "3.7.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "djangorestframework" version))
+       (sha256
+        (base32
+         "11qv117gqwswxjljs7wafxg1hyzzlx3qrviwlk9hw41bsbl997lz"))))
+    (build-system python-build-system)
+    (arguments
+     '(;; No included tests
+       #:tests? #f))
+    (propagated-inputs
+     `(("python-django" ,python-django)))
+    (home-page "https://www.django-rest-framework.org")
+    (synopsis "Toolkit for building Web APIs with Django")
+    (description
+     "The Django REST framework is for building Web APIs with Django.  It
+provides features like a web browseable API and authentication policies.")
+    (license license:bsd-2)))
+
+(define-public python-django-crispy-forms
+  (package
+    (name "python-django-crispy-forms")
+    (version "1.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "django-crispy-forms" version))
+       (sha256
+        (base32
+         "16s05jx86jmimlvnwpq73kl0mqw1v9lryc8zi61a9qwl25krm6mj"))))
+    (build-system python-build-system)
+    (arguments
+     '(;; No included tests
+       #:tests? #f))
+    (propagated-inputs
+     `(("python-django" ,python-django)))
+    (home-page
+     "http://github.com/maraujop/django-crispy-forms")
+    (synopsis "Tool to control Django forms without custom templates")
+    (description
+     "@code{django-crispy-forms} lets you easily build, customize and reuse
+forms using your favorite CSS framework, without writing template code.")
+    (license license:expat)))

gnu/packages/dns.scm

@@ -99,7 +99,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
 (define-public isc-bind
   (package
     (name "bind")
-    (version "9.12.0")
+    (version "9.12.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -107,7 +107,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "10iwkghl5g50b7wc17bsb9wa0dh2gd57bjlk6ynixhywz6dhx1r9"))))
+                "043mjcw405qa0ghm5dkhfsq35gsy279724fz3mjqpr1mbi14dr0n"))))
     (build-system gnu-build-system)
     (outputs `("out" "utils"))
     (inputs
@@ -149,7 +149,8 @@ and BOOTP/TFTP for network booting of diskless machines.")
          ;;          (system "bin/tests/system/ifconfig.sh up")))
          (replace 'check
            (lambda _
-             (zero? (system* "make" "force-test")))))))
+             (invoke "make" "force-test")
+             #t)))))
     (synopsis "An implementation of the Domain Name System")
     (description "BIND is an implementation of the @dfn{Domain Name System}
 (DNS) protocols for the Internet.  It is a reference implementation of those

gnu/packages/emacs.scm

@@ -3773,7 +3773,7 @@ programming language.")
                                         texlive-latex-seminar
                                         texlive-latex-hyperref
                                         texlive-tex-texinfo)))))
-    (home-page "http://ess.r-project.org/")
+    (home-page "https://ess.r-project.org/")
     (synopsis "Emacs mode for statistical analysis programs")
     (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU
 Emacs.  It is designed to support editing of scripts and interaction with
@@ -7361,3 +7361,48 @@ highlighting and indentation support.")
 @uref{https://www.terraform.io/, Terraform} configuration files.  Most of the
 functionality is inherited from @code{hcl-mode}.")
     (license license:gpl3+)))
+
+(define-public emacs-exec-path-from-shell
+  (package
+    (name "emacs-exec-path-from-shell")
+    (version "1.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://stable.melpa.org/packages/exec-path-from-shell-"
+             version ".el"))
+       (sha256
+        (base32
+         "03qjgb81cq1l3j54lvlf98r75vmmgd06mj6qh5wa6mz4xzp4w26r"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/purcell/exec-path-from-shell")
+    (synopsis "Get environment variables such as @var{PATH} from the shell")
+    (description
+     "This library allows the user to set Emacs @var{exec-path} and @var{PATH}
+from the shell @var{PATH}, so that @code{shell-command}, @code{compile} and
+the like work as expected on systems on which Emacs is not guaranteed to
+inherit a login shell's environment variables.  It also allows other
+environment variables to be retrieved from the shell, so that Emacs will see
+the same values you get in a terminal.")
+    (license license:gpl3+)))
+
+(define-public emacs-deft
+  (package
+    (name "emacs-deft")
+    (version "0.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://stable.melpa.org/packages/deft-"
+                           version ".el"))
+       (sha256
+        (base32
+         "1vb9cjxskc7c0yyf9pvxy1fzypg1vrcgwnjz0m3hslinsgdyig58"))))
+    (build-system emacs-build-system)
+    (home-page "https://jblevins.org/projects/deft/")
+    (synopsis "Quickly browse, filter, and edit plain text notes")
+    (description
+     "Deft is an Emacs mode for quickly browsing, filtering, and editing
+directories of plain text notes, inspired by Notational Velocity.")
+    (license license:bsd-3)))

gnu/packages/emulators.scm

@@ -1095,7 +1095,7 @@ emulation community.  It provides highly accurate emulation.")
        ("sdl" ,sdl2)
        ("udev" ,eudev)
        ("vulkan-icd-loader" ,vulkan-icd-loader)
-       ("wayland", wayland)
+       ("wayland" ,wayland)
        ("zlib" ,zlib)))
     (native-inputs
      `(("pkg-config" ,pkg-config)

gnu/packages/engineering.scm

@@ -696,12 +696,12 @@ language.")
       (arguments
        `(#:out-of-source? #t
          #:tests? #f ; no tests
+         #:build-type "Release"
          #:configure-flags
          (list "-DKICAD_STABLE_VERSION=ON"
                "-DKICAD_REPO_NAME=stable"
                ,(string-append "-DKICAD_BUILD_VERSION=4.0-"
                                (string-take commit 7))
-               "-DCMAKE_BUILD_TYPE=Release"
                "-DKICAD_SKIP_BOOST=ON"; Use our system's boost library.
                "-DKICAD_SCRIPTING=ON"
                "-DKICAD_SCRIPTING_MODULES=ON"
@@ -862,7 +862,7 @@ the 'showing the effect of'-style of operation.")
     (inputs
      `(("boost" ,boost)))
     (native-inputs
-     `(("python-2", python-2)
+     `(("python-2" ,python-2)
        ("python2-cheetah" ,python2-cheetah)))
     (home-page "http://libvolk.org/")
     (synopsis "Vector-Optimized Library of Kernels")

gnu/packages/enlightenment.scm

@@ -286,9 +286,10 @@ Libraries with some extra bells and whistles.")
                  (("/bin/mount") (string-append utils "/bin/mount"))
                  (("/bin/umount") (string-append utils "/bin/umount"))
                  (("/usr/bin/eject") (string-append utils "/bin/eject"))
-                 ; TODO: Replace suspend and hibernate also.
+                 (("/etc/acpi/sleep.sh force") "/run/current-system/profile/bin/loginctl suspend")
-                 (("/sbin/shutdown -h now") "/run/current-system/profile/sbin/halt")
+                 (("/etc/acpi/hibernate.sh force") "/run/current-system/profile/bin/loginctl hibernate")
-                 (("/sbin/shutdown -r now") "/run/current-system/profile/sbin/reboot"))
+                 (("/sbin/shutdown -h now") "/run/current-system/profile/bin/loginctl poweroff now")
+                 (("/sbin/shutdown -r now") "/run/current-system/profile/bin/loginctl reboot now"))
                #t))))))
     (native-inputs
      `(("gettext" ,gettext-minimal)

gnu/packages/file-systems.scm

@@ -236,7 +236,7 @@ All of this is accomplished without a centralized metadata server.")
     (inputs
      `(("curl" ,curl)
        ("glib" ,glib)
-       ("fuse", fuse)))
+       ("fuse" ,fuse)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (home-page "http://curlftpfs.sourceforge.net/")

gnu/packages/flashing-tools.scm

@@ -104,7 +104,7 @@ programmer devices.")
         "1g4032c81wkk37wvbg1dxcqq6mnd76y9x7f2crmzqi6z4q9jcxmj"))))
     (build-system gnu-build-system)
     (inputs
-     `(("libusb",libusb-0.1))) ; doesn't work with libusb-compat
+     `(("libusb" ,libusb-0.1))) ; doesn't work with libusb-compat
     (arguments
      '(#:phases
        (modify-phases %standard-phases
@@ -300,8 +300,8 @@ RK3036, RK3066, RK312X, RK3168, RK3188, RK3288, RK3368.")
                 "1y7gwg3lipyp2zcysm2vid1qg5nwin9bxbvgzs28lz2rya4fz6sq"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release")
+     `(#:build-type "Release"
-       #:tests? #f; no tests
+       #:tests? #f                      ; no tests
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-invocations

gnu/packages/freedesktop.scm

@@ -367,7 +367,7 @@ of a the system to know what users are logged in, and where.")
        ("glib:bin" ,glib "bin")))
     (inputs
      `(("glib" ,glib)
-       ("bash-completion", bash-completion)
+       ("bash-completion" ,bash-completion)
        ("polkit" ,polkit)))
     (propagated-inputs
      `(("sqlite" ,sqlite)))
@@ -1097,13 +1097,13 @@ update-desktop-database: updates the database containing a cache of MIME types
 (define-public xdg-user-dirs
   (package
     (name "xdg-user-dirs")
-    (version "0.16")
+    (version "0.17")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://user-dirs.freedesktop.org/releases/"
                                     name "-" version ".tar.gz"))
               (sha256
-               (base32 "1rp3c94hxjlfsryvwajklynfnrcvxplhwnjqc7395l89i0nb83vp"))))
+               (base32 "13216b8rfkzak5k6bvpx6jvqv3cnbgpijnjwj8a8d3kq4cl0a1ra"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)

gnu/packages/fvwm.scm

@@ -45,6 +45,27 @@
                (base32
                 "0wzghjgy65pkn31rgl14fngizw7nbkzbxsfa670xmrndpmd4sr81"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-xsession
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (xsessions (string-append out "/share/xsessions")))
+               (mkdir-p xsessions)
+               (with-output-to-file
+                   (string-append xsessions "/fvwm2.desktop")
+                 (lambda _
+                   (format #t
+                           "[Desktop Entry]~@
+                    Name=FVWM~@
+                    Comment=FVWM~@
+                    Exec=~a/bin/fvwm~@
+                    TryExec=~@*~a/bin/fvwm~@
+                    Icon=~@
+                    Type=Application~%"
+                           out))))
+             #t)))))
     (native-inputs
      `(("perl" ,perl)
        ("pkg-config" ,pkg-config)

gnu/packages/game-development.scm

@@ -386,7 +386,7 @@ support.")
 (define-public tiled
   (package
     (name "tiled")
-    (version "1.1.2")
+    (version "1.1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/bjorn/tiled/archive/v"
@@ -394,7 +394,7 @@ support.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0l4wc10d10fi0a5spbi318kjfzlizmycpr4wwlq04sk3b5kra0w0"))))
+                "08bxl6vc7ynnji4r6ij9ayr2jixvfhv4daplw5p96s0gkhdqd90k"))))
     (build-system gnu-build-system)
     (inputs
      `(("qtbase" ,qtbase)

gnu/packages/games.scm

@@ -234,7 +234,7 @@ settings to tweak as well.")
        ("libvorbis" ,libvorbis)
        ("ncurses" ,ncurses)
        ("sdl2" ,sdl2)
-       ("sdl2-image", sdl2-image)
+       ("sdl2-image" ,sdl2-image)
        ("sdl2-ttf" ,sdl2-ttf)
        ("sdl2-mixer" ,sdl2-mixer)))
     (home-page "http://en.cataclysmdda.com/")
@@ -2230,19 +2230,19 @@ Transport Tycoon Deluxe.")
               (substitute* "cmake_install.cmake"
                 (("EXPECTED_HASH SHA1=b587d83de508d0b104d14c599b76f8565900fce0")
                 "")))))))
-    (inputs `(("curl", curl)
+    (inputs `(("curl" ,curl)
-              ("fontconfig", fontconfig)
+              ("fontconfig" ,fontconfig)
-              ("freetype", freetype)
+              ("freetype" ,freetype)
-              ("jansson", jansson)
+              ("jansson" ,jansson)
-              ("libpng", libpng)
+              ("libpng" ,libpng)
-              ("libzip", libzip)
+              ("libzip" ,libzip)
-              ("mesa", mesa)
+              ("mesa" ,mesa)
-              ("openssl", openssl)
+              ("openssl" ,openssl)
-              ("sdl2", sdl2)
+              ("sdl2" ,sdl2)
-              ("speexdsp", speexdsp)
+              ("speexdsp" ,speexdsp)
-              ("zlib", zlib)))
+              ("zlib" ,zlib)))
     (native-inputs
-      `(("pkg-config", pkg-config)))
+      `(("pkg-config" ,pkg-config)))
     (home-page "https://github.com/OpenRCT2/OpenRCT2")
     (synopsis "Free software re-implementation of RollerCoaster Tycoon 2")
     (description "OpenRCT2 is a free software re-implementation of

gnu/packages/geo.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,6 +27,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python)
   #:use-module (guix build-system scons)
+  #:use-module (guix build-system r)
   #:use-module (guix download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
@@ -35,6 +37,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages cran)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gtk)
@@ -42,6 +45,8 @@
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages web)
   #:use-module (gnu packages webkit)
   #:use-module (gnu packages wxwidgets)
   #:use-module (gnu packages xml))
@@ -490,3 +495,119 @@ development.")
  construct common SQL queries, or craft your own SQL queries.")
     (home-page "https://www.gaia-gis.it/fossil/spatialite_gui/index")
     (license license:gpl3+)))
+
+(define-public r-maps
+  (package
+   (name "r-maps")
+   (version "3.2.0")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "maps" version))
+       (sha256
+        (base32
+         "0577f3b5d3a7djl7r0miy9mzr6xq6jb32p8nyrma7m2azasbwyj3"))))
+   (build-system r-build-system)
+   (home-page "https://cran.r-project.org/web/packages/maps")
+   (synopsis "Draw geographical maps")
+   (description "This package provies an R module for display of maps.
+Projection code and larger maps are in separate packages ('mapproj' and
+'mapdata').")
+   (license license:gpl2)))
+
+(define-public r-mapproj
+  (package
+   (name "r-mapproj")
+   (version "1.2-5")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mapproj" version))
+       (sha256
+        (base32
+         "0rjz37r4rizk2c6jaf54f0kfb60dqv6b262cnhiwjl55d4x6l0pk"))))
+   (build-system r-build-system)
+   (propagated-inputs `(("r-maps" ,r-maps)))
+   (home-page "https://cran.r-project.org/web/packages/mapproj")
+   (synopsis "Map projection in R")
+   (description "This package converts latitude/longitude into projected
+coordinates.")
+   (license (list license:gpl2 ; The R interface
+                  (license:non-copyleft ; The C code
+                    "https://www.gnu.org/licenses/license-list.en.html#lucent102"
+                    "Lucent Public License Version 1.02")))))
+
+(define-public r-rgooglemaps
+  (package
+   (name "r-rgooglemaps")
+   (version "1.4.1")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RgoogleMaps" version))
+       (sha256
+        (base32
+         "0fsmlnhl4kw2j4972kfanzw9njhnzk695gsyw8g6yppsmz2clcaq"))))
+   (properties `((upstream-name . "RgoogleMaps")))
+   (build-system r-build-system)
+   (propagated-inputs `(("r-png" ,r-png)))
+   (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
+   (synopsis "Use Google Maps in R")
+   (description "This package serves two purposes: (i) Provide a comfortable R
+interface to query the Google server for static maps, and (ii) Use the map as a
+background image to overlay plots within R.  This requires proper coordinate
+scaling.")
+   (license license:gpl2+)))
+
+(define-public r-geosphere
+  (package
+   (name "r-geosphere")
+   (version "1.5-7")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "geosphere" version))
+       (sha256
+        (base32
+         "186qdm5niq7v3d4w4rngx71znsgi44hnam7698bsx9ar5mg5b6wx"))))
+   (build-system r-build-system)
+   (propagated-inputs `(("r-sp" ,r-sp)))
+   (home-page "https://cran.r-project.org/web/packages/geosphere")
+   (synopsis "Spherical trigonometry")
+   (description "This package computes spherical trigonometry for geographic
+applications.  That is, compute distances and related measures for angular
+(longitude/latitude) locations.")
+   (license license:gpl3+)))
+
+(define-public r-ggmap
+  (package
+   (name "r-ggmap")
+   (version "2.6.1")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggmap" version))
+       (sha256
+        (base32
+         "0mssb09w818jv58h7mly9y181pzv22sgcd4a079cfpq04bs0wigw"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-digest" ,r-digest)
+      ("r-geosphere" ,r-geosphere)
+      ("r-ggplot2" ,r-ggplot2)
+      ("r-jpeg" ,r-jpeg)
+      ("r-mapproj" ,r-mapproj)
+      ("r-plyr" ,r-plyr)
+      ("r-png" ,r-png)
+      ("r-proto" ,r-proto)
+      ("r-reshape2" ,r-reshape2)
+      ("r-rgooglemaps" ,r-rgooglemaps)
+      ("r-rjson" ,r-rjson)
+      ("r-scales" ,r-scales)))
+   (home-page "https://github.com/dkahle/ggmap")
+   (synopsis "Spatial visualization with ggplot2")
+   (description "This package provides a collection of functions to visualize
+spatial data and models on top of static maps from various online sources (e.g
+Google Maps and Stamen Maps).  It includes tools common to those tasks,
+including functions for geolocation and routing.")
+   (license license:gpl2)))

gnu/packages/gimp.scm

@@ -175,12 +175,12 @@ buffers.")
        ("libjpeg" ,libjpeg-8)
        ("atk" ,atk)
        ("gtk+" ,gtk+-2)
-       ("exif" ,libexif)                         ;optional, EXIF + XMP support
+       ("exif" ,libexif)                ; optional, EXIF + XMP support
-       ("lcms" ,lcms)                            ;optional, color management
+       ("lcms" ,lcms)                   ; optional, color management
-       ("librsvg" ,librsvg)                      ;optional, SVG support
+       ("librsvg" ,librsvg)             ; optional, SVG support
-       ("poppler", poppler)             ; optional, PDF support
+       ("poppler" ,poppler)             ; optional, PDF support
-       ("python" ,python-2)                      ;optional, Python support
+       ("python" ,python-2)             ; optional, Python support
-       ("python2-pygtk" ,python2-pygtk)          ;optional, Python support
+       ("python2-pygtk" ,python2-pygtk) ; optional, Python support
        ("gegl" ,gegl)))
     (native-inputs
      `(("pkg-config" ,pkg-config)

gnu/packages/gl.scm

@@ -752,7 +752,7 @@ mixed vector/bitmap output.")
               ("libjpeg-turbo" ,libjpeg-turbo)
               ("mesa" ,mesa)
               ("openssl" ,openssl)))
-    (native-inputs `(("pkg-config", pkg-config)))
+    (native-inputs `(("pkg-config" ,pkg-config)))
     (home-page "https://www.virtualgl.org")
     (synopsis "Redirects 3D commands from an OpenGL application onto a 3D
 graphics card")

gnu/packages/gnome.scm

@@ -273,7 +273,7 @@ features to enable users to create their discs easily and quickly.")
        ("gettext" ,gettext-minimal)
        ("itstool" ,itstool)
        ("intltool" ,intltool)
-       ("cmake", cmake)))
+       ("cmake" ,cmake)))
     (home-page "https://launchpad.net/deja-dup")
     (synopsis "Simple backup tool, for regular encrypted backups")
     (description
@@ -2450,7 +2450,7 @@ libxml to ease remote use of the RESTful API.")
 (define-public libsoup
   (package
     (name "libsoup")
-    (version "2.60.3")
+    (version "2.62.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/libsoup/"
@@ -2458,7 +2458,7 @@ libxml to ease remote use of the RESTful API.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "08lawrdkkzycvpb1h0wfiqfz6dgx77jp0wxp546lxgisy9icf38v"))))
+                "1b5aff1igbsx1h4v3wmkffvzgiy8rscibqka7fmjf2lxs7l7lz5b"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (arguments
@@ -2691,7 +2691,7 @@ floating in an ocean using only your brain and a little bit of luck.")
 (define-public gnome-sudoku
   (package
     (name "gnome-sudoku")
-    (version "3.26.0")
+    (version "3.28.0")
     (source
      (origin
        (method url-fetch)
@@ -2700,7 +2700,7 @@ floating in an ocean using only your brain and a little bit of luck.")
                            name "-" version ".tar.xz"))
        (sha256
         (base32
-         "186k2axryn3ic8blc9ddnvyrqqf88khg2hlisfa1n4wp784wfx47"))))
+         "07b4lzniaf3gjsss6zl1lslv18smwc4nrijykvn2z90f423q2xav"))))
     (build-system glib-or-gtk-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -4647,7 +4647,7 @@ javascript engine and the GObject introspection framework.")
 (define-public gedit
   (package
     (name "gedit")
-    (version "3.22.1")
+    (version "3.28.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -4655,7 +4655,7 @@ javascript engine and the GObject introspection framework.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0as9r5zvnyrxh699q6jnd0p9ddqy5qamfbxggpdjzagzixhw6yxa"))))
+                "0pyam0zi44xq776x20ycqnvmf86l98jns8ldv4m81gnp9wnhmycv"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      `(#:phases
@@ -5619,7 +5619,7 @@ like switching to windows and launching applications.")
 (define-public gtk-vnc
   (package
     (name "gtk-vnc")
-    (version "0.7.0")
+    (version "0.7.1")
     (source
      (origin
        (method url-fetch)
@@ -5628,7 +5628,7 @@ like switching to windows and launching applications.")
                            name "-" version ".tar.xz"))
        (sha256
         (base32
-         "0gj8dpy3sj4dp810gy67spzh5f0jd8aqg69clcwqjcskj1yawbiw"))))
+         "1cdaywj5lqnl5b22qzd7k7lmacsnmk8b8rc4drk6gvqmcrlsljzk"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--with-gtk=3.0")))
@@ -5644,6 +5644,7 @@ like switching to windows and launching applications.")
        ("gobject-introspection" ,gobject-introspection)
        ("intltool" ,intltool)
        ("pkg-config" ,pkg-config)
+       ("python-wrapper" ,python-wrapper)
        ("vala" ,vala)))
     (home-page "https://wiki.gnome.org/Projects/gtk-vnc")
     (synopsis "VNC viewer widget for GTK+")

gnu/packages/gnunet.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Sree Harsha Totakura <sreeharsha@totakura.in>
-;;; Copyright © 2015, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
@@ -327,7 +327,7 @@ kinds of basic applications for the foundation of a GNU internet.")
                       (lambda _
                         (invoke "autoreconf" "-vfi"))))))
       (native-inputs `(("pkg-config" ,pkg-config)
-                       ("autoconf" ,(autoconf-wrapper))
+                       ("autoconf" ,autoconf-wrapper)
                        ("automake" ,automake)))
       (inputs `(("guile" ,guile-2.0)
                 ("gnunet" ,gnunet)))

gnu/packages/gnupg.scm

@@ -1,10 +1,10 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016, 2017 ng0 <ng0@infotropique.org>
@@ -618,7 +618,7 @@ PGP keysigning parties.")
                      "1n5bpcfpl9vg1xp6r1jhbyahrgdyxp05b5pria1rh4m0qnv8sifr"))))
    (build-system gnu-build-system)
    (native-inputs
-    `(("autoconf" ,(autoconf-wrapper))
+    `(("autoconf" ,autoconf-wrapper)
       ("automake" ,automake)))
    (inputs `(("perl" ,perl)
              ("perl-text-template" ,perl-text-template)
@@ -929,3 +929,58 @@ keyring content.  Parcimonie is a daemon that fetches one key at a time using
 the Tor network, waits a bit, changes the Tor circuit being used, and starts
 over.")
     (license license:gpl1+)))
+
+(define-public jetring
+  (package
+    (name "jetring")
+    (version "0.25")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "mirror://debian/pool/main/j/" name "/"
+                            name "_" version ".tar.xz"))
+        (sha256
+         (base32
+          "0shcnnw0h31b08vmnvf18ni33dg40w18wv9smb69vkklz3h4jhpw"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; no configure script
+         (add-before 'install 'hardlink-gnupg
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((gpg (string-append (assoc-ref inputs "gnupg")
+                                       "/bin/gpg")))
+               (substitute* (find-files "." "jetring-[[:alpha:]]+$")
+                 (("gpg -") (string-append gpg " -"))
+                 (("\\\"gpg\\\"") (string-append "\"" gpg "\"")))
+               #t)))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (man (string-append out "/share/man")))
+               (for-each (lambda (file)
+                           (install-file file (string-append out "/bin/")))
+                         (find-files "." "jetring-[[:alpha:]]+$"))
+               (for-each (lambda (file)
+                           (install-file file (string-append man "/man1/")))
+                         (find-files "." ".*\\.1$"))
+               (install-file "jetring.7" (string-append man "/man7/"))
+               #t))))
+       #:tests? #f)) ; no test phase
+    (inputs
+     `(("gnupg" ,gnupg)
+       ("perl" ,perl)))
+    (home-page "https://joeyh.name/code/jetring/")
+    (synopsis "GnuPG keyring maintenance using changesets")
+    (description
+     "Jetring is a collection of tools that allow for gpg keyrings to be
+maintained using changesets.  It was developed with the Debian keyring in mind,
+and aims to solve the problem that a gpg keyring is a binary blob that's hard
+for multiple people to collaboratively edit.
+
+With jetring, changesets can be submitted, reviewed to see exactly what they
+will do, applied, and used to build a keyring.  The origin of every change made
+to the keyring is available for auditing, and gpg signatures can be used for
+integrity guarantees.")
+    (license license:gpl2+)))

gnu/packages/gnuzilla.scm

@@ -278,7 +278,7 @@ in C/C++.")
     (home-page
      "https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR")
     (synopsis "Netscape API for system level and libc-like functions")
-    (description "Netscape Portable Runtime (NSPR) provides a
+    (description "Netscape Portable Runtime (@dfn{NSPR}) provides a
 platform-neutral API for system level and libc-like functions.  It is used
 in the Mozilla clients.")
     (license license:mpl2.0)))
@@ -424,24 +424,32 @@ security standards.")
         (mozilla-patch "icecat-bug-1350152.patch"        "f822bda79c28" "1wf56169ca874shr6r7qx40s17h2gwj7ngmpyylrpmd1c6hipvsj")
         (mozilla-patch "icecat-bug-1411708.patch"        "34c968767eb7" "0l2jy201ikj3m3h66mvlsj4y0ki7cpm7x7nnfygbwnfxg42s1sip")
         (mozilla-patch "icecat-bug-1375217.patch"        "00fc630c9a46" "17pcprp452nslk6sac6sili0p74zh8w3g0v1wsdn0ikm9xmnphhv")
-        (mozilla-patch "icecat-bug-1261175.patch"        "f0ec180993d2" "0jiazxcwki83wr00fyh2g518ynsd33p7nk65zk4d1682gn22lc8v")
+        (mozilla-patch "icecat-CVE-2018-5145.patch"      "f0ec180993d2" "0jiazxcwki83wr00fyh2g518ynsd33p7nk65zk4d1682gn22lc8v")
-        (mozilla-patch "icecat-bug-1433005.patch"        "a6a9e26688c1" "0cvizvilb4k422j2gzqcbakznvsffmk6n6xn1ayj5rgxfaizkkqk")
+        (mozilla-patch "icecat-CVE-2018-5130.patch"      "a6a9e26688c1" "0cvizvilb4k422j2gzqcbakznvsffmk6n6xn1ayj5rgxfaizkkqk")
-        (mozilla-patch "icecat-bug-1434580.patch"        "198ad052621e" "1721zx8hifdlflrhvw6hmkdgjbvsmxl9n84iji5qywhlp2krdk9r")
+        (mozilla-patch "icecat-CVE-2018-5125-pt1.patch"  "198ad052621e" "1721zx8hifdlflrhvw6hmkdgjbvsmxl9n84iji5qywhlp2krdk9r")
         (mozilla-patch "icecat-bug-1426087.patch"        "391ea77ebfdb" "1fhkvd0z6mvdkj7m0d3jlj42rsdw5r4x122c1wb1i428228ifw6n")
         (mozilla-patch "icecat-bug-1416307.patch"        "54f2f7f93b30" "1ncjir16mqya37wgf6fy2rqki3vl433c4grjr3fypmlig6xfgg1l")
-        (mozilla-patch "icecat-bug-1430557.patch"        "2c4d7a59041b" "178c6gid89cvw52yqs43i6x6s5w0hslj0rfa2r8b4762ij3civ92")
+        (mozilla-patch "icecat-CVE-2018-5127.patch"      "2c4d7a59041b" "178c6gid89cvw52yqs43i6x6s5w0hslj0rfa2r8b4762ij3civ92")
-        (mozilla-patch "icecat-bug-1416529.patch"        "f87ef3774d5e" "0payf3az2w93nzl5qknqx290jbxk8v39rwhdgq7wyd5f245dywxk")
+        (mozilla-patch "icecat-CVE-2018-5125-pt2.patch"  "f87ef3774d5e" "0payf3az2w93nzl5qknqx290jbxk8v39rwhdgq7wyd5f245dywxk")
-        (mozilla-patch "icecat-bug-1324042.patch"        "ac743923f81d" "0msyr45xr1j5q4x6ah4r907pwjngyi0k6pp9y8ixk21cnwbzrdwx")
+        (mozilla-patch "icecat-CVE-2018-5125-pt3.patch"  "ac743923f81d" "0msyr45xr1j5q4x6ah4r907pwjngyi0k6pp9y8ixk21cnwbzrdwx")
-        (mozilla-patch "icecat-bug-1428947.patch"        "456913d7e8b5" "0fx0s06kxxj7g4hllinaskgh41z3k48zml6yqqzxx485qk3hdh9x")
+        (mozilla-patch "icecat-CVE-2018-5129.patch"      "456913d7e8b5" "0fx0s06kxxj7g4hllinaskgh41z3k48zml6yqqzxx485qk3hdh9x")
         (mozilla-patch "icecat-bug-1334465-pt1.patch"    "f95c5b881442" "0iaddhf65jd9cycj4bw0b207n2jiqkr4q84jifzyqn4ygs75wdqd")
         (mozilla-patch "icecat-bug-1334465-pt2.patch"    "8a4265c8fb41" "1d9zfdbrlw9wzr84b7pj7lxgy487lsx0kfd89287hjk0al8m6vrw")
         (mozilla-patch "icecat-bug-1398021.patch"        "28855df568d8" "1kmq836gniplxpjnvq8lhbcc1aqi56al628r1mzdy94b5yb0lis3")
         (mozilla-patch "icecat-bug-1388020.patch"        "e8ab2736499b" "0n28vcd65rxsyq3z22rfcfksryfndhm1i3g6ah3akg11jnagqf5v")
-        (mozilla-patch "icecat-bug-1437087.patch"        "014877bf17ea" "0hk90pnf7h7kvidji6ydvva1zpyraipn03pjhvprdqr7k2fqzmsz")
+        (mozilla-patch "icecat-CVE-2018-5125-pt4.patch"  "014877bf17ea" "0hk90pnf7h7kvidji6ydvva1zpyraipn03pjhvprdqr7k2fqzmsz")
-        (mozilla-patch "icecat-bug-1437507.patch"        "5b3a5de48912" "1ifya05rcd34ryp9zawdacihhkkf2m0xn2q8m8c6v78bvxj0mgig")
+        (mozilla-patch "icecat-CVE-2018-5125-pt5.patch"  "5b3a5de48912" "1ifya05rcd34ryp9zawdacihhkkf2m0xn2q8m8c6v78bvxj0mgig")
-        (mozilla-patch "icecat-bug-1440926.patch"        "1df9b4404acd" "1sd59vsarfsbh3vlrzrqv6n1ni7vxdzm83j6s6g0fygl1h8kwijg")
+        (mozilla-patch "icecat-CVE-2018-5144.patch"      "1df9b4404acd" "1sd59vsarfsbh3vlrzrqv6n1ni7vxdzm83j6s6g0fygl1h8kwijg")
         (mozilla-patch "icecat-bug-1430173-pt1.patch"    "9124c3972e2b" "13ns5yy39yzfx7lrkv4rgwdz6s6q0z4i09wkbxdvnkfsz17cd17i")
-        (mozilla-patch "icecat-bug-1430173-pt2.patch"    "9f6dc031be51" "0bv2p98z5ahp3x9wxnhwxn87g21djvzzp7jy55ik90hqixsbhwdl")))
+        (mozilla-patch "icecat-bug-1430173-pt2.patch"    "9f6dc031be51" "0bv2p98z5ahp3x9wxnhwxn87g21djvzzp7jy55ik90hqixsbhwdl")
+        (mozilla-patch "icecat-CVE-2018-5131.patch"      "3102fbb97b32" "0kg0183v92gxjb9255xjwhxyd6gl77l9c0civx3040k975fybwlp")
+        (mozilla-patch "icecat-CVE-2018-5125-pt6.patch"  "4904c0f4a645" "0lsq62ynksy1fbw0m87f1d741fyvrrp1vrznx5hx0l2p4g4frhv3")
+        (mozilla-patch "icecat-CVE-2018-5125-pt7.patch"  "16b8073d5c30" "1dv94qqah1wjd3bxjvrkmjbb2f95d3d11zpm8mggdk52il575bwl")
+        (mozilla-patch "icecat-bug-1442127-pt1.patch"    "f931f85b09da" "02s380w8a73g4w2wm810lbigh4z4rrlfy10ywwhv4lpkbk8xg7pr")
+        (mozilla-patch "icecat-bug-1442127-pt2.patch"    "da5792b70f30" "116k9qja5ir9b3laazasp43f5jx59qq72nknmq5bn5v1ixya9r4l")
+        (mozilla-patch "icecat-CVE-2018-5125-pt8.patch"  "62b831df8269" "109pn0hqn7s27580glv4z7qv1pmjzii9szvf3wkn97k5wybrzgkx")
+        (mozilla-patch "icecat-bug-1442504.patch"        "8954ce68a364" "0bl65zw82bwqg0mmcri94pxqq6ibff7y5rclkzapb081p6yvf73q")
+        (mozilla-patch "icecat-CVE-2018-5125-pt9.patch"  "8a16f439117c" "108iarql6z7h1r4rlzac6n6lrzs78x7kcdbfa0b5dbr5xc66jmgb")))
       (modules '((guix build utils)))
       (snippet
        '(begin

gnu/packages/golang.scm

@@ -8,6 +8,7 @@
 ;;; Copyright © 2017 Sergei Trofimovich <slyfox@inbox.ru>
 ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -639,3 +640,54 @@ termination.")
 per-goroutine.")
     (home-page "https://github.com/jtolds/gls")
     (license license:expat)))
+
+(define-public go-github-com-tj-docopt
+  (package
+    (name "go-github-com-tj-docopt")
+    (version "1.0.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/tj/docopt")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "06h8hdg1mh3s78zqlr01g4si7k0f0g6pr7fj7lnvfg446hgc7080"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/tj/docopt"))
+    (synopsis "Go implementation of docopt")
+    (description
+     "This library allows the user to define a command-line interface from a
+program's help message rather than specifying it programatically with
+command-line parsers.")
+    (home-page "https://github.com/tj/docopt")
+    (license license:expat)))
+
+(define-public go-github-com-hashicorp-hcl
+  (let ((commit "23c074d0eceb2b8a5bfdbb271ab780cde70f05a8")
+        (revision "0"))
+    (package
+      (name "go-github-com-hashicorp-hcl")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/hashicorp/hcl")
+                       (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                  (base32
+                    "0db4lpqb5m130rmfy3s3gjjf4dxllypmyrzxv6ggqhkmwmc7w4mc"))))
+      (build-system go-build-system)
+      (arguments
+       '(#:tests? #f
+         #:import-path "github.com/hashicorp/hcl"))
+      (synopsis "Go implementation of HashiCorp Configuration Language")
+      (description
+       "This package contains the main implementation of the @acronym{HCL,
+HashiCorp Configuration Language}.  HCL is designed to be a language for
+expressing configuration which is easy for both humans and machines to read.")
+      (home-page "https://github.com/hashicorp/hcl")
+      (license license:mpl2.0))))

gnu/packages/gps.scm

@@ -108,6 +108,7 @@ manipulate maps.")
                 (uri (git-reference
                       (url "https://github.com/freefoote/gpscorrelate")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "006a6l8p38a4h7y2959sqrmjjn29d8pd50zj9nypcp5ph18nybjb"))))

gnu/packages/graph.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -33,7 +34,10 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages statistics)
+  #:use-module (gnu packages time)
   #:use-module (gnu packages xml))
 
 (define-public igraph
@@ -138,7 +142,7 @@ more.")
      `(("r-igraph" ,r-igraph)
        ("r-matrix" ,r-matrix)
        ("r-scatterplot3d" ,r-scatterplot3d)))
-    (home-page "http://www.r-project.org")
+    (home-page "https://www.r-project.org")
     (synopsis "Diffusion map")
     (description "This package implements the diffusion map method of data
 parametrization, including creation and visualization of diffusion maps,
@@ -199,3 +203,34 @@ objects from the @code{graph} package.")
 represented by horizontal lines, and edges are represented by vertical
 lines.")
       (license license:expat))))
+
+(define-public python-plotly
+  (package
+    (name "python-plotly")
+    (version "2.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "plotly" version))
+        (sha256
+         (base32
+          "0n18116jz6bl5n9cq23vabv1gcbh1x3yficdnfq55v0z4cwy0zlf"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:tests? #f)) ; The tests are not distributed in the release
+    (propagated-inputs
+     `(("python-decorator" ,python-decorator)
+       ("python-nbformat" ,python-nbformat)
+       ("python-pytz" ,python-pytz)
+       ("python-requests" ,python-requests)
+       ("python-six" ,python-six)))
+    (home-page "https://plot.ly/python/")
+    (synopsis "Interactive plotting library for Python")
+    (description "Plotly's Python graphing library makes interactive,
+publication-quality graphs online.  Examples of how to make line plots, scatter
+plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
+subplots, multiple-axes, polar charts, and bubble charts. ")
+    (license license:expat)))
+
+(define-public python2-plotly
+  (package-with-python2 python-plotly))

gnu/packages/graphics.scm

@@ -6,8 +6,8 @@
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
-;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -251,7 +251,7 @@ exception-handling library.")
 (define-public ogre
   (package
     (name "ogre")
-    (version "1.10.7")
+    (version "1.10.11")
     (source
      (origin
        (method url-fetch)
@@ -259,7 +259,7 @@ exception-handling library.")
                            "/archive/v" version ".tar.gz"))
        (sha256
         (base32
-         "1p0c91cc7zg3c00wjaibnxb0a0xm14mkg0h65pzpw93m0d6nc8wd"))
+         "13bdh9v4026qf8w8rbfln2rmwf0rby1a8fz55zpdvpy105i6cbpz"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system cmake-build-system)
     (arguments
@@ -423,25 +423,24 @@ visual effects work for film.")
        (file-name (string-append name "-" version ".zip"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f ;; No test target available.
+     `(#:tests? #f ; no test target available
+       ;; Without this flag, 'rd' will be added to the name of the
+       ;; library binaries and break linking with other programs.
+       #:build-type "Release"
        #:configure-flags
        (list (string-append "-DCMAKE_INSTALL_RPATH="
                             (assoc-ref %outputs "out") "/lib:"
-                            (assoc-ref %outputs "out") "/lib64")
+                            (assoc-ref %outputs "out") "/lib64"))))
-             ;; We need to set this flag or otherwise 'rd' will be added
-             ;; to the name of the library binaries and break linking
-             ;; with other programs.
-             "-DCMAKE_BUILD_TYPE=Release")))
     (native-inputs
      `(("unzip" ,unzip)))
     (inputs
-     `(("giflib", giflib)
+     `(("giflib" ,giflib)
-       ("jasper", jasper)
+       ("jasper" ,jasper)
-       ("librsvg", librsvg)
+       ("librsvg" ,librsvg)
-       ("pth", pth)
+       ("pth" ,pth)
-       ("qtbase", qtbase)
+       ("qtbase" ,qtbase)
-       ("ffmpeg", ffmpeg)
+       ("ffmpeg" ,ffmpeg)
-       ("mesa", mesa)))
+       ("mesa" ,mesa)))
     (synopsis "High performance real-time graphics toolkit")
     (description
      "The OpenSceneGraph is a high performance 3D graphics toolkit

gnu/packages/gtk.scm

@@ -322,6 +322,7 @@ diagrams.")
                 (uri (git-reference
                       (url "http://git.drobilla.net/ganv.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1cr8w02lr6bk9mkxa12j3imq721b2an2yn4bj5wnwmpm91ddn2gi")))))))
@@ -384,7 +385,7 @@ printing and other features typical of a source code editor.")
 (define-public gtksourceview
  (package
    (name "gtksourceview")
-   (version "3.24.6")
+   (version "3.24.7")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnome/sources/" name "/"
@@ -392,7 +393,7 @@ printing and other features typical of a source code editor.")
                                  name "-" version ".tar.xz"))
              (sha256
               (base32
-               "1261fwjpwn3qizmvjns9z3k3a264j3ql5anyvmisfwywpkzbv9ks"))))
+               "1rp8zspwyw3mmdgccsas3pa6v7s0hqjaaglg6n4kcls7ccx0vhm5"))))
    (build-system gnu-build-system)
    (arguments
     '(#:phases

gnu/packages/guile.scm

@@ -769,7 +769,7 @@ format is also supported.")
                       (symlink "README.org" "README")
                       (zero? (system* "autoreconf" "-fi")))))))
     (native-inputs
-     `(("autoconf" ,(autoconf-wrapper))
+     `(("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
        ("texinfo" ,texinfo)
        ;; Gettext brings 'AC_LIB_LINKFLAGS_FROM_LIBS'.
@@ -1259,14 +1259,14 @@ Guile's foreign function interface.")
 (define-public haunt
   (package
     (name "haunt")
-    (version "0.2.1")
+    (version "0.2.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://files.dthompson.us/haunt/haunt-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1fpaf1vm6s7j13fs35barjh5yajcc2rc3pi8r7278wpgp4i2vs3w"))))
+                "0nm00krmqq4zmqi2irh35dbf2cn6al58s620hijmhfvhgvdqznlp"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 match) (ice-9 ftw)
@@ -1283,12 +1283,15 @@ Guile's foreign function interface.")
                                     out "/share/guile/site")))
                         (match (scandir site)
                           (("." ".." version)
-                           (let ((modules (string-append site "/" version)))
+                           (let ((modules (string-append site "/" version))
+                                 (compiled-modules (string-append
+                                                    out "/lib/guile/" version
+                                                    "/site-ccache")))
                              (wrap-program (string-append bin "/haunt")
                                `("GUILE_LOAD_PATH" ":" prefix
                                  (,modules))
                                `("GUILE_LOAD_COMPILED_PATH" ":" prefix
-                                 (,modules)))
+                                 (,compiled-modules)))
                              #t)))))))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -1856,7 +1859,7 @@ dictionary and suggesting spelling corrections.")
                (string-append "--libdir=" (assoc-ref %outputs "out")
                               "/lib/bash"))))
       (native-inputs `(("pkg-config" ,pkg-config)
-                       ("autoconf" ,(autoconf-wrapper))
+                       ("autoconf" ,autoconf-wrapper)
                        ("automake" ,automake)
                        ("libtool" ,libtool)
                        ;; Gettext brings 'AC_LIB_LINKFLAGS_FROM_LIBS'.
@@ -1957,8 +1960,8 @@ is not available for Guile 2.0.")
     (license license:lgpl3+)))
 
 (define-public guile-git
-  (let ((revision "4")
+  (let ((revision "5")
-        (commit "951a32c56cc4d80f8836e3c7394783e69c1fcbad"))
+        (commit "2bb9fbbf93cf93496718efc85ad9394aefa21029"))
     (package
       (name "guile-git")
       (version (string-append "0.0-" revision "." (string-take commit 7)))
@@ -1968,7 +1971,7 @@ is not available for Guile 2.0.")
                 (uri (git-reference (url home-page) (commit commit)))
                 (sha256
                  (base32
-                  "0qri9x73ij6g40ijs4hyhj8knxw39ydgghiafq74dp99bc8hh0qc"))
+                  "0z3v0v89dyp35zx2h2gsq6v29lba3wbzabc5n2g4hx2fcb6q5qqy"))
                 (file-name (git-file-name name version))))
       (build-system gnu-build-system)
       (arguments
@@ -2008,31 +2011,21 @@ manipulate repositories of the Git version control system.")
   (package-for-guile-2.0 guile-git))
 
 (define-public guile-syntax-highlight
-  (let ((commit "a047675e66861b647426372aa2ba7820f749616d")
-        (revision "0"))
   (package
     (name "guile-syntax-highlight")
-      (version (string-append "0.0." revision "."
+    (version "0.1")
-                              (string-take commit 7)))
     (source (origin
-                (method git-fetch)
+              (method url-fetch)
-                (uri (git-reference
+              (uri (string-append "https://files.dthompson.us/"
-                      (url "git://dthompson.us/guile-syntax-highlight.git")
+                                  "guile-syntax-highlight/"
-                      (commit commit)))
+                                  "guile-syntax-highlight-"
-                (file-name (string-append name "-" version "-checkout"))
+                                  version ".tar.gz"))
               (sha256
                (base32
-                  "1zjr6sg3n7xbdsliy45i39dqanxvcms58ayx36wxrz72zpq58vq3"))))
+                "1p771kq15x83483m23bhah1sz6vkalg3drm7x279f4j1cxligkzi"))))
     (build-system gnu-build-system)
-      (arguments
-       '(#:phases (modify-phases %standard-phases
-                    (add-after 'unpack 'bootstrap
-                      (lambda _
-                        (zero? (system* "sh" "bootstrap")))))))
     (native-inputs
-       `(("autoconf" ,autoconf)
+     `(("pkg-config" ,pkg-config)))
-         ("automake" ,automake)
-         ("pkg-config" ,pkg-config)))
     (inputs
      `(("guile" ,guile-2.2)))
       (synopsis "General-purpose syntax highlighter for GNU Guile")
@@ -2040,8 +2033,8 @@ manipulate repositories of the Git version control system.")
 highlighting library for GNU Guile.  It can parse code written in various
 programming languages into a simple s-expression that can be converted to
 HTML (via SXML) or any other format for rendering.")
-      (home-page "http://dthompson.us/software/guile-syntax-highlight")
+    (home-page "http://dthompson.us/projects/guile-syntax-highlight.html")
-      (license license:lgpl3+))))
+    (license license:lgpl3+)))
 
 (define-public guile-sjson
   (package

gnu/packages/haskell-web.scm

@@ -777,6 +777,18 @@ for Haskell, optimized for ease of use and high performance.  (A note on
 naming: in Greek mythology, Aeson was the father of Jason.)")
     (license license:bsd-3)))
 
+(define-public ghc-aeson-for-pandoc-1
+  (package (inherit ghc-aeson)
+    (version "1.1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/aeson/aeson-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1zy5z8pzvh53qkjm0nm3f4rwqfqg3867ck8ncd6mrxpcyvxqqj1p"))))))
+
 (define-public ghc-aeson-pretty
   (package
     (name "ghc-aeson-pretty")

gnu/packages/haskell.scm

@@ -63,7 +63,8 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix utils)
-  #:use-module (ice-9 regex))
+  #:use-module (ice-9 regex)
+  #:use-module ((srfi srfi-1) #:select (alist-delete)))
 
 (define-public cl-yale-haskell
   (let ((commit "85f94c72a16c5f70301dd8db04cde9de2d7dd270")
@@ -4980,6 +4981,22 @@ pandoc to represent structured documents.  It also provides functions for
 building up, manipulating and serialising @code{Pandoc} structures.")
     (license license:bsd-3)))
 
+(define-public ghc-pandoc-types-for-pandoc-1
+  (package (inherit ghc-pandoc-types)
+    (version "1.17.0.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://hackage.haskell.org/package/"
+                                  "pandoc-types/pandoc-types-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1csipjdq00iiq77k2wlrg4i7afrzlh8nl585q785xzw7nn45b0n8"))))
+    (inputs
+     `(("ghc-syb" ,ghc-syb)
+       ("ghc-aeson" ,ghc-aeson-for-pandoc-1)
+       ("ghc-string-qq" ,ghc-string-qq)))))
+
 (define-public ghc-texmath
   (package
     (name "ghc-texmath")
@@ -5013,6 +5030,27 @@ markup formats).  The TeX reader supports basic LaTeX and AMS extensions, and
 it can parse and apply LaTeX macros.")
     (license license:gpl2+)))
 
+(define-public ghc-texmath-for-pandoc-1
+  (package (inherit ghc-texmath)
+    (version "0.9.4.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://hackage.haskell.org/package/"
+                                  "texmath/texmath-" version ".tar.gz"))
+              (sha256
+               (base32
+                "129q33m56diiv35kdwfb07838wrg0mm88kxdqxfyl1zvf9nzkqkd"))))
+    (inputs
+     `(("ghc-mtl" ,ghc-mtl)
+       ("ghc-network-uri" ,ghc-network-uri)
+       ("ghc-pandoc-types" ,ghc-pandoc-types-for-pandoc-1)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-split" ,ghc-split)
+       ("ghc-syb" ,ghc-syb)
+       ("ghc-temporary" ,ghc-temporary)
+       ("ghc-utf8-string" ,ghc-utf8-string)
+       ("ghc-xml" ,ghc-xml)))))
+
 (define-public ghc-regex-pcre-builtin
   (package
     (name "ghc-regex-pcre-builtin")
@@ -5562,6 +5600,12 @@ back-ends.")
      "This package provides a library to parse and render YAML documents.")
     (license license:bsd-3)))
 
+(define-public ghc-yaml-for-pandoc-1
+  (package (inherit ghc-yaml)
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
+       ,@(alist-delete "ghc-aeson" (package-inputs ghc-yaml))))))
+
 (define-public ghc-filemanip
   (package
     (name "ghc-filemanip")
@@ -5666,6 +5710,27 @@ TIFF and GIF formats.")
 described in @url{https://www.lua.org/}.")
     (license license:expat)))
 
+(define-public ghc-hslua-for-pandoc-1
+  (package (inherit ghc-hslua)
+    (version "0.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://hackage.haskell.org/package/"
+                                  "hslua/hslua-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0gqp6qhp4v24kzv2j49kgk7bxqzw0w10x0zr0r2j9wkfavqb9wid"))))
+    (inputs
+     `(("lua" ,lua-5.1)
+       ("ghc-text" ,ghc-text)))
+    (native-inputs
+     `(("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-quickcheck-instances" ,ghc-quickcheck-instances)
+       ("ghc-hspec" ,ghc-hspec)
+       ("ghc-hspec-contrib" ,ghc-hspec-contrib)
+       ("ghc-hunit" ,ghc-hunit)
+       ("hspec-discover" ,hspec-discover)))))
+
 (define-public ghc-hslua-module-text
   (package
     (name "ghc-hslua-module-text")
@@ -5892,6 +5957,57 @@ supported by that framework can be added.  An optional command-line program is
 provided.  Skylighting is intended to be the successor to highlighting-kate.")
     (license license:gpl2)))
 
+(define-public ghc-skylighting-for-pandoc-1
+  (package (inherit ghc-skylighting)
+    (version "0.1.1.5")
+    (source (origin
+              (method git-fetch)
+              ;; We take the sources from Github, because the tarball on
+              ;; hackage does not include the XML files.
+              (uri (git-reference
+                    (url "https://github.com/jgm/skylighting.git")
+                    (commit version)))
+              (file-name (string-append "ghc-skylighting-" version "-checkout"))
+              (sha256
+               (base32
+                "0z3yv8v2fqqgv6lsf0ff3ld0h2vkg97b2jiry9wn2f1rizwdqmzl"))))
+    (arguments
+     `(#:configure-flags '("-fbootstrap")
+       #:phases
+       (modify-phases %standard-phases
+         ;; After building the skylighting-extract tool we use it to generate
+         ;; syntax source files from the included XML files.  These are then
+         ;; added to the skylighting.cabal file.
+         (add-after 'build 'extract-xml
+           (lambda _
+             (make-file-writable "skylighting.cabal")
+             (apply invoke "./dist/build/skylighting-extract/skylighting-extract"
+                    (find-files "xml" "\\.xml$"))
+             #t))
+         ;; Reconfigure without bootstrap flag
+         (add-after 'extract-xml 'configure-again
+           (lambda* (#:key outputs inputs tests? #:allow-other-keys)
+             ((assoc-ref %standard-phases 'configure)
+              #:outputs outputs
+              #:inputs inputs
+              #:tests? tests?
+              #:configure-flags '("-f-bootstrap"))))
+         (add-after 'configure-again 'build-again
+           (assoc-ref %standard-phases 'build)))))
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
+       ("ghc-ansi-terminal" ,ghc-ansi-terminal)
+       ("ghc-blaze-html" ,ghc-blaze-html)
+       ("ghc-case-insensitive" ,ghc-case-insensitive)
+       ("ghc-diff" ,ghc-diff)
+       ("ghc-hxt" ,ghc-hxt)
+       ("ghc-mtl" ,ghc-mtl)
+       ("ghc-pretty-show" ,ghc-pretty-show)
+       ("ghc-regex-pcre-builtin" ,ghc-regex-pcre-builtin)
+       ("ghc-safe" ,ghc-safe)
+       ("ghc-text" ,ghc-text)
+       ("ghc-utf8-string" ,ghc-utf8-string)))))
+
 (define-public ghc-doctemplates
   (package
     (name "ghc-doctemplates")
@@ -5923,6 +6039,29 @@ provided.  Skylighting is intended to be the successor to highlighting-kate.")
      "This package provides a simple text templating system used by pandoc.")
     (license license:bsd-3)))
 
+(define-public ghc-doctemplates-for-pandoc-1
+  (package (inherit ghc-doctemplates)
+    (version "0.1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "doctemplates/doctemplates-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0swal6rjya1293mwvl63jch5fx9ghpsil7qs4v7rpansa0izalmp"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
+       ("ghc-blaze-markup" ,ghc-blaze-markup)
+       ("ghc-blaze-html" ,ghc-blaze-html)
+       ("ghc-text" ,ghc-text)
+       ("ghc-vector" ,ghc-vector)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-scientific" ,ghc-scientific)))))
+
 (define-public ghc-pandoc
   (package
     (name "ghc-pandoc")
@@ -5999,6 +6138,67 @@ definition lists, tables, and other features.  A compatibility mode is
 provided for those who need a drop-in replacement for Markdown.pl.")
     (license license:gpl2+)))
 
+;; This is the last version of Pandoc 1.x, which is preferred for Rmarkdown.
+(define-public ghc-pandoc-1
+  (package (inherit ghc-pandoc)
+    (version "1.19.2.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/pandoc/pandoc-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0mim429mpakrcnm50csxyqk3ljcx2l26r5grk6w9isnggwgqrq5v"))))
+    (arguments
+     `(#:configure-flags (list "--allow-newer=skylighting")))
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
+       ("ghc-ansi-terminal" ,ghc-ansi-terminal)
+       ("ghc-base64-bytestring" ,ghc-base64-bytestring)
+       ("ghc-blaze-html" ,ghc-blaze-html)
+       ("ghc-blaze-markup" ,ghc-blaze-markup)
+       ("ghc-cmark" ,ghc-cmark)
+       ("ghc-data-default" ,ghc-data-default)
+       ("ghc-deepseq-generics" ,ghc-deepseq-generics)
+       ("ghc-diff" ,ghc-diff)
+       ("ghc-doctemplates" ,ghc-doctemplates-for-pandoc-1)
+       ("ghc-executable-path" ,ghc-executable-path)
+       ("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
+       ("ghc-filemanip" ,ghc-filemanip)
+       ("ghc-haddock-library" ,ghc-haddock-library)
+       ("ghc-hslua" ,ghc-hslua-for-pandoc-1)
+       ("ghc-http" ,ghc-http)
+       ("ghc-http-client" ,ghc-http-client)
+       ("ghc-http-client-tls" ,ghc-http-client-tls)
+       ("ghc-http-types" ,ghc-http-types)
+       ("ghc-juicypixels" ,ghc-juicypixels)
+       ("ghc-mtl" ,ghc-mtl)
+       ("ghc-network" ,ghc-network)
+       ("ghc-network-uri" ,ghc-network-uri)
+       ("ghc-old-time" ,ghc-old-time)
+       ("ghc-pandoc-types" ,ghc-pandoc-types-for-pandoc-1)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-random" ,ghc-random)
+       ("ghc-scientific" ,ghc-scientific)
+       ("ghc-sha" ,ghc-sha)
+       ("ghc-skylighting" ,ghc-skylighting-for-pandoc-1)
+       ("ghc-syb" ,ghc-syb)
+       ("ghc-tagsoup" ,ghc-tagsoup)
+       ("ghc-temporary" ,ghc-temporary)
+       ("ghc-texmath" ,ghc-texmath-for-pandoc-1)
+       ("ghc-text" ,ghc-text)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-vector" ,ghc-vector)
+       ("ghc-xml" ,ghc-xml)
+       ("ghc-yaml" ,ghc-yaml-for-pandoc-1)
+       ("ghc-zip-archive" ,ghc-zip-archive)
+       ("ghc-zlib" ,ghc-zlib)))
+    (native-inputs
+     `(("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))))
+
 (define-public ghc-hs-bibutils
   (package
     (name "ghc-hs-bibutils")
@@ -7681,7 +7881,7 @@ files in Haskell.")
     (inputs
      `(("ghc-mtl" ,ghc-mtl)
        ("ghc-network" ,ghc-network)
-       ("ghc-directory", ghc-directory)
+       ("ghc-directory" ,ghc-directory)
        ("ghc-old-locale" ,ghc-old-locale)))
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)))
@@ -8258,7 +8458,7 @@ that are much lighter weight than IO-threads.")
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)
        ("ghc-quickcheck" ,ghc-quickcheck)
-       ("ghc-ieee754", ghc-ieee754)
+       ("ghc-ieee754" ,ghc-ieee754)
        ("ghc-test-framework" ,ghc-test-framework)
        ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
        ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
@@ -8382,7 +8582,7 @@ statically known size.")
     (build-system haskell-build-system)
     (inputs `(("ghc-tuple-th" ,ghc-tuple-th)
               ("ghc-contravariant" ,ghc-contravariant)
-              ("ghc-base-prelude",ghc-base-prelude)))
+              ("ghc-base-prelude" ,ghc-base-prelude)))
     (home-page "https://github.com/nikita-volkov/contravariant-extras")
     (synopsis "Extras for the @code{ghc-contravariant} Haskell package")
     (description "This Haskell package provides extras for the
@@ -8697,7 +8897,7 @@ and are often as efficient as hand-written folds.")
               ("ghc-vector-algorithms" ,ghc-vector-algorithms)
               ("ghc-split" ,ghc-split)))
     (native-inputs `(("ghc-hspec" ,ghc-hspec)
-                     ("ghc-hunit",ghc-hunit)
+                     ("ghc-hunit" ,ghc-hunit)
                      ("ghc-quickcheck" ,ghc-quickcheck)
                      ("ghc-semigroups" ,ghc-semigroups)
                      ("ghc-foldl" ,ghc-foldl)))

gnu/packages/idris.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2016, 2017 David Craven <david@craven.ch>
+;;; Copyright © 2018 Alex ter Weele <alex.ter.weele@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,6 +31,52 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages))
 
+(define ghc-aeson-1.1.2.0
+  (package (inherit ghc-aeson)
+    (version "1.1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/aeson/aeson-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "1zy5z8pzvh53qkjm0nm3f4rwqfqg3867ck8ncd6mrxpcyvxqqj1p"))))))
+
+(define ghc-trifecta-1.6.2.1
+  (package (inherit ghc-trifecta)
+    (version "1.6.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/trifecta/"
+             "trifecta-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1rgv62dlmm4vkdymx5rw5jg3w8ifpzg1745rvs1m4kzdx16p5cxs"))))))
+
+;; ghc-cheapskate appeared too new. This follows LTS Haskell.
+(define ghc-cheapskate-0.1.0.5
+  (package
+    (inherit ghc-cheapskate)
+    (version "0.1.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/cheapskate/cheapskate-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "0cpsmfx5z2xykg71sv8j7pl8ga6pzyjnjdb9bxn00vcpqkzvfqvs"))))
+    (arguments
+     ;; LTS Haskell says data-default >=0.5 && <0.8
+     `(#:configure-flags (list "--allow-newer=data-default")))))
+
 (define-public idris
   (package
     (name "idris")
@@ -46,15 +93,15 @@
     (inputs
      `(("gmp" ,gmp)
        ("ncurses" ,ncurses)
-       ("ghc-aeson" ,ghc-aeson)
+       ("ghc-aeson" ,ghc-aeson-1.1.2.0)
-       ("ghc-async" ,ghc-async)
        ("ghc-annotated-wl-pprint" ,ghc-annotated-wl-pprint)
        ("ghc-ansi-terminal" ,ghc-ansi-terminal)
        ("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint)
+       ("ghc-async" ,ghc-async)
        ("ghc-base64-bytestring" ,ghc-base64-bytestring)
        ("ghc-blaze-html" ,ghc-blaze-html)
        ("ghc-blaze-markup" ,ghc-blaze-markup)
-       ("ghc-cheapskate" ,ghc-cheapskate)
+       ("ghc-cheapskate" ,ghc-cheapskate-0.1.0.5)
        ("ghc-code-page" ,ghc-code-page)
        ("ghc-fingertree" ,ghc-fingertree)
        ("ghc-fsnotify" ,ghc-fsnotify)
@@ -62,23 +109,18 @@
        ("ghc-mtl" ,ghc-mtl)
        ("ghc-network" ,ghc-network)
        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
-       ("ghc-parsers" ,ghc-parsers)
        ("ghc-regex-tdfa" ,ghc-regex-tdfa)
        ("ghc-safe" ,ghc-safe)
        ("ghc-split" ,ghc-split)
-       ("ghc-tasty" ,ghc-tasty)
-       ("ghc-tasty-golden" ,ghc-tasty-golden)
-       ("ghc-tasty-rerun" ,ghc-tasty-rerun)
        ("ghc-terminal-size" ,ghc-terminal-size)
        ("ghc-text" ,ghc-text)
-       ("ghc-trifecta" ,ghc-trifecta)
+       ("ghc-trifecta" ,ghc-trifecta-1.6.2.1)
        ("ghc-uniplate" ,ghc-uniplate)
        ("ghc-unordered-containers" ,ghc-unordered-containers)
        ("ghc-utf8-string" ,ghc-utf8-string)
-       ("ghc-vector-binary-instances" ,ghc-vector-binary-instances)
        ("ghc-vector" ,ghc-vector)
-       ("ghc-zip-archive" ,ghc-zip-archive)
+       ("ghc-vector-binary-instances" ,ghc-vector-binary-instances)
-       ("ghc-zlib" ,ghc-zlib)))
+       ("ghc-zip-archive" ,ghc-zip-archive)))
     (arguments
      `(#:tests? #f ; FIXME: Test suite doesn't run in a sandbox.
        #:configure-flags

gnu/packages/image.scm

@@ -16,6 +16,7 @@
 ;;; Copyright © 2017 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -58,6 +59,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
+  #:use-module (gnu packages qt)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -1252,3 +1254,65 @@ such as images.  This metadata can include captions and keywords, often used by
 popular photo management applications.  The library provides routines for
 parsing, viewing, modifying, and saving this metadata.")
     (license license:lgpl2.0+)))
+
+(define-public flameshot
+  (package
+    (name "flameshot")
+    (version "0.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/lupoDharkael/flameshot/archive/"
+                           "v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0kp451bqgssvg8n3sg60s3fifplm9l5kxiij0yxkl864p2mhw8im"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("qttools" ,qttools)))
+    (inputs
+     `(("qtbase" ,qtbase)))
+    (arguments
+     `(#:tests? #f ; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (invoke "qmake"
+                     "CONFIG+=packaging"
+                     (string-append "BASEDIR=" (assoc-ref outputs "out"))
+                     "PREFIX=/"))))))
+    (home-page "https://github.com/lupoDharkael/flameshot")
+    (synopsis "Powerful yet simple to use screenshot software")
+    (description "Flameshot is a screenshot program.
+Features:
+
+@itemize
+@item Customizable appearance.
+@item Easy to use.
+@item In-app screenshot edition.
+@item DBus interface.
+@item Upload to Imgur.
+@end itemize\n")
+    (license license:gpl3+)))
+
+(define-public r-jpeg
+  (package
+   (name "r-jpeg")
+   (version "0.1-8")
+   (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "jpeg" version))
+       (sha256
+        (base32
+         "05hawv5qcb82ljc1l2nchx1wah8mq2k2kfkhpzyww554ngzbwcnh"))))
+   (build-system r-build-system)
+   (inputs `(("libjpeg" ,libjpeg)))
+   (home-page "http://www.rforge.net/jpeg/")
+   (synopsis "Read and write JPEG images with R")
+   (description "This package provides a way to read, write and display bitmap
+images stored in the JPEG format with R.  It can read and write both files and
+in-memory raw vectors.")
+   (license license:gpl2+)))

gnu/packages/inkscape.scm

@@ -46,25 +46,15 @@
 (define-public inkscape
   (package
     (name "inkscape")
-    (version "0.92.2")
+    (version "0.92.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://media.inkscape.org/dl/"
                                   "resources/file/"
                                   "inkscape-" version ".tar.bz2"))
-              (patches
-               (list
-                ;; Fix compatibility with poppler >= 0.58.
-                (origin
-                  (method url-fetch)
-                  (uri (string-append "https://gitlab.com/inkscape/inkscape/commit/"
-                                      "9418824967eb4c53371ef8588243fed4cab496e0.patch"))
               (sha256
                (base32
-                    "0wwyhkqb1qyazz5f6wqrc223l6k8qnmadiw28q8gihlgvh38rvll")))))
+                "1chng2yw8dsjxc9gf92aqv7plj11cav8ax321wmakmv5bb09cch6"))))
-              (sha256
-               (base32
-                "1lyghk6yarcv9nwkh6k366p6hb7rfilqcvbyji09hki59khd0a56"))))
     (build-system cmake-build-system)
     (inputs
      `(("aspell" ,aspell)
@@ -78,6 +68,7 @@
        ("libgc" ,libgc)
        ("freetype" ,freetype)
        ("popt" ,popt)
+       ("potrace" ,potrace)
        ("python" ,python-2)
        ("lcms" ,lcms)
        ("boost" ,boost)))

gnu/packages/irc.scm

@@ -100,7 +100,7 @@
        ("qttools" ,qttools)))
     (inputs
      `(("qca" ,qca)
-       ("qtbase", qtbase)
+       ("qtbase" ,qtbase)
        ("qtscript" ,qtscript)
        ("snorenotify" ,snorenotify)
        ("zlib" ,zlib)))

gnu/packages/java.scm

@@ -1074,7 +1074,7 @@ bootstrapping purposes.")
     (license license:gpl2+)))
 
 (define-public icedtea-7
-  (let* ((version "2.6.12")
+  (let* ((version "2.6.13")
          (drop (lambda (name hash)
                  (origin
                    (method url-fetch)
@@ -1092,7 +1092,7 @@ bootstrapping purposes.")
                       version ".tar.xz"))
                 (sha256
                  (base32
-                  "0s0zh0mj1sab99kb516lsgq3859vsc951phc565gwix4l5g9zppk"))
+                  "1w331rdqx1dcx2xb0fmjmrkdc71xqn20fxsgw8by4xhiblh88khh"))
                 (modules '((guix build utils)))
                 (snippet
                  '(substitute* "Makefile.in"
@@ -1502,25 +1502,25 @@ bootstrapping purposes.")
       (native-inputs
        `(("openjdk-src"
           ,(drop "openjdk"
-                 "15qf3nfidgnigh2zny6djfp8bhfwjnwk9i06mxs2jbq6na953ql2"))
+                 "0l34ikyf62hbzlf9032alzkkqvf7bpmckz4gvirvph755w7gka8l"))
          ("corba-drop"
           ,(drop "corba"
-                 "1phvn8fyl5mw2n2sn97f17nm442k75xsz2023bfw4h66ywzkqhqy"))
+                 "050gv2jbg1pi6qkn8w18bwpbklfa5b0kymjvan9pncddbj8m84fz"))
          ("jaxp-drop"
           ,(drop "jaxp"
-                 "0j4ms6lmnfa2cwfh9yfqdfg1bnn3fc40ay4x6k8zqa8yvspik5w5"))
+                 "1k6yldwnxfzdg5926r1nlfv8d1r1j7rlp2nkz6gqh05vgyamnfhl"))
          ("jaxws-drop"
           ,(drop "jaxws"
-                 "09sddj73k7n29s39hvdk14r130mvlknbxkpd2w58f34sq5sgpdrg"))
+                 "110j7jlz47x2gg6f7653x12mssan5kvj9l9h1m1c8c92drfxbqyk"))
          ("jdk-drop"
           ,(drop "jdk"
-                 "0q896zz8wyswmksy225q1k27nz3v3l27052dcvvpv20ryykz8yp7"))
+                 "0d1mca38ksxvdskp9im3pp7fdijhj1n3lwq9w13r9s4v3qyskgdd"))
          ("langtools-drop"
           ,(drop "langtools"
-                 "0niicyfccim4a9is4akh87jd7wbl8jrazdaab957mcv9l1x3bnqc"))
+                 "0nq5236fzxn3p6x8cgncl56mzcmsj07q9gymysnws4c8byc6n0qj"))
          ("hotspot-drop"
           ,(drop "hotspot"
-                 "1jw42qhbm3wfavk39304m53lmqipcllrvjqiab2f42mjs10i8gfx"))
+                 "17bdv39n4lh8l5737c96f3xgamx4y305m067p01cywgp7zaddqws"))
          ("ant" ,ant-bootstrap)
          ("attr" ,attr)
          ("coreutils" ,coreutils)
@@ -1570,7 +1570,7 @@ IcedTea build harness.")
       (license license:gpl2+))))
 
 (define-public icedtea-8
-  (let* ((version "3.6.0")
+  (let* ((version "3.7.0")
          (drop (lambda (name hash)
                  (origin
                    (method url-fetch)
@@ -1579,7 +1579,7 @@ IcedTea build harness.")
                          "/icedtea8/" version "/" name ".tar.xz"))
                    (sha256 (base32 hash))))))
     (package (inherit icedtea-7)
-      (version "3.6.0")
+      (version "3.7.0")
       (source (origin
                 (method url-fetch)
                 (uri (string-append
@@ -1587,11 +1587,12 @@ IcedTea build harness.")
                       version ".tar.xz"))
                 (sha256
                  (base32
-                  "0zj192zrrxqh6j1ywc3399gk2ycay9w8pvzcvvr2kvdkb37ak86h"))
+                  "09yqzn8rpccs7cyv89hhy5zlznpgqw5x3jz0w1ccp0cz1vgs8l5w"))
                 (modules '((guix build utils)))
                 (snippet
                  '(begin
-                    (substitute* "acinclude.m4"
+                    (substitute* '("configure"
+                                   "acinclude.m4")
                       ;; Do not embed build time
                       (("(DIST_ID=\"Custom build).*$" _ prefix)
                        (string-append prefix "\"\n"))
@@ -1600,10 +1601,22 @@ IcedTea build harness.")
                        "DIST_NAME=\"guix\""))
                     #t))))
       (arguments
-       (substitute-keyword-arguments (package-arguments icedtea-7)
+       `(#:imported-modules
+         ((guix build ant-build-system)
+          (guix build syscalls)
+          ,@%gnu-build-system-modules)
+         ,@(substitute-keyword-arguments (package-arguments icedtea-7)
+             ((#:modules modules)
+              `((guix build utils)
+                (guix build gnu-build-system)
+                ((guix build ant-build-system) #:prefix ant:)
+                (ice-9 match)
+                (ice-9 popen)
+                (srfi srfi-19)
+                (srfi srfi-26)))
              ((#:configure-flags flags)
               `(let ((jdk (assoc-ref %build-inputs "jdk")))
-             `(;;"--disable-bootstrap"
+                 `( ;;"--disable-bootstrap"
                    "--enable-bootstrap"
                    "--enable-nss"
                    "--disable-downloading"
@@ -1618,6 +1631,17 @@ IcedTea build harness.")
                  (delete 'patch-paths)
                  (delete 'set-additional-paths)
                  (delete 'patch-patches)
+                 ;; Prevent the keytool from recording the current time when
+                 ;; adding certificates at build time.
+                 (add-after 'unpack 'patch-keystore
+                   (lambda _
+                     (substitute* "openjdk.src/jdk/src/share/classes/sun/security/provider/JavaKeyStore.java"
+                       (("date = new Date\\(\\);")
+                        "\
+date = (System.getenv(\"SOURCE_DATE_EPOCH\") != null) ?\
+new Date(Long.parseLong(System.getenv(\"SOURCE_DATE_EPOCH\"))) :\
+new Date();"))
+                     #t))
                  (add-after 'unpack 'patch-jni-libs
                    ;; Hardcode dynamically loaded libraries.
                    (lambda _
@@ -1658,39 +1682,41 @@ IcedTea build harness.")
                        ;; support via NSS.
                        (copy-file (string-append jdk "/jre/lib/security/nss.cfg")
                                   (string-append jre "/lib/security/nss.cfg"))
-                   #t)))))))
+                       #t)))
+                 (add-after 'install 'strip-jar-timestamps
+                   (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))))
       (native-inputs
        `(("jdk" ,icedtea-7 "jdk")
          ("openjdk-src"
           ,(drop "openjdk"
-                 "0mqxh81kq05z4wydkik0yrr81ibf84xmwsdcw9n2gfrzs4f5jxnb"))
+                 "1mj6xgmw31i6qd30qi9dmv7160fbcfq5ikz1jwjihdg2793il19p"))
          ("aarch32-drop"
           ,(drop "aarch32"
-                 "0b207g2n6kn510zf5vwh58bsxgqrmkvrna4p20r74v9cwcwx83n2"))
+                 "1wb8k5zm40zld0986dvmlh5xh3gyixbg9h26sl662zy92amhmyyg"))
          ("corba-drop"
           ,(drop "corba"
-                 "0qinc1q4w01nkr9klhfyd8caxvyrrfxjrz32nd7kgyja2bj8x7dd"))
+                 "11ma4zz0599cy70xd219v7a8vin7p96xrhhz3wsaw6cjhkzpagah"))
          ("jaxp-drop"
           ,(drop "jaxp"
-                 "07azrp3g86vk2laybmr5xfn0yrljkxs0rlm1q48385br225bgdxi"))
+                 "14m1y0z0fbm5z5zjw3vnq85py8dma84bi3f9cw8rhdyc6skk8q4i"))
          ("jaxws-drop"
           ,(drop "jaxws"
-                 "018fd2hq57zp3pq06wlxy5pabqcyk36xi8hk0d6xk3a90wsjvyik"))
+                 "09andnm6xaasnp963hgx42yiflifiljp9z7z85jrfyc5z8a5whmf"))
          ("jdk-drop"
           ,(drop "jdk"
-                 "0vs488kq5j2cc6kplc78jbhfxwq4fn06l34xrbq4d6y17777arg8"))
+                 "0s6lcpc0zckz2fnq98aqf28nz9y3wbi41a3kyaqqa2abwbkm1zwl"))
          ("langtools-drop"
           ,(drop "langtools"
-                 "04f6d1wvck5jrpvrcw5gsbzxnihcry9zrf1v85czdm959q21zv9c"))
+                 "15wizy123vhk40chl1b4p552jf2pw2hdww0myf11qab425axz4nw"))
          ("hotspot-drop"
           ,(drop "hotspot"
-                 "1mfgpzyr6zzy9klf8nn3z6d41fydb9ghpfpqzjq3cl95axfbdl1g"))
+                 "1ciz1w9j0kz7s1dxdhyqq71nla9icyz6qvn0b9z2zgkklqa98qmm"))
          ("nashorn-drop"
           ,(drop "nashorn"
-                 "1a26cmzbs50gkh4rmmmxls7zljx62vfp1wq02gsfd5jqs4xvlibj"))
+                 "19pzl3ppaw8j6r5cnyp8qiw3hxijh3hdc46l39g5yfhdl4pr4hpa"))
          ("shenandoah-drop"
           ,(drop "shenandoah"
-                 "11hmn9mwmvryfddcanzx3qffjm8bbiv18nwv3iy9cswrvxjy010f"))
+                 "0k33anxdzw1icn072wynfmmdjhsv50hay0j1sfkfxny12rb3vgdy"))
          ,@(fold alist-delete (package-native-inputs icedtea-7)
                  '("jdk" "openjdk-src" "corba-drop" "jaxp-drop" "jaxws-drop"
                    "jdk-drop" "langtools-drop" "hotspot-drop")))))))
@@ -3860,15 +3886,8 @@ The jMock library
   (package (inherit java-hamcrest-core)
     (name "java-hamcrest-all")
     (arguments
-     (substitute-keyword-arguments (package-arguments java-hamcrest-core)
+     `(#:jdk ,icedtea-8
-       ;; FIXME: a unit test fails because org.hamcrest.SelfDescribing is not
+       ,@(substitute-keyword-arguments (package-arguments java-hamcrest-core)
-       ;; found, although it is part of the hamcrest-core library that has
-       ;; just been built.
-       ;;
-       ;; Fixing this one test is insufficient, though, and upstream confirmed
-       ;; that the latest hamcrest release fails its unit tests when built
-       ;; with Java 7.  See https://github.com/hamcrest/JavaHamcrest/issues/30
-       ((#:tests? _) #f)
            ((#:build-target _) "bigjar")
            ((#:phases phases)
             `(modify-phases ,phases
@@ -3882,17 +3901,15 @@ The jMock library
                       (string-join
                        (cons line
                              (append
-                          (find-files (assoc-ref inputs "java-hamcrest-core") "\\.jar$")
                               (find-files (assoc-ref inputs "java-junit") "\\.jar$")
                               (find-files (assoc-ref inputs "java-jmock") "\\.jar$")
                               (find-files (assoc-ref inputs "java-easymock") "\\.jar$")))
                        ";")))
-               #t))))))
+                   #t)))))))
     (inputs
      `(("java-junit" ,java-junit)
        ("java-jmock" ,java-jmock-1)
        ("java-easymock" ,java-easymock)
-       ("java-hamcrest-core" ,java-hamcrest-core)
        ,@(package-inputs java-hamcrest-core)))))
 
 (define-public java-jopt-simple
@@ -7290,6 +7307,7 @@ configuration.")
               (method url-fetch)
               (uri (string-append "https://bitbucket.org/asomov/snakeyaml/get/v"
                                   version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "0rf5ha6w0waz50jz2479jsrbgmd0dnx0gs337m126j5z7zlmg7mg"))))
@@ -7965,6 +7983,7 @@ to use.")
                 (uri (git-reference
                       (url "https://github.com/neilalexander/jnacl.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1d6g6xhn83byv5943n7935wwjsk0ibk0qdvqgr699qqgqqmwisbb"))))
@@ -8561,7 +8580,8 @@ protocol-independent framework to build mail and messaging applications.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "1gxkp7lv2ahymgrqdw94ncq54bmp4m4sw5m1x9gkp7l5bxn0xsyj"))))
+                "1gxkp7lv2ahymgrqdw94ncq54bmp4m4sw5m1x9gkp7l5bxn0xsyj"))
+              (patches (search-patches "java-jeromq-fix-tests.patch"))))
     (build-system ant-build-system)
     (arguments
      `(#:jar-name "java-jeromq.jar"
@@ -8575,7 +8595,13 @@ protocol-independent framework to build mail and messaging applications.")
          ;; Failures
          "**/DealerSpecTest.java"
          "**/CustomDecoderTest.java"
-         "**/CustomEncoderTest.java")))
+         "**/CustomEncoderTest.java"
+         "**/ConnectRidTest.java"
+         "**/ReqSpecTest.java"
+         "**/PushPullSpecTest.java"
+         "**/PubSubHwmTest.java"
+         "**/RouterSpecTest.java"
+         "**/ProxyTest.java")))
     (inputs
      `(("java-jnacl" ,java-jnacl)))
     (native-inputs

gnu/packages/julia.scm

@@ -315,7 +315,12 @@
         "USE_SYSTEM_OPENSPECFUN=1")))
     (inputs
      `(("llvm" ,llvm)
-       ("arpack-ng" ,arpack-ng)
+
+       ;; The bundled version is 3.3.0 so stick to that version.  With other
+       ;; versions, we get test failures in 'linalg/arnoldi' as described in
+       ;; <https://bugs.gnu.org/30282>.
+       ("arpack-ng" ,arpack-ng-3.3.0)
+
        ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
        ("lapack" ,lapack)
        ("openblas" ,openblas) ;Julia does not build with Atlas

gnu/packages/kde-frameworks.scm

@@ -157,7 +157,7 @@ common build settings used in software produced by the KDE community.")
      ;; TODO: Add building the super experimental QML support
      `(("extra-cmake-modules" ,extra-cmake-modules)
        ("pkg-config" ,pkg-config)
-       ("qttools", qttools)))
+       ("qttools" ,qttools)))
     (inputs
      `(("qtbase" ,qtbase)))
     (arguments
@@ -1186,7 +1186,7 @@ lower level classes for interaction with the X Windowing System.")
        ("pkg-config" ,pkg-config)))
     (propagated-inputs
      ;; Headers contain #include <ModemManager/ModemManager.h>
-     `(("modem-manager", modem-manager)))
+     `(("modem-manager" ,modem-manager)))
     (inputs
      `(("qtbase" ,qtbase)))
     (arguments
@@ -1284,7 +1284,7 @@ which are used in DBus communication.")
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)))
     (inputs
-     `(("libdmtx", libdmtx)
+     `(("libdmtx" ,libdmtx)
        ("qrencode" ,qrencode)
        ("qtbase" ,qtbase))) ;; TODO: rethink: nix propagates this
     (home-page "https://api.kde.org/frameworks/prison/html/index.html")
@@ -2209,7 +2209,7 @@ their settings.")
        ("kwidgetsaddons" ,kwidgetsaddons)
        ("kwindowsystem" ,kwindowsystem)
        ("kxmlgui" ,kxmlgui)
-       ("libepoxy", libepoxy)
+       ("libepoxy" ,libepoxy)
        ("qtbase" ,qtbase)
        ("qtdeclarative" ,qtdeclarative)
        ("solid" ,solid)))
@@ -3003,7 +3003,7 @@ types or handled by application specific code.")
        ("libgit2" ,libgit2)
        ("perl" ,perl)
        ("qtbase" ,qtbase)
-       ("qtdeclarative", qtdeclarative)
+       ("qtdeclarative" ,qtdeclarative)
        ("qtscript" ,qtscript)
        ("qtxmlpatterns" ,qtxmlpatterns)
        ("solid" ,solid)
@@ -3071,7 +3071,7 @@ library.")
        ("kwidgetsaddons" ,kwidgetsaddons)
        ("kwindowsystem" ,kwindowsystem)
        ("qtbase" ,qtbase)
-       ("qtspeech", qtspeech)))
+       ("qtspeech" ,qtspeech)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -3150,7 +3150,7 @@ the passwords on KDE work spaces.")
      `(("extra-cmake-modules" ,extra-cmake-modules)))
     (inputs
      `(("attica" ,attica)
-       ("kauth", kauth)
+       ("kauth" ,kauth)
        ("kcodecs" ,kcodecs)
        ("kcoreaddons" ,kcoreaddons)
        ("kglobalaccel" ,kglobalaccel)
@@ -3395,7 +3395,7 @@ workspace.")
      `(("dbus" ,dbus)
        ("docbook-xml" ,docbook-xml-4.4) ; optional
        ("extra-cmake-modules" ,extra-cmake-modules)
-       ("perl", perl)
+       ("perl" ,perl)
        ("perl-uri" ,perl-uri)
        ("pkg-config" ,pkg-config)
        ("shared-mime-info" ,shared-mime-info)
@@ -3421,7 +3421,7 @@ workspace.")
        ("knotifications" ,knotifications)
        ("kparts" ,kparts)
        ("ktextwidgets" ,ktextwidgets)
-       ("kunitconversion", kunitconversion)
+       ("kunitconversion" ,kunitconversion)
        ("kwindowsystem" ,kwindowsystem)
        ("qtbase" ,qtbase)))
     (inputs
@@ -3434,9 +3434,9 @@ workspace.")
        ("kservice" ,kservice)
        ("kwidgetsaddons" ,kwidgetsaddons)
        ("kxmlgui" ,kxmlgui)
-       ("libsm", libsm)
+       ("libsm" ,libsm)
-       ("networkmanager-qt", networkmanager-qt)
+       ("networkmanager-qt" ,networkmanager-qt)
-       ("openssl", openssl)
+       ("openssl" ,openssl)
        ("qtsvg" ,qtsvg)
        ("qttools" ,qttools)
        ("qtx11extras" ,qtx11extras)))
@@ -3507,7 +3507,7 @@ http://community.kde.org/Frameworks/Porting_Notes should help with this.")
     (build-system cmake-build-system)
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
-       ("perl", perl)))
+       ("perl" ,perl)))
     (inputs
      `(("giflib" ,giflib)
        ("gperf" ,gperf)
@@ -3521,14 +3521,14 @@ http://community.kde.org/Frameworks/Porting_Notes should help with this.")
        ("knotifications" ,knotifications)
        ("kparts" ,kparts)
        ("ktextwidgets" ,ktextwidgets)
-       ("kwallet", kwallet)
+       ("kwallet" ,kwallet)
        ("kwidgetsaddons" ,kwidgetsaddons)
        ("kwindowsystem" ,kwindowsystem)
        ("kxmlgui" ,kxmlgui)
-       ("libjpeg", libjpeg)
+       ("libjpeg" ,libjpeg)
-       ("libpng", libpng)
+       ("libpng" ,libpng)
-       ("openssl", openssl)
+       ("openssl" ,openssl)
-       ("phonon", phonon)
+       ("phonon" ,phonon)
        ("qtbase" ,qtbase)
        ("qtx11extras" ,qtx11extras)
        ("sonnet" ,sonnet)))

gnu/packages/language.scm

@@ -98,7 +98,7 @@ converting a word to singular or plural.")
 (define-public perl-lingua-en-inflect-phrase
   (package
     (name "perl-lingua-en-inflect-phrase")
-    (version "0.18")
+    (version "0.20")
     (source
      (origin
        (method url-fetch)
@@ -106,7 +106,7 @@ converting a word to singular or plural.")
                            "Lingua-EN-Inflect-Phrase-" version ".tar.gz"))
        (sha256
         (base32
-         "19prg6pkgnznrc82ymdkdi3l9schg815axjig7adca5yqa7mn2i9"))))
+         "1a6y1l2pjim2242wcpgz066di4pbzfgsjjdl7vg5a5wzm48qj1am"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-test-nowarnings" ,perl-test-nowarnings)))
@@ -365,7 +365,7 @@ stemmer at http://snowball.sourceforge.net.")
 (define-public perl-string-toidentifier-en
   (package
     (name "perl-string-toidentifier-en")
-    (version "0.11")
+    (version "0.12")
     (source
      (origin
        (method url-fetch)
@@ -373,7 +373,7 @@ stemmer at http://snowball.sourceforge.net.")
                            "String-ToIdentifier-EN-" version ".tar.gz"))
        (sha256
         (base32
-         "1bawghkgkkx7j3avnrj5sg3vix1z5564ks6wf9az3jc2knh8s5nh"))))
+         "12nw7h2yiybhdw0vnnpc7bif8ylhsn6kqf6s39dsrf9h54iq9yrs"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-lingua-en-inflect-phrase" ,perl-lingua-en-inflect-phrase)

gnu/packages/libevent.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015, 2017 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
@@ -140,7 +140,7 @@ limited support for fork events.")
 
        ;; XXX: Some tests want /dev/tty, attempt to make connections, etc.
        #:tests? #f))
-    (native-inputs `(("autoconf" ,(autoconf-wrapper))
+    (native-inputs `(("autoconf" ,autoconf-wrapper)
                      ("automake" ,automake)
                      ("libtool" ,libtool)
 

gnu/packages/libusb.scm

@@ -124,6 +124,7 @@ version of libusb to run with newer libusb.")
                 (uri (git-reference
                       (url "https://github.com/usb4java/libusb4java.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "0wqgapalhfh9v38ycbl6i2f5lh1wpr6fzwn5dwd0rdacypkd1gml"))))

gnu/packages/linux.scm

@@ -383,8 +383,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.15.7")
+(define %linux-libre-version "4.15.10")
-(define %linux-libre-hash "1h17wc12lvva5vcm2z06cf57ywxb6i2snm9vxixw1lwibnksrb6l")
+(define %linux-libre-hash "10fp8jmy0fxq8l01m1nnagpq1hznl9jmhcwknk8izjmdcb5snq6c")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
@@ -392,8 +392,8 @@ It has been modified to remove all non-free binary blobs.")
                     %linux-compatible-systems
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.24")
+(define %linux-libre-4.14-version "4.14.27")
-(define %linux-libre-4.14-hash "1i14djw3rmxb6syl6vfd5w76rjksbbaviynwj2dwwp9ki1h6p1hr")
+(define %linux-libre-4.14-hash "0mgkka9niyd0lj4qliy4v7jjh9lg1a5jwlv60yw7z0s4k7ajyyrp")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
@@ -402,20 +402,20 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.86"
+  (make-linux-libre "4.9.87"
-                    "0fqixx3yyvznianygk8bfxzfqj8zpnjcalifhpfyb7rm3dyvi3wd"
+                    "1p8phvmxp04npzqzqcfmv8k9l5l65s7vpjcakdm0fxfkzvnswsp6"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.120"
+  (make-linux-libre "4.4.121"
-                    "17zk5dbpa3kilf8m8i6r2jifjgi4yjim42gyk9j6n4218jjcszv6"
+                    "1d7djrhiib0ds9ssjkali6b5w6rzap4zgj5hf9jq1jmqpp54jkm4"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.1
-  (make-linux-libre "4.1.49"
+  (make-linux-libre "4.1.50"
-                    "0dklmqj6ayjlkz97b811zdvpgb3yppahinji9l9jmkz4ssi7a1gs"
+                    "1hl1pk724v2waa55bhxfmxyz9nl6pkcj4dc3l80jfvqdfgr55mm2"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
@@ -547,6 +547,7 @@ providing the system administrator with some help in common tasks.")
 (define-public util-linux
   (package
     (name "util-linux")
+    (replacement util-linux/fixed)
     (version "2.31")
     (source (origin
               (method url-fetch)
@@ -634,6 +635,15 @@ block devices, UUIDs, TTYs, and many other tools.")
     (license (list license:gpl3+ license:gpl2+ license:gpl2 license:lgpl2.0+
                    license:bsd-4 license:public-domain))))
 
+(define util-linux/fixed
+  (package
+    (inherit util-linux)
+    (source
+      (origin
+        (inherit (package-source util-linux))
+        (patches (append (origin-patches (package-source util-linux))
+                         (search-patches "util-linux-CVE-2018-7738.patch")))))))
+
 (define-public ddate
   (package
     (name "ddate")
@@ -1758,7 +1768,7 @@ file system is as easy as logging into the server with an SSH client.")
 (define-public archivemount
   (package
     (name "archivemount")
-    (version "0.8.7")
+    (version "0.8.9")
     (source
      (origin
        (method url-fetch)
@@ -1766,11 +1776,11 @@ file system is as easy as logging into the server with an SSH client.")
                            "archivemount-" version ".tar.gz"))
        (sha256
         (base32
-         "1diiw6pnlnrnikn6l5ld92dx59lhrxjlqms8885vwbynsjl5q127"))))
+         "0v4si1ri6lhnq9q87gkx7fsh6lv6xz4bynknwndqncpvfp5cy1jg"))))
     (build-system gnu-build-system)
-    (inputs `(("fuse", fuse)
+    (inputs `(("fuse" ,fuse)
-              ("libarchive", libarchive)))
+              ("libarchive" ,libarchive)))
-    (native-inputs `(("pkg-config", pkg-config)))
+    (native-inputs `(("pkg-config" ,pkg-config)))
     (home-page "http://www.cybernoia.de/software/archivemount")
     (synopsis "Tool for mounting archive files with FUSE")
     (description "archivemount is a FUSE-based file system for Unix variants,
@@ -2024,7 +2034,7 @@ from the module-init-tools project.")
        ("docbook-xml" ,docbook-xml-4.2)
        ("docbook-xsl" ,docbook-xsl)
        ("libxml2" ,libxml2)             ;for $XML_CATALOG_FILES
-       ("xsltproc", libxslt)))
+       ("xsltproc" ,libxslt)))
     (inputs
      ;; When linked against libblkid, eudev can populate /dev/disk/by-label
      ;; and similar; it also installs the '60-persistent-storage.rules' file,
@@ -3394,8 +3404,8 @@ The package provides additional NTFS tools.")
        ;; Upstream uses the "ninja" build system and encourage distros
        ;; to do the same for consistency. They also recommend using the
        ;; "Release" build type.
-       #:configure-flags (list "-GNinja"
+       #:build-type "Release"
-                               "-DCMAKE_BUILD_TYPE=Release")
+       #:configure-flags (list "-GNinja")
        #:phases
        (modify-phases %standard-phases
          (replace 'build
@@ -3697,7 +3707,7 @@ are exceeded.")
     (inputs
      `(("acl" ,acl)
        ("libuuid" ,util-linux)
-       ("lzo", lzo)
+       ("lzo" ,lzo)
        ("zlib" ,zlib)))
     (build-system gnu-build-system)
     (arguments
@@ -4127,13 +4137,13 @@ used by nftables.")
         (base32
          "1i1gfy8l7qyhc5vlrpp63s0n5kybmc9pi4dywiq8rmkhrrnddsla"))))
     (build-system gnu-build-system)
-    (inputs `(("bison", bison)
+    (inputs `(("bison" ,bison)
-              ("flex", flex)
+              ("flex" ,flex)
-              ("gmp", gmp)
+              ("gmp" ,gmp)
-              ("libmnl", libmnl)
+              ("libmnl" ,libmnl)
-              ("libnftnl", libnftnl)
+              ("libnftnl" ,libnftnl)
-              ("readline", readline)))
+              ("readline" ,readline)))
-    (native-inputs `(("pkg-config", pkg-config)))
+    (native-inputs `(("pkg-config" ,pkg-config)))
     (home-page "http://www.nftables.org")
     (synopsis "Userspace utility for Linux packet filtering")
     (description "nftables is the project that aims to replace the existing

gnu/packages/lisp.scm

@@ -1370,6 +1370,7 @@ It is similar to the @code{CL:LOOP} macro, with these distinguishing marks:
          (uri (git-reference
                (url "https://github.com/mishoo/cl-uglify-js.git")
                (commit commit)))
+         (file-name (git-file-name name version))
          (sha256
           (base32
            "0k39y3c93jgxpr7gwz7w0d8yknn1fdnxrjhd03057lvk5w8js27a"))))

gnu/packages/logging.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -73,7 +73,7 @@ staying as close to their API as is reasonable.")
     (build-system gnu-build-system)
     (native-inputs
      `(("perl" ,perl)                             ;for tests
-       ("autoconf" ,(autoconf-wrapper))
+       ("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
        ("libtool" ,libtool)))
     (arguments

gnu/packages/lua.scm

@@ -354,12 +354,12 @@ secure session between the peers.")
     (inputs
      `(("gobject-introspection" ,gobject-introspection)
        ("glib" ,glib)
-       ("pango", pango)
+       ("pango" ,pango)
-       ("gtk", gtk+-2)
+       ("gtk" ,gtk+-2)
        ("lua" ,lua)
        ("cairo" ,cairo)
        ("libffi" ,libffi)
-       ("xorg-server", xorg-server)))
+       ("xorg-server" ,xorg-server)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("dbus" ,dbus)))                          ;tests use 'dbus-run-session'
@@ -397,7 +397,7 @@ Notable examples are GTK+, GStreamer and Webkit.")
                              (string-append out "/share/lua/" lua-version))
                #t))))
        #:test-target "test"))
-    (inputs `(("lua", lua)))
+    (inputs `(("lua" ,lua)))
     (synopsis "Pattern-matching library for Lua")
     (description
      "LPeg is a pattern-matching library for Lua, based on Parsing Expression
@@ -436,7 +436,7 @@ Grammars (PEGs).")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure))))
-    (inputs `(("lua", lua)))
+    (inputs `(("lua" ,lua)))
     (home-page "https://bitop.luajit.org/index.html")
     (synopsis "Bitwise operations on numbers for Lua")
     (description

gnu/packages/mail.scm

@@ -931,7 +931,7 @@ useful features.")
              (sha256
                (base32 "1sxnaglp5hb0z78sgnfzva4x8m4flqhicvm1dz0krkxdmfsafrsf"))))
     (build-system gnu-build-system)
-    (native-inputs `(("autoconf" ,(autoconf-wrapper))
+    (native-inputs `(("autoconf" ,autoconf-wrapper)
                      ("automake" ,automake)
                      ("libtool" ,libtool)
                      ("pkg-config" ,pkg-config)))
@@ -1812,7 +1812,7 @@ in Perl.")
              (patch-shebang "mb2md" (list (string-append perl "/bin")))
              (chmod "mb2md" #o555))
            #t))))
-    (native-inputs `(("gzip", gzip)))
+    (native-inputs `(("gzip" ,gzip)))
     (inputs `(("perl" ,perl)
               ("perl-timedate" ,perl-timedate)))
     (home-page "http://batleth.sapienti-sat.org/projects/mb2md/")

gnu/packages/make-bootstrap.scm

@@ -108,7 +108,7 @@ for `sh' in $PATH, and without nscd, and with static NSS modules."
           ("gcc" ,(package (inherit gcc)
                     (outputs '("out")) ; all in one so libgcc_s is easily found
                     (inputs
-                     `(("libc",(glibc-for-bootstrap))
+                     `(("libc" ,(glibc-for-bootstrap))
                        ("libc:static" ,(glibc-for-bootstrap) "static")
                        ,@(package-inputs gcc)))))
           ,@(fold alist-delete (%final-inputs) '("libc" "gcc")))))

gnu/packages/man.scm

@@ -58,14 +58,14 @@ a flexible and convenient way.")
 (define-public man-db
   (package
     (name "man-db")
-    (version "2.7.6.1")
+    (version "2.8.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://savannah/man-db/man-db-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0gqgs4zc3r87apns0k5qp689p2ylxx2596s2mkmkxjjay99brv88"))))
+                "0p0cvv5ykvyzq33qyfik11p2s0d2j75ans1avj9xv3c8vy3zzga5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -131,6 +131,9 @@ a flexible and convenient way.")
        ("groff-minimal" ,groff-minimal)
        ("less" ,less)
        ("libpipeline" ,libpipeline)
+       ;; FIXME: 4.8 and later can use libseccomp, but it causes test
+       ;; failures in the build chroot.
+       ;;("libseccomp" ,libseccomp)
        ("util-linux" ,util-linux)))
     (native-search-paths
      (list (search-path-specification

gnu/packages/mate.scm

@@ -135,7 +135,7 @@ MATE applications.")
              (setenv "CONFIG_SHELL" (which "sh"))
              (invoke "sh" "autogen.sh"))))))
     (native-inputs
-     `(("autoconf" ,(autoconf-wrapper))
+     `(("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
        ("intltool" ,intltool)
        ("icon-naming-utils" ,icon-naming-utils)
@@ -1191,7 +1191,7 @@ Re-decorates windows on un-maximise.
                (("dbus-1") ""))))))))
     (native-inputs
      `(("automake" ,automake)
-       ("autoconf" ,(autoconf-wrapper))
+       ("autoconf" ,autoconf-wrapper)
        ("gettext" ,gettext-minimal)
        ("intltool" ,intltool)
        ("kbproto" ,kbproto)

gnu/packages/maths.scm

@@ -12,7 +12,7 @@
 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
@@ -23,6 +23,7 @@
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
 ;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -418,18 +419,26 @@ computing convex hulls.")
 (define-public arpack-ng
   (package
     (name "arpack-ng")
-    (version "3.2.0")
+    (version "3.5.0")
+    (home-page "https://github.com/opencollab/arpack-ng")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
+       (uri (string-append home-page "/archive/" version ".tar.gz"))
-                           version ".tar.gz"))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
+         "0f8jx3fifmj9qdp289zr7r651y1q48k1jya859rqxq62mvis7xsh"))))
     (build-system gnu-build-system)
-    (home-page "https://github.com/opencollab/arpack-ng")
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'autoreconf
+                    (lambda _
+                      (invoke "autoreconf" "-vfi"))))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
     (inputs
      `(("lapack" ,lapack)
        ("fortran" ,gfortran)))
@@ -440,6 +449,21 @@ large scale eigenvalue problems.")
     (license (license:non-copyleft "file://COPYING"
                                 "See COPYING in the distribution."))))
 
+(define-public arpack-ng-3.3.0
+  (package
+    (inherit arpack-ng)
+    (version "3.3.0")
+    (name (package-name arpack-ng))
+    (home-page (package-home-page arpack-ng))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append home-page "/archive/" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
+
 (define-public arpack-ng-openmpi
   (package (inherit arpack-ng)
     (name "arpack-ng-openmpi")
@@ -724,7 +748,11 @@ incompatible with HDF5.")
              ;; unnecessary store references to those compilers:
              (substitute* "src/libhdf5.settings"
               (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
-               (string-append prefix (string-take hash 10) "...")))
+               (string-append prefix (string-take hash 10) "..."))
+              ;; Don't record the build-time kernel version to make the
+              ;; settings file reproducible.
+              (("Uname information:.*")
+               "Uname information: Linux\n"))
              #t))
          (add-after 'install 'patch-references
            (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -1280,7 +1308,7 @@ can solve two kinds of problems:
 (define-public octave
   (package
     (name "octave")
-    (version "4.2.1")
+    (version "4.2.2")
     (source
      (origin
       (method url-fetch)
@@ -1288,7 +1316,7 @@ can solve two kinds of problems:
                           version ".tar.lz"))
       (sha256
        (base32
-        "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92"))))
+        "0pkkz1vazsh7ipffb09q0nc2jgx6q27pkkngygjij6jrpcly5zsp"))))
     (build-system gnu-build-system)
     (inputs
      `(("lapack" ,lapack)
@@ -3727,3 +3755,54 @@ specifications.  Also, state spaces can be manipulated, visualised and
 analysed.")
     (home-page "http://mcrl2.org")
     (license license:boost1.0)))
+
+(define-public r-subplex
+  (package
+    (name "r-subplex")
+    (version "1.5-2")
+    (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "subplex" version))
+      (sha256
+       (base32
+        "1v9xrnkapnq7v1jbhlg32ignklzf2vn8rqpayc8pzk8wvz53r33g"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/subplex")
+    (synopsis "Unconstrained optimization using the subplex algorithm")
+    (description "This package implements the Subplex optimization algorithm.
+It solves unconstrained optimization problems using a simplex method on
+subspaces.  The method is well suited for optimizing objective functions that
+are noisy or are discontinuous at the solution.")
+    (license license:gpl3+)))
+
+(define-public r-desolve
+  (package
+    (name "r-desolve")
+    (version "1.20")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "deSolve" version))
+        (sha256
+         (base32
+          "18nx3maww979a8p8ly4hv63y65mnjx8vbj2fpipd6rhcbf1lbsan"))))
+    (properties `((upstream-name . "deSolve")))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://desolve.r-forge.r-project.org/")
+    (synopsis "Solvers for initial value problems of differential equations")
+    (description "This package provides functions that solve initial
+value problems of a system of first-order ordinary differential equations (ODE),
+of partial differential equations (PDE), of differential algebraic equations
+(DAE), and of delay differential equations.  The functions provide an interface
+to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
+to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
+the Runge-Kutta family with fixed or variable time steps.  The package contains
+routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
+differential equations (PDE) that have been converted to ODEs by numerical
+differencing.")
+    (license license:gpl2+)))

gnu/packages/messaging.scm

@@ -144,9 +144,9 @@ keys, no previous conversation is compromised.")
      #:configure-flags '("-DBUILD_SHARED_LIBS=on" "-DBUILD_TESTING=1")))
   (build-system cmake-build-system)
   (inputs `( ;; Required for tests:
-            ("check", check)
+            ("check" ,check)
-            ("openssl", openssl)))
+            ("openssl" ,openssl)))
-  (native-inputs `(("pkg-config", pkg-config)))
+  (native-inputs `(("pkg-config" ,pkg-config)))
   (home-page "https://github.com/WhisperSystems/libsignal-protocol-c")
   (synopsis "Implementation of a ratcheting forward secrecy protocol")
   (description "libsignal-protocol-c is an implementation of a ratcheting
@@ -613,8 +613,8 @@ end-to-end encryption support; XML console.")
              (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
       (inputs
        `(("libgee" ,libgee)
-         ("libsignal-protocol-c", libsignal-protocol-c)
+         ("libsignal-protocol-c" ,libsignal-protocol-c)
-         ("libgcrypt", libgcrypt)
+         ("libgcrypt" ,libgcrypt)
          ("libsoup" ,libsoup)
          ("sqlite" ,sqlite)
          ("gpgme" ,gpgme)
@@ -623,7 +623,7 @@ end-to-end encryption support; XML console.")
          ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)))
       (native-inputs
        `(("pkg-config" ,pkg-config)
-         ("libsignal-protocol-c-source", (package-source libsignal-protocol-c))
+         ("libsignal-protocol-c-source" ,(package-source libsignal-protocol-c))
          ("glib" ,glib "bin")
          ("vala" ,vala)
          ("gettext" ,gettext-minimal)))
@@ -874,10 +874,18 @@ instant messenger with audio and video chat capabilities.")
                (("__DATE__") "\"\"")
                (("__TIME__") "\"\"")
                (("TIMESTAMP") "\"\""))
-             #t)))))
+             #t))
+         ;; Ensure that icons are found at runtime.
+         (add-after 'install 'wrap-executable
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/qtox")
+                 `("QT_PLUGIN_PATH" prefix
+                   ,(list (string-append (assoc-ref inputs "qtsvg")
+                                         "/lib/qt5/plugins/"))))))))))
     (inputs
      `(("ffmpeg" ,ffmpeg)
-       ("filteraudio", filteraudio)
+       ("filteraudio" ,filteraudio)
        ("glib" ,glib)
        ("gtk+" ,gtk+-2)
        ("libsodium" ,libsodium)

gnu/packages/mingw.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -36,14 +37,14 @@
 (define-public mingw-w64
   (package
     (name "mingw-w64")
-    (version "5.0-rc2")
+    (version "5.0.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
                     "https://sourceforge.net/projects/mingw-w64/files/mingw-w64/"
                     "mingw-w64-release/mingw-w64-v" version ".tar.bz2"))
               (sha256
-               (base32 "0imdary8j07if8ih73pfgxiclpf2ax8h3mz8mxln07i8sbbd30c9"))
+               (base32 "1d4wrjfdlq5xqpv9zg6ssw4lm8jnv6522xf7d6zbjygmkswisq1a"))
               (patches (search-patches "mingw-w64-5.0rc2-gcc-4.9.3.patch"))))
     (native-inputs `(("xgcc-core" ,(cross-gcc %mingw-triplet))
                      ("xbinutils" ,(cross-binutils %mingw-triplet))))
@@ -76,9 +77,16 @@
        #:make-flags (list "DEFS=-DHAVE_CONFIG_H -D__MINGW_HAS_DXSDK=1")
        #:tests? #f ; compiles and includes glibc headers
        #:strip-binaries? #f))
-    (home-page "http://mingw.org")
+    (home-page "https://mingw-w64.org")
     (synopsis "Minimalist GNU for Windows")
-    (description "MinGW provides a complete programming tool set which is
+    (description
-suitable for the development of native MS-Windows applications, and which does
+     "Minimalist GNU for Windows (@dfn{MinGW}) is a complete software
-not depend on any 3rd-party C-Runtime dlls.")
+development environment for creating native Microsoft Windows applications.
+
+It includes a set of Windows-specific header files and static import libraries
+which enable the use of the Windows API.  It does not rely on any third-party C
+runtime dynamic-link libraries (@dfn{DLL}s).
+
+Mingw-w64 is an advancement of the original mingw.org project and provides
+several new APIs such as DirectX and DDK, and 64-bit support.")
     (license license:fdl1.3+)))

gnu/packages/monitoring.scm

@@ -28,6 +28,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages admin)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages django)
   #:use-module (gnu packages gd)
@@ -262,3 +263,33 @@ and persisting them to disk using the Whisper time-series library.")
 two things: store numeric time-series data, and render graphs of this data on
 demand.")
     (license license:asl2.0)))
+
+(define-public python-prometheus-client
+  (package
+    (name "python-prometheus-client")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "prometheus_client" version))
+       (sha256
+        (base32
+         "164qzzg8q8awqk0angcm87p2sjiibaj1wgjz0xk6j0klvqi5q2mz"))))
+    (build-system python-build-system)
+    (arguments
+     '(;; No included tests.
+       #:tests? #f))
+    (home-page
+     "https://github.com/prometheus/client_python")
+    (synopsis "Python client for the Prometheus monitoring system")
+    (description
+     "The @code{prometheus_client} package supports exposing metrics from
+software written in Python, so that they can be scraped by a Prometheus
+service.
+
+Metrics can be exposed through a standalone web server, or through Twisted,
+WSGI and the node exporter textfile collector.")
+    (license license:asl2.0)))
+
+(define-public python2-prometheus-client
+  (package-with-python2 python-prometheus-client))

gnu/packages/music.scm

@@ -399,7 +399,7 @@ many input formats and provides a customisable Vi-style user interface.")
                             "Clarinet in Bb.denemo"))
              #t)))))
     (native-inputs
-     `(("glib:bin", glib "bin")   ; for gtester
+     `(("glib:bin" ,glib "bin")   ; for gtester
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("alsa-lib" ,alsa-lib)
@@ -417,7 +417,7 @@ many input formats and provides a customisable Vi-style user interface.")
        ("libsndfile" ,libsndfile)
        ("libtool" ,libtool)
        ("libxml2" ,libxml2)
-       ("lilypond", lilypond)
+       ("lilypond" ,lilypond)
        ("portaudio" ,portaudio)
        ("portmidi" ,portmidi)
        ("rubberband" ,rubberband)))
@@ -441,6 +441,7 @@ background while you work.")
               (uri (string-append
                     "https://github.com/hydrogen-music/hydrogen/archive/"
                     version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "1dy2jfkdw0nchars4xi4isrz66fqn53a9qk13bqza7lhmsg3s3qy"))))
@@ -1754,9 +1755,9 @@ projects.")
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; tests cannot be linked
+       #:build-type "Release"           ; needed to have PMALSA set
        #:configure-flags
        (list "-DPORTMIDI_ENABLE_JAVA=Off"
-             "-DCMAKE_BUILD_TYPE=Release"    ; needed to have PMALSA set
              "-DPORTMIDI_ENABLE_TEST=Off"))) ; tests fail linking
     (inputs
      `(("alsa-lib" ,alsa-lib)))
@@ -2517,7 +2518,7 @@ websites such as Libre.fm.")
     (build-system python-build-system)
     (propagated-inputs
      `(("python-requests" ,python-requests)
-       ("eyed3", eyed3)
+       ("eyed3" ,eyed3)
        ("python-beautifulsoup4" ,python-beautifulsoup4)
        ("youtube-dl" ,youtube-dl)))
     (arguments

gnu/packages/networking.scm

@@ -87,17 +87,22 @@
   #:use-module (gnu packages xml)
   #:use-module (ice-9 match))
 
+;; The gnu.org ‘home’ for this GNU project is a directory listing with 1.6.0 as
+;; the latest version.  The author's git repository, mentioned in the 1.6.0
+;; README and otherwise legit-looking, contains a proper 1.7.0 release tarball
+;; with many OUI updates.  Use it, even though it's also several years old now.
 (define-public macchanger
   (package
     (name "macchanger")
-    (version "1.6.0")
+    (version "1.7.0")
-    (source (origin
+    (source
+     (origin
        (method url-fetch)
-              (uri (string-append "mirror://gnu/"
+       (uri (string-append "https://github.com/alobbs/macchanger/"
-                                  name "/" name "-" version ".tar.gz"))
+                           "releases/download/" version "/"
+                           name "-" version ".tar.gz"))
        (sha256
-               (base32
+        (base32 "1gs5m0jxyprdp00w2qkbnaqm3ilkjz0q1gqdg4nzdm8g4xy73qns"))))
-                "1xsiivjjyhqcs6dyjcshrnxlgypvyfzacjz7gcjgl88xiw9lylri"))))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/macchanger/")
     (synopsis "Viewing and manipulating MAC addresses of network interfaces")
@@ -1220,11 +1225,11 @@ gone wild and are suddenly taking up your bandwidth.")
                        (assoc-ref %build-inputs "ncurses") "/lib")
         (string-append "--with-tlslib=GnuTLS"))))
     (build-system gnu-build-system)
-    (inputs `(("gnutls", gnutls)
+    (inputs `(("gnutls" ,gnutls)
-              ("libxml2", libxml2)
+              ("libxml2" ,libxml2)
-              ("ncurses", ncurses)
+              ("ncurses" ,ncurses)
-              ("zlib", zlib)))
+              ("zlib" ,zlib)))
-    (native-inputs `(("pkg-config", pkg-config)))
+    (native-inputs `(("pkg-config" ,pkg-config)))
     (home-page "https://github.com/nzbget/nzbget")
     (synopsis "Usenet binary file downloader")
     (description
@@ -1450,11 +1455,11 @@ does not use SSH and requires a pre-shared symmetric key.")
               (patches
                (search-patches "quagga-reproducible-build.patch"))))
     (build-system gnu-build-system)
-    (native-inputs `(("pkg-config",pkg-config)
+    (native-inputs `(("pkg-config" ,pkg-config)
-                     ("perl",perl)
+                     ("perl" ,perl)
-                     ("dejagnu",dejagnu)))
+                     ("dejagnu" ,dejagnu)))
-    (inputs `(("readline",readline)
+    (inputs `(("readline" ,readline)
-              ("c-ares",c-ares)))
+              ("c-ares" ,c-ares)))
     (synopsis "Routing Software Suite")
     (description "Quagga is a routing software suite, providing implementations
 of OSPFv2, OSPFv3, RIP v1 and v2, RIPng and BGP-4 for Unix platforms.

gnu/packages/node.scm

@@ -31,9 +31,11 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages icu4c)
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web))
@@ -41,23 +43,43 @@
 (define-public node
   (package
     (name "node")
-    (version "9.4.0")
+    (version "9.8.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://nodejs.org/dist/v" version
                                   "/node-v" version ".tar.gz"))
               (sha256
                (base32
-                "0rx947ibcfpa0lf93nayfrmjls7r7svqsq87z0xmjzf8fb9361r4"))))
+                "1mjr1rm5w26c0yb4zq6z5yv3zbvqk18lwbswhwn1sha8hapinjp8"))
+              (modules '((guix build utils)))
+              (snippet
+               `(begin
+                  ;; Remove bundled software.
+                  (for-each delete-file-recursively
+                            '("deps/cares"
+                              "deps/http_parser"
+                              "deps/icu-small"
+                              "deps/nghttp2"
+                              "deps/openssl"
+                              "deps/uv"
+                              "deps/zlib"))
+                  (substitute* "Makefile"
+                    ;; Remove references to bundled software
+                    (("deps/http_parser/http_parser.gyp") "")
+                    (("deps/uv/include/\\*.h") "")
+                    (("deps/uv/uv.gyp") "")
+                    (("deps/zlib/zlib.gyp") ""))))))
     (build-system gnu-build-system)
     (arguments
      ;; TODO: Purge the bundled copies from the source.
-     '(#:configure-flags '("--shared-openssl"
+     '(#:configure-flags '("--shared-cares"
-                           "--shared-zlib"
-                           "--shared-libuv"
-                           "--shared-cares"
                            "--shared-http-parser"
-                           "--without-snapshot")
+                           "--shared-libuv"
+                           "--shared-nghttp2"
+                           "--shared-openssl"
+                           "--shared-zlib"
+                           "--without-snapshot"
+                           "--with-intl=system-icu")
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'patch-files
@@ -77,29 +99,13 @@
                (("'/usr/bin/env'")
                 (string-append "'" (which "env") "'")))
 
-
-             ;; test-make-doc needs doc-only target, which is inhibited below
-             (for-each delete-file
-                       '("test/doctool/test-make-doc.js"))
              ;; FIXME: These tests depend on being able to install eslint.
              ;; See https://github.com/nodejs/node/issues/17098.
              (for-each delete-file
-                       '("test/parallel/test-eslint-crypto-check.js"
+                       '("test/parallel/test-eslint-alphabetize-errors.js"
-                         "test/parallel/test-eslint-alphabetize-errors.js"
                          "test/parallel/test-eslint-buffer-constructor.js"
                          "test/parallel/test-eslint-documented-errors.js"
-                         "test/parallel/test-eslint-inspector-check.js"
+                         "test/parallel/test-eslint-inspector-check.js"))
-                         "test/parallel/test-eslint-lowercase-name-for-primitive.js"
-                         "test/parallel/test-eslint-no-unescaped-regexp-dot.js"
-                         "test/parallel/test-eslint-no-let-in-for-declaration.js"
-                         "test/parallel/test-eslint-number-isnan.js"
-                         "test/parallel/test-eslint-prefer-assert-iferror.js"
-                         "test/parallel/test-eslint-prefer-assert-methods.js"
-                         "test/parallel/test-eslint-prefer-common-expectserror.js"
-                         "test/parallel/test-eslint-prefer-common-mustnotcall.js"
-                         "test/parallel/test-eslint-prefer-util-format-errors.js"
-                         "test/parallel/test-eslint-require-buffer.js"
-                         "test/parallel/test-eslint-required-modules.js"))
 
              ;; FIXME: These tests fail in the build container, but they don't
              ;; seem to be indicative of real problems in practice.
@@ -135,14 +141,6 @@
                              (string-append (assoc-ref inputs "python")
                                             "/bin/python")
                              "configure" flags)))))
-         (add-before 'check 'skip-check-doc-only
-           (lambda _
-             (substitute* "Makefile"
-               ;; requires js-yaml, which is not part of the distribution,
-               ;; and falls back to using npm to download it
-               (("\\$\\(MAKE\\) doc-only" all)
-                (string-append "#" all)))
-             #t))
          (add-after 'patch-shebangs 'patch-npm-shebang
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((bindir (string-append (assoc-ref outputs "out")
@@ -155,6 +153,7 @@
     (native-inputs
      `(("python" ,python-2)
        ("perl" ,perl)
+       ("pkg-config" ,pkg-config)
        ("procps" ,procps)
        ("util-linux" ,util-linux)
        ("which" ,which)))
@@ -165,7 +164,9 @@
     (inputs
      `(("c-ares" ,c-ares)
        ("http-parser" ,http-parser)
+       ("icu4c" ,icu4c)
        ("libuv" ,libuv)
+       ("nghttp2" ,nghttp2 "lib")
        ("openssl" ,openssl)
        ("zlib" ,zlib)))
     (synopsis "Evented I/O for V8 JavaScript")

gnu/packages/ocaml.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 David Hashe <david.hashe@dhashe.com>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -1123,14 +1123,15 @@ instances and printing them.")
 (define-public ocaml-qtest
   (package
     (name "ocaml-qtest")
-    (version "2.5")
+    (version "2.8")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://github.com/vincent-hugot/iTeML/"
+              (uri (string-append "https://github.com/vincent-hugot/qtest/"
-                                  "archive/v" version ".tar.gz"))
+                                  "archive/" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1hw3jqir7w79payy4knc38fa3nxcvl7ap6y6hnqavrhpi8zqb59j"))))
+                "1ff4if64mc9c7wmhjdgnlnh6k6a713piqzr4043zzj4s5pw7smxk"))))
     (build-system ocaml-build-system)
     (native-inputs
      `(("findlib" ,ocaml-findlib)))
@@ -1144,7 +1145,7 @@ instances and printing them.")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure))))
-    (home-page "https://github.com/vincent-hugot/iTeML")
+    (home-page "https://github.com/vincent-hugot/qtest")
     (synopsis "Inline (Unit) Tests for OCaml")
     (description "Qtest extracts inline unit tests written using a special
 syntax in comments.  Those tests are then run using the oUnit framework and the
@@ -1163,6 +1164,7 @@ to use -- to sophisticated random generation of test cases.")
               (method url-fetch)
               (uri (string-append "https://github.com/rgrinberg/stringext"
                                   "/archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "19g6lfn03iki9f8h91hi0yiqn0b3wkxyq08b3y23wgv6jw6mssfh"))))
@@ -1242,6 +1244,7 @@ coverage information.")
               (method url-fetch)
               (uri (string-append "https://github.com/xguerin/bitstring"
                                   "/archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "0vy8ibrxccii1jbsk5q6yh1kxjigqvi7lhhcmizvd5gfhf7mfyc8"))
@@ -1307,6 +1310,7 @@ powerful.")
               (method url-fetch)
               (uri (string-append "https://github.com/janestreet/result"
                                   "/archive/" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "1pgpfsgvhxnh0i37fkvp9j8nadns9hz9iqgabj4dr519j2gr1xvw"))))
@@ -1644,6 +1648,7 @@ lets the client choose the concrete timeline.")
         (method url-fetch)
         (uri (string-append "https://github.com/savonet/ocaml-ssl/archive/"
                             version ".tar.gz"))
+        (file-name (string-append name "-" version ".tar.gz"))
         (sha256 (base32
                   "15p7652cvzdrlqxc1af11mg07wasxr1fsaj44gcmmh6bmav7wfzq"))))
     (build-system ocaml-build-system)
@@ -1678,6 +1683,7 @@ through Transport Layer Security (@dfn{TLS}) encrypted connections.")
         (method url-fetch)
         (uri (string-append "https://github.com/ocsigen/lwt/archive/" version
                             ".tar.gz"))
+        (file-name (string-append name "-" version ".tar.gz"))
         (sha256 (base32
                   "1gbw0g8a5a4b16diqrmlhc8ilnikrm4w3jjm1zq310maqg8z0zxz"))))
     (build-system ocaml-build-system)
@@ -3448,6 +3454,7 @@ and 4 (random based) according to RFC 4122.")
               (method url-fetch)
               (uri (string-append "https://github.com/alavrik/piqi-ocaml/"
                                   "archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "0ngz6y8i98i5v2ma8nk6mc83pdsmf2z0ks7m3xi6clfg3zqbddrv"))))
@@ -3748,7 +3755,7 @@ sensitive completion, colors, and more.")
          (delete 'configure))))
     (inputs
      `(("topkg" ,ocaml-topkg)
-       ("opam", opam)))
+       ("opam" ,opam)))
     (synopsis "Various signed and unsigned integer types for OCaml")
     (description "The ocaml-integers library provides a number of 8-, 16-, 32-
 and 64-bit signed and unsigned integer types, together with aliases such as
@@ -3782,7 +3789,7 @@ long and size_t whose sizes depend on the host platform.")
       ("integers" ,ocaml-integers)
       ("lwt" ,ocaml-lwt)
       ("topkg" ,ocaml-topkg)
-      ("opam", opam)))
+      ("opam" ,opam)))
    (synopsis "Library for binding to C libraries using pure OCaml")
    (description "Ctypes is a library for binding to C libraries using pure
 OCaml.  The primary aim is to make writing C extensions as straightforward as
@@ -3815,7 +3822,7 @@ without writing or generating any C!")
         (delete 'configure))))
    (inputs
     `(("topkg" ,ocaml-topkg)
-      ("opam", opam)))
+      ("opam" ,opam)))
    (native-inputs
     `(("astring" ,ocaml-astring)))
    (synopsis "OCamlbuild plugin for C stubs")

gnu/packages/openstack.scm

@@ -646,14 +646,14 @@ from the OpenStack project.")
 (define-public python-oslotest
   (package
     (name "python-oslotest")
-    (version "3.2.0")
+    (version "3.3.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "oslotest" version))
         (sha256
           (base32
-            "1xay6wjxzqm4bg87fahqas84dhvhgf1gghzldkcczsfx897mqdkh"))))
+            "006i73w8kbc9s0av2v5mbni6mnkb91c2nq17wa0lz7bwk5zss992"))))
     (build-system python-build-system)
     (propagated-inputs
       `(("python-fixtures" ,python-fixtures)

gnu/packages/package-management.scm

@@ -239,7 +239,7 @@
                        ;; XXX: Keep the development inputs here even though
                        ;; they're unnecessary, just so that 'guix environment
                        ;; guix' always contains them.
-                       ("autoconf" ,(autoconf-wrapper))
+                       ("autoconf" ,autoconf-wrapper)
                        ("automake" ,automake)
                        ("gettext" ,gettext-minimal)
                        ("texinfo" ,texinfo)

gnu/packages/password-utils.scm

@@ -458,14 +458,14 @@ winner of the 2015 Password Hashing Competition.")
 (define-public python-bcrypt
   (package
     (name "python-bcrypt")
-    (version "3.1.0")
+    (version "3.1.4")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "bcrypt" version))
         (sha256
          (base32
-          "1giy0dvd8gvq6flxh44np1v2nqwsji5qsnrz038mgwzgp7c20j75"))))
+          "13cyrnqwkhc70rs6dg65z4yrrr3dc42fhk11804fqmci9hvimvb7"))))
         (build-system python-build-system)
     (native-inputs
      `(("python-pycparser" ,python-pycparser)

gnu/packages/patches/java-jeromq-fix-tests.patch

@@ -0,0 +1,253 @@
+From 5803aadd3f209eba1ffbb2cf7bf16778019dbee1 Mon Sep 17 00:00:00 2001
+From: fredoboulo <fredoboulo@users.noreply.github.com>
+Date: Fri, 23 Feb 2018 23:55:57 +0100
+Subject: [PATCH] Fix #524 : V1 and V2 protocol downgrades handle received data
+ in handshake buffer
+
+This patch is upstream pull request, see:
+https://gihub.com/zeromq/jeromq/pull/527.
+
+It is merged on commit c2afa9c, and we can drop it on the
+0.4.4 release.
+
+---
+ src/main/java/zmq/io/StreamEngine.java            | 21 ++++++++++--
+ src/test/java/zmq/io/AbstractProtocolVersion.java | 41 +++++++++++++----------
+ src/test/java/zmq/io/V0ProtocolTest.java          | 12 +++++++
+ src/test/java/zmq/io/V1ProtocolTest.java          | 16 +++++++--
+ src/test/java/zmq/io/V2ProtocolTest.java          | 16 +++++++--
+ 5 files changed, 81 insertions(+), 25 deletions(-)
+
+diff --git a/src/main/java/zmq/io/StreamEngine.java b/src/main/java/zmq/io/StreamEngine.java
+index b8933c92..fe2f2d8d 100644
+--- a/src/main/java/zmq/io/StreamEngine.java
++++ b/src/main/java/zmq/io/StreamEngine.java
+@@ -816,9 +816,7 @@ private boolean handshake()
+             assert (bufferSize == headerSize);
+ 
+             //  Make sure the decoder sees the data we have already received.
+-            greetingRecv.flip();
+-            inpos = greetingRecv;
+-            insize = greetingRecv.limit();
++            decodeDataAfterHandshake(0);
+ 
+             //  To allow for interoperability with peers that do not forward
+             //  their subscriptions, we inject a phantom subscription message
+@@ -846,6 +844,8 @@ else if (greetingRecv.get(revisionPos) == Protocol.V1.revision) {
+             }
+             encoder = new V1Encoder(errno, Config.OUT_BATCH_SIZE.getValue());
+             decoder = new V1Decoder(errno, Config.IN_BATCH_SIZE.getValue(), options.maxMsgSize, options.allocator);
++
++            decodeDataAfterHandshake(V2_GREETING_SIZE);
+         }
+         else if (greetingRecv.get(revisionPos) == Protocol.V2.revision) {
+             //  ZMTP/2.0 framing.
+@@ -859,6 +859,8 @@ else if (greetingRecv.get(revisionPos) == Protocol.V2.revision) {
+             }
+             encoder = new V2Encoder(errno, Config.OUT_BATCH_SIZE.getValue());
+             decoder = new V2Decoder(errno, Config.IN_BATCH_SIZE.getValue(), options.maxMsgSize, options.allocator);
++
++            decodeDataAfterHandshake(V2_GREETING_SIZE);
+         }
+         else {
+             zmtpVersion = Protocol.V3;
+@@ -904,6 +906,19 @@ else if (greetingRecv.get(revisionPos) == Protocol.V2.revision) {
+         return true;
+     }
+ 
++    private void decodeDataAfterHandshake(int greetingSize)
++    {
++        final int pos = greetingRecv.position();
++        if (pos > greetingSize) {
++            // data is present after handshake
++            greetingRecv.position(greetingSize).limit(pos);
++
++            //  Make sure the decoder sees this extra data.
++            inpos = greetingRecv;
++            insize = greetingRecv.remaining();
++        }
++    }
++
+     private Msg identityMsg()
+     {
+         Msg msg = new Msg(options.identitySize);
+diff --git a/src/test/java/zmq/io/AbstractProtocolVersion.java b/src/test/java/zmq/io/AbstractProtocolVersion.java
+index e60db403..aa06b4a7 100644
+--- a/src/test/java/zmq/io/AbstractProtocolVersion.java
++++ b/src/test/java/zmq/io/AbstractProtocolVersion.java
+@@ -18,15 +18,18 @@
+ import zmq.SocketBase;
+ import zmq.ZError;
+ import zmq.ZMQ;
++import zmq.ZMQ.Event;
+ import zmq.util.Utils;
+ 
+ public abstract class AbstractProtocolVersion
+ {
++    protected static final int REPETITIONS = 1000;
++
+     static class SocketMonitor extends Thread
+     {
+-        private final Ctx             ctx;
+-        private final String          monitorAddr;
+-        private final List<ZMQ.Event> events = new ArrayList<>();
++        private final Ctx         ctx;
++        private final String      monitorAddr;
++        private final ZMQ.Event[] events = new ZMQ.Event[1];
+ 
+         public SocketMonitor(Ctx ctx, String monitorAddr)
+         {
+@@ -41,15 +44,15 @@ public void run()
+             boolean rc = s.connect(monitorAddr);
+             assertThat(rc, is(true));
+             // Only some of the exceptional events could fire
+-            while (true) {
+-                ZMQ.Event event = ZMQ.Event.read(s);
+-                if (event == null && s.errno() == ZError.ETERM) {
+-                    break;
+-                }
+-                assertThat(event, notNullValue());
+-
+-                events.add(event);
++
++            ZMQ.Event event = ZMQ.Event.read(s);
++            if (event == null && s.errno() == ZError.ETERM) {
++                s.close();
++                return;
+             }
++            assertThat(event, notNullValue());
++
++            events[0] = event;
+             s.close();
+         }
+     }
+@@ -69,11 +72,12 @@ public void run()
+         boolean rc = ZMQ.setSocketOption(receiver, ZMQ.ZMQ_LINGER, 0);
+         assertThat(rc, is(true));
+ 
+-        SocketMonitor monitor = new SocketMonitor(ctx, "inproc://monitor");
+-        monitor.start();
+         rc = ZMQ.monitorSocket(receiver, "inproc://monitor", ZMQ.ZMQ_EVENT_HANDSHAKE_PROTOCOL);
+         assertThat(rc, is(true));
+ 
++        SocketMonitor monitor = new SocketMonitor(ctx, "inproc://monitor");
++        monitor.start();
++
+         rc = ZMQ.bind(receiver, host);
+         assertThat(rc, is(true));
+ 
+@@ -81,17 +85,18 @@ public void run()
+         OutputStream out = sender.getOutputStream();
+         for (ByteBuffer raw : raws) {
+             out.write(raw.array());
+-            ZMQ.msleep(100);
+         }
+ 
+         Msg msg = ZMQ.recv(receiver, 0);
+         assertThat(msg, notNullValue());
+         assertThat(new String(msg.data(), ZMQ.CHARSET), is(payload));
+ 
+-        ZMQ.msleep(500);
+-        assertThat(monitor.events.size(), is(1));
+-        assertThat(monitor.events.get(0).event, is(ZMQ.ZMQ_EVENT_HANDSHAKE_PROTOCOL));
+-        assertThat((Integer) monitor.events.get(0).arg, is(version));
++        monitor.join();
++
++        final Event event = monitor.events[0];
++        assertThat(event, notNullValue());
++        assertThat(event.event, is(ZMQ.ZMQ_EVENT_HANDSHAKE_PROTOCOL));
++        assertThat((Integer) event.arg, is(version));
+ 
+         InputStream in = sender.getInputStream();
+         byte[] data = new byte[255];
+diff --git a/src/test/java/zmq/io/V0ProtocolTest.java b/src/test/java/zmq/io/V0ProtocolTest.java
+index bd547d23..1a5b7aef 100644
+--- a/src/test/java/zmq/io/V0ProtocolTest.java
++++ b/src/test/java/zmq/io/V0ProtocolTest.java
+@@ -10,6 +10,18 @@
+ 
+ public class V0ProtocolTest extends AbstractProtocolVersion
+ {
++    @Test
++    public void testFixIssue524() throws IOException, InterruptedException
++    {
++        for (int idx = 0; idx < REPETITIONS; ++idx) {
++            if (idx % 100 == 0) {
++                System.out.print(idx + " ");
++            }
++            testProtocolVersion0short();
++        }
++        System.out.println();
++    }
++
+     @Test(timeout = 2000)
+     public void testProtocolVersion0short() throws IOException, InterruptedException
+     {
+diff --git a/src/test/java/zmq/io/V1ProtocolTest.java b/src/test/java/zmq/io/V1ProtocolTest.java
+index e1045f34..764159d0 100644
+--- a/src/test/java/zmq/io/V1ProtocolTest.java
++++ b/src/test/java/zmq/io/V1ProtocolTest.java
+@@ -10,7 +10,19 @@
+ 
+ public class V1ProtocolTest extends AbstractProtocolVersion
+ {
+-    @Test(timeout = 2000)
++    @Test
++    public void testFixIssue524() throws IOException, InterruptedException
++    {
++        for (int idx = 0; idx < REPETITIONS; ++idx) {
++            if (idx % 100 == 0) {
++                System.out.print(idx + " ");
++            }
++            testProtocolVersion1short();
++        }
++        System.out.println();
++    }
++
++    @Test
+     public void testProtocolVersion1short() throws IOException, InterruptedException
+     {
+         List<ByteBuffer> raws = raws(0);
+@@ -25,7 +37,7 @@ public void testProtocolVersion1short() throws IOException, InterruptedException
+         assertProtocolVersion(1, raws, "abcdefg");
+     }
+ 
+-    @Test(timeout = 2000)
++    @Test
+     public void testProtocolVersion1long() throws IOException, InterruptedException
+     {
+         List<ByteBuffer> raws = raws(0);
+diff --git a/src/test/java/zmq/io/V2ProtocolTest.java b/src/test/java/zmq/io/V2ProtocolTest.java
+index d5e64bce..7fda31bc 100644
+--- a/src/test/java/zmq/io/V2ProtocolTest.java
++++ b/src/test/java/zmq/io/V2ProtocolTest.java
+@@ -21,7 +21,19 @@ protected ByteBuffer identity()
+                 .put((byte) 0);
+     }
+ 
+-    @Test(timeout = 2000)
++    @Test
++    public void testFixIssue524() throws IOException, InterruptedException
++    {
++        for (int idx = 0; idx < REPETITIONS; ++idx) {
++            if (idx % 100 == 0) {
++                System.out.print(idx + " ");
++            }
++            testProtocolVersion2short();
++        }
++        System.out.println();
++    }
++
++    @Test
+     public void testProtocolVersion2short() throws IOException, InterruptedException
+     {
+         List<ByteBuffer> raws = raws(1);
+@@ -38,7 +50,7 @@ public void testProtocolVersion2short() throws IOException, InterruptedException
+         assertProtocolVersion(2, raws, "abcdefg");
+     }
+ 
+-    @Test(timeout = 2000)
++    @Test
+     public void testProtocolVersion2long() throws IOException, InterruptedException
+     {
+         List<ByteBuffer> raws = raws(1);

gnu/packages/patches/java-simple-xml-fix-tests.patch

@@ -0,0 +1,37 @@
+From b3b7a305f1278ec414500bf96c4c7a7f634c941b Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Jens=20Thee=C3=9F?= <theess@subshell.com>
+Date: Thu, 15 Sep 2016 13:08:26 +0200
+Subject: [PATCH] Dictionary uses stable order. This fixes unit tests.
+
+This is upstream pull request #15:
+https://github.com/ngallagher/simplexml/pull/15
+This software is unmaintained, this pull request will no get merged.
+The patch is modified, to match the directory layout of the tarball.
+
+---
+ src/main/java/org/simpleframework/xml/util/Dictionary.java | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/src/main/java/org/simpleframework/xml/util/Dictionary.java b/src/main/java/org/simpleframework/xml/util/Dictionary.java
+index 077d2514..c7327426 100644
+--- a/src/org/simpleframework/xml/util/Dictionary.java
++++ b/src/org/simpleframework/xml/util/Dictionary.java
+@@ -19,8 +19,8 @@
+ package org.simpleframework.xml.util;
+ 
+ import java.util.AbstractSet;
+-import java.util.HashMap;
+ import java.util.Iterator;
++import java.util.LinkedHashMap;
+ 
+ /**
+  * The <code>Dictionary</code> object represents a mapped set of entry
+@@ -134,7 +134,7 @@ public T remove(String name) {
+     *
+     * @see org.simpleframework.xml.util.Entry
+     */
+-   private static class Table<T> extends HashMap<String, T> {
++   private static class Table<T> extends LinkedHashMap<String, T> {
+       
+       /**
+        * Constructor for the <code>Table</code> object. This will

gnu/packages/patches/lrzip-CVE-2017-8842.patch

@@ -0,0 +1,23 @@
+From 38386bd482c0a8102a79958cb3eddcb97a167ca3 Mon Sep 17 00:00:00 2001
+From: Con Kolivas <kernel@kolivas.org>
+Date: Fri, 9 Mar 2018 17:39:40 +1100
+Subject: [PATCH] CVE-2017-8842 Fix divide-by-zero in bufRead::get
+
+---
+ libzpaq/libzpaq.h | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/libzpaq/libzpaq.h b/libzpaq/libzpaq.h
+index 93387da..cbe211d 100644
+--- a/libzpaq/libzpaq.h
++++ b/libzpaq/libzpaq.h
+@@ -465,7 +465,8 @@ struct bufRead: public libzpaq::Reader {
+ 
+ 	int get() {
+ 		if (progress && !(*s_len % 128)) {
+-			int pct = (total_len - *s_len) * 100 / total_len;
++			int pct = (total_len > 0) ?
++				(total_len - *s_len) * 100 / total_len : 100;
+ 
+ 			if (pct / 10 != *last_pct / 10) {
+ 				int i;

gnu/packages/patches/shadow-CVE-2018-7169.patch

@@ -0,0 +1,191 @@
+Fix CVE-2018-7169:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7169
+
+Patch copied from upstream source repository:
+
+https://github.com/shadow-maint/shadow/commit/fb28c99b8a66ff2605c5cb96abc0a4d975f92de0
+
+From fb28c99b8a66ff2605c5cb96abc0a4d975f92de0 Mon Sep 17 00:00:00 2001
+From: Aleksa Sarai <asarai@suse.de>
+Date: Thu, 15 Feb 2018 23:49:40 +1100
+Subject: [PATCH] newgidmap: enforce setgroups=deny if self-mapping a group
+
+This is necessary to match the kernel-side policy of "self-mapping in a
+user namespace is fine, but you cannot drop groups" -- a policy that was
+created in order to stop user namespaces from allowing trivial privilege
+escalation by dropping supplementary groups that were "blacklisted" from
+certain paths.
+
+This is the simplest fix for the underlying issue, and effectively makes
+it so that unless a user has a valid mapping set in /etc/subgid (which
+only administrators can modify) -- and they are currently trying to use
+that mapping -- then /proc/$pid/setgroups will be set to deny. This
+workaround is only partial, because ideally it should be possible to set
+an "allow_setgroups" or "deny_setgroups" flag in /etc/subgid to allow
+administrators to further restrict newgidmap(1).
+
+We also don't write anything in the "allow" case because "allow" is the
+default, and users may have already written "deny" even if they
+technically are allowed to use setgroups. And we don't write anything if
+the setgroups policy is already "deny".
+
+Ref: https://bugs.launchpad.net/ubuntu/+source/shadow/+bug/1729357
+Fixes: CVE-2018-7169
+Reported-by: Craig Furman <craig.furman89@gmail.com>
+Signed-off-by: Aleksa Sarai <asarai@suse.de>
+---
+ src/newgidmap.c | 89 +++++++++++++++++++++++++++++++++++++++++++++++++++------
+ 1 file changed, 80 insertions(+), 9 deletions(-)
+
+diff --git a/src/newgidmap.c b/src/newgidmap.c
+index b1e33513..59a2e75c 100644
+--- a/src/newgidmap.c
++++ b/src/newgidmap.c
+@@ -46,32 +46,37 @@
+  */
+ const char *Prog;
+ 
+-static bool verify_range(struct passwd *pw, struct map_range *range)
++
++static bool verify_range(struct passwd *pw, struct map_range *range, bool *allow_setgroups)
+ {
+ 	/* An empty range is invalid */
+ 	if (range->count == 0)
+ 		return false;
+ 
+-	/* Test /etc/subgid */
+-	if (have_sub_gids(pw->pw_name, range->lower, range->count))
++	/* Test /etc/subgid. If the mapping is valid then we allow setgroups. */
++	if (have_sub_gids(pw->pw_name, range->lower, range->count)) {
++		*allow_setgroups = true;
+ 		return true;
++	}
+ 
+-	/* Allow a process to map its own gid */
+-	if ((range->count == 1) && (pw->pw_gid == range->lower))
++	/* Allow a process to map its own gid. */
++	if ((range->count == 1) && (pw->pw_gid == range->lower)) {
++		/* noop -- if setgroups is enabled already we won't disable it. */
+ 		return true;
++	}
+ 
+ 	return false;
+ }
+ 
+ static void verify_ranges(struct passwd *pw, int ranges,
+-	struct map_range *mappings)
++	struct map_range *mappings, bool *allow_setgroups)
+ {
+ 	struct map_range *mapping;
+ 	int idx;
+ 
+ 	mapping = mappings;
+ 	for (idx = 0; idx < ranges; idx++, mapping++) {
+-		if (!verify_range(pw, mapping)) {
++		if (!verify_range(pw, mapping, allow_setgroups)) {
+ 			fprintf(stderr, _( "%s: gid range [%lu-%lu) -> [%lu-%lu) not allowed\n"),
+ 				Prog,
+ 				mapping->upper,
+@@ -89,6 +94,70 @@ static void usage(void)
+ 	exit(EXIT_FAILURE);
+ }
+ 
++void write_setgroups(int proc_dir_fd, bool allow_setgroups)
++{
++	int setgroups_fd;
++	char *policy, policy_buffer[4096];
++
++	/*
++	 * Default is "deny", and any "allow" will out-rank a "deny". We don't
++	 * forcefully write an "allow" here because the process we are writing
++	 * mappings for may have already set themselves to "deny" (and "allow"
++	 * is the default anyway). So allow_setgroups == true is a noop.
++	 */
++	policy = "deny\n";
++	if (allow_setgroups)
++		return;
++
++	setgroups_fd = openat(proc_dir_fd, "setgroups", O_RDWR|O_CLOEXEC);
++	if (setgroups_fd < 0) {
++		/*
++		 * If it's an ENOENT then we are on too old a kernel for the setgroups
++		 * code to exist. Emit a warning and bail on this.
++		 */
++		if (ENOENT == errno) {
++			fprintf(stderr, _("%s: kernel doesn't support setgroups restrictions\n"), Prog);
++			goto out;
++		}
++		fprintf(stderr, _("%s: couldn't open process setgroups: %s\n"),
++			Prog,
++			strerror(errno));
++		exit(EXIT_FAILURE);
++	}
++
++	/*
++	 * Check whether the policy is already what we want. /proc/self/setgroups
++	 * is write-once, so attempting to write after it's already written to will
++	 * fail.
++	 */
++	if (read(setgroups_fd, policy_buffer, sizeof(policy_buffer)) < 0) {
++		fprintf(stderr, _("%s: failed to read setgroups: %s\n"),
++			Prog,
++			strerror(errno));
++		exit(EXIT_FAILURE);
++	}
++	if (!strncmp(policy_buffer, policy, strlen(policy)))
++		goto out;
++
++	/* Write the policy. */
++	if (lseek(setgroups_fd, 0, SEEK_SET) < 0) {
++		fprintf(stderr, _("%s: failed to seek setgroups: %s\n"),
++			Prog,
++			strerror(errno));
++		exit(EXIT_FAILURE);
++	}
++	if (dprintf(setgroups_fd, "%s", policy) < 0) {
++		fprintf(stderr, _("%s: failed to setgroups %s policy: %s\n"),
++			Prog,
++			policy,
++			strerror(errno));
++		exit(EXIT_FAILURE);
++	}
++
++out:
++	close(setgroups_fd);
++}
++
+ /*
+  * newgidmap - Set the gid_map for the specified process
+  */
+@@ -103,6 +172,7 @@ int main(int argc, char **argv)
+ 	struct stat st;
+ 	struct passwd *pw;
+ 	int written;
++	bool allow_setgroups = false;
+ 
+ 	Prog = Basename (argv[0]);
+ 
+@@ -145,7 +215,7 @@ int main(int argc, char **argv)
+ 				(unsigned long) getuid ()));
+ 		return EXIT_FAILURE;
+ 	}
+-	
++
+ 	/* Get the effective uid and effective gid of the target process */
+ 	if (fstat(proc_dir_fd, &st) < 0) {
+ 		fprintf(stderr, _("%s: Could not stat directory for target %u\n"),
+@@ -177,8 +247,9 @@ int main(int argc, char **argv)
+ 	if (!mappings)
+ 		usage();
+ 
+-	verify_ranges(pw, ranges, mappings);
++	verify_ranges(pw, ranges, mappings, &allow_setgroups);
+ 
++	write_setgroups(proc_dir_fd, allow_setgroups);
+ 	write_mapping(proc_dir_fd, ranges, mappings, "gid_map");
+ 	sub_gid_close();
+ 
+-- 
+2.16.2
+

gnu/packages/patches/util-linux-CVE-2018-7738.patch

@@ -0,0 +1,49 @@
+Fix CVE-2018-7738:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7738
+
+Patch copied from upstream source repository:
+
+https://github.com/karelzak/util-linux/commit/75f03badd7ed9f1dd951863d75e756883d3acc55
+
+From 75f03badd7ed9f1dd951863d75e756883d3acc55 Mon Sep 17 00:00:00 2001
+From: Karel Zak <kzak@redhat.com>
+Date: Thu, 16 Nov 2017 16:27:32 +0100
+Subject: [PATCH] bash-completion: (umount) use findmnt, escape a space in
+ paths
+
+ # mount /dev/sdc1 /mnt/test/foo\ bar
+ # umount <tab>
+
+has to return "/mnt/test/foo\ bar".
+
+Changes:
+
+ * don't use mount | awk output, we have findmnt
+ * force compgen use \n as entries separator
+
+Addresses: https://github.com/karelzak/util-linux/issues/539
+Signed-off-by: Karel Zak <kzak@redhat.com>
+---
+ bash-completion/umount | 9 +++++----
+ 1 file changed, 5 insertions(+), 4 deletions(-)
+
+diff --git a/bash-completion/umount b/bash-completion/umount
+index d76cb9fff..98c90d61a 100644
+--- a/bash-completion/umount
++++ b/bash-completion/umount
+@@ -40,9 +40,10 @@ _umount_module()
+ 			return 0
+ 			;;
+ 	esac
+-	local DEVS_MPOINTS
+-	DEVS_MPOINTS="$(mount | awk '{print $1, $3}')"
+-	COMPREPLY=( $(compgen -W "$DEVS_MPOINTS" -- $cur) )
+-	return 0
++
++	local oldifs=$IFS
++	IFS=$'\n'
++	COMPREPLY=( $( compgen -W '$(findmnt -lno TARGET | sed "s/\([[:blank:]]\)/\\\\\1/g")' -- "$cur" ) )
++	IFS=$oldifs
+ }
+ complete -F _umount_module umount

gnu/packages/patches/zsh-CVE-2018-7548.patch

@@ -0,0 +1,48 @@
+Fix CVE-2018-7548:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7548
+
+Patch copied from upstream source repository:
+
+https://sourceforge.net/p/zsh/code/ci/110b13e1090bc31ac1352b28adc2d02b6d25a102
+
+From 110b13e1090bc31ac1352b28adc2d02b6d25a102 Mon Sep 17 00:00:00 2001
+From: Joey Pabalinas <joeypabalinas@gmail.com>
+Date: Tue, 23 Jan 2018 22:28:08 -0800
+Subject: [PATCH] 42313: avoid null-pointer deref when using ${(PA)...} on an
+ empty array result
+
+---
+ ChangeLog   | 5 +++++
+ Src/subst.c | 2 +-
+ 2 files changed, 6 insertions(+), 1 deletion(-)
+
+#diff --git a/ChangeLog b/ChangeLog
+#index d2ba94afc..3037edda4 100644
+#--- a/ChangeLog
+#+++ b/ChangeLog
+#@@ -1,3 +1,8 @@
+#+2018-01-23  Barton E. Schaefer  <schaefer@zsh.org>
+#+
+#+       * Joey Pabalinas: 42313: Src/subst.c: avoid null-pointer deref
+#+       when using ${(PA)...} on an empty array result
+#+
+# 2018-01-23  Oliver Kiddle  <okiddle@yahoo.co.uk>
+# 
+#        * 42317: Completion/Linux/Command/_cryptsetup,
+diff --git a/Src/subst.c b/Src/subst.c
+index d027e3d83..a265a187e 100644
+--- a/Src/subst.c
++++ b/Src/subst.c
+@@ -2430,7 +2430,7 @@ paramsubst(LinkList l, LinkNode n, char **str, int qt, int pf_flags,
+ 		val = aval[0];
+ 		isarr = 0;
+ 	    }
+-	    s = dyncat(val, s);
++	    s = val ? dyncat(val, s) : dupstring(s);
+ 	    /* Now behave po-faced as if it was always like that... */
+ 	    subexp = 0;
+ 	    /*
+-- 
+2.16.2
+

gnu/packages/patches/zsh-CVE-2018-7549.patch

@@ -0,0 +1,56 @@
+Fix CVE-2018-7549:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7549
+
+Patch copied from upstream source repository:
+
+https://sourceforge.net/p/zsh/code/ci/c2cc8b0fbefc9868fa83537f5b6d90fc1ec438dd
+
+From c2cc8b0fbefc9868fa83537f5b6d90fc1ec438dd Mon Sep 17 00:00:00 2001
+From: Stephane Chazelas <stephane.chazelas@gmail.com>
+Date: Fri, 22 Dec 2017 22:17:09 +0000
+Subject: [PATCH] Avoid crash copying empty hash table.
+
+Visible with typeset -p.
+---
+ ChangeLog    |  2 ++
+ Src/params.c | 11 +++++++----
+ 2 files changed, 9 insertions(+), 4 deletions(-)
+
+#diff --git a/ChangeLog b/ChangeLog
+#index f74c26b88..e3628cfa7 100644
+#--- a/ChangeLog
+#+++ b/ChangeLog
+#@@ -1,5 +1,7 @@
+# 2018-01-04  Peter Stephenson  <p.stephenson@samsung.com>
+# 
+#+       * Stephane: 42159: Src/params.c: avoid crash copying empty hash table.
+#+
+#        * Sebastian: 42188: Src/Modules/system.c: It is necessary to
+#        close the lock descriptor in some failure cases.
+#
+diff --git a/Src/params.c b/Src/params.c
+index 31ff0445b..de7730ae7 100644
+--- a/Src/params.c
++++ b/Src/params.c
+@@ -549,10 +549,13 @@ scancopyparams(HashNode hn, UNUSED(int flags))
+ HashTable
+ copyparamtable(HashTable ht, char *name)
+ {
+-    HashTable nht = newparamtable(ht->hsize, name);
+-    outtable = nht;
+-    scanhashtable(ht, 0, 0, 0, scancopyparams, 0);
+-    outtable = NULL;
++    HashTable nht = 0;
++    if (ht) {
++	nht = newparamtable(ht->hsize, name);
++	outtable = nht;
++	scanhashtable(ht, 0, 0, 0, scancopyparams, 0);
++	outtable = NULL;
++    }
+     return nht;
+ }
+ 
+-- 
+2.16.2
+

gnu/packages/perl.scm

@@ -831,7 +831,7 @@ the Carp.pm module doesn't help.")
 (define-public perl-class-accessor
   (package
     (name "perl-class-accessor")
-    (version "0.34")
+    (version "0.51")
     (source
      (origin
        (method url-fetch)
@@ -839,7 +839,7 @@ the Carp.pm module doesn't help.")
                            "Class-Accessor-" version ".tar.gz"))
        (sha256
         (base32
-         "1z6fqg0yz8gay15r1iasslv8f1n1mzjkrhs47fvbj3rqz36y1cfd"))))
+         "07215zzr4ydf49832vn54i3gf2q5b97lydkv8j56wb2svvjs64mz"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-sub-name" ,perl-sub-name)))
@@ -1681,7 +1681,7 @@ short and handy (e.g. to use it as part of a URL).")
 (define-public perl-data-dump
   (package
     (name "perl-data-dump")
-    (version "1.22")
+    (version "1.23")
     (source
      (origin
        (method url-fetch)
@@ -1689,7 +1689,7 @@ short and handy (e.g. to use it as part of a URL).")
                            "Data-Dump-" version ".tar.gz"))
        (sha256
         (base32
-         "1ciqlwsy1q35s94dry9bjy1pwanbq6b7q4rhxm9z8prgkzbslg2k"))))
+         "0r9ba52b7p8nnn6nw0ygm06lygi8g68piri78jmlqyrqy5gb0lxg"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Data-Dump/")
     (synopsis "Pretty printing of data structures")
@@ -2043,7 +2043,7 @@ Date::Calc.")
 (define-public perl-date-manip
   (package
     (name "perl-date-manip")
-    (version "6.50")
+    (version "6.70")
     (source
      (origin
        (method url-fetch)
@@ -2051,7 +2051,7 @@ Date::Calc.")
                            "Date-Manip-" version ".tar.gz"))
        (sha256
         (base32
-         "0zd0wbf91i49753rnf7m1lw197hdl5r97mxy0n43zdmcmhvkb3qq"))))
+         "0r4k4ypb09xwhvq6das0vpx2c0xbhhhx83knq6jfpf8m55h8qi9r"))))
     (build-system perl-build-system)
     (native-inputs `(("perl-module-build" ,perl-module-build)))
     (arguments
@@ -2091,7 +2091,7 @@ hours, minutes, seconds, and time zones.")
 (define-public perl-datetime
   (package
     (name "perl-datetime")
-    (version "1.43")
+    (version "1.46")
     (source
      (origin
        (method url-fetch)
@@ -2099,7 +2099,7 @@ hours, minutes, seconds, and time zones.")
                            "DateTime-" version ".tar.gz"))
        (sha256
         (base32
-         "0xgrcqs7zza7646g81j54z3fcxb8rw11ynlfm02afr436lgfnfql"))))
+         "1247d2q2gm912bxj88a0sr5gvj2nx4a7n6z1smkq16iy21cziz79"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-cpan-meta-check" ,perl-cpan-meta-check)
@@ -2332,7 +2332,7 @@ parsing logic.")
 (define-public perl-datetime-format-strptime
   (package
     (name "perl-datetime-format-strptime")
-    (version "1.73")
+    (version "1.75")
     (source
      (origin
        (method url-fetch)
@@ -2340,7 +2340,7 @@ parsing logic.")
                            "DateTime-Format-Strptime-" version ".tar.gz"))
        (sha256
         (base32
-         "1gmjcmvh81cla6yn2pvlkr7i25bspg90pzzsizrfb0c5xc37h1vd"))))
+         "069wmgbchydgx3nm9klqw0g6ksnja28g61d4allgzmvr9ynb5ksg"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-datetime" ,perl-datetime)
@@ -2361,7 +2361,7 @@ takes a string and a pattern and returns the `DateTime` object associated.")
 (define-public perl-datetime-locale
   (package
     (name "perl-datetime-locale")
-    (version "1.16")
+    (version "1.17")
     (source
      (origin
        (method url-fetch)
@@ -2369,7 +2369,7 @@ takes a string and a pattern and returns the `DateTime` object associated.")
                            "DateTime-Locale-" version ".tar.gz"))
        (sha256
         (base32
-         "1zkc0wggbsczbj4qadahh197imr9fa6knxr10zl241lw2i14rbyz"))))
+         "1jawnci23kik5x4gln6ixvv9bxznd5f6ira024yjxsc97y5mk9hc"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-file-sharedir" ,perl-file-sharedir)
@@ -2392,7 +2392,7 @@ the DateTime.pm class.")
 (define-public perl-datetime-timezone
   (package
     (name "perl-datetime-timezone")
-    (version "2.13")
+    (version "2.17")
     (source
      (origin
        (method url-fetch)
@@ -2400,7 +2400,7 @@ the DateTime.pm class.")
                            "DateTime-TimeZone-" version ".tar.gz"))
        (sha256
         (base32
-         "1371sk4p9clygfwxzvivfqz6q9dy8gn3n4dr1424d0xqsv63jg9k"))))
+         "1ckhjw7h545306b02p6ra60y8zxqnbqr2lsy7c1wib8libf0l2hx"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-test-fatal" ,perl-test-fatal)
@@ -3722,7 +3722,7 @@ single-letter approach, is provided but not enabled by default.")
 (define-public perl-getopt-long-descriptive
   (package
     (name "perl-getopt-long-descriptive")
-    (version "0.100")
+    (version "0.102")
     (source
      (origin
        (method url-fetch)
@@ -3730,7 +3730,7 @@ single-letter approach, is provided but not enabled by default.")
                            "Getopt-Long-Descriptive-" version ".tar.gz"))
        (sha256
         (base32
-         "1dpz5nhg5glmrpq46nkc90dg19cfqfjspqwhfvihsqyi229yfl8l"))))
+         "0ii8xafvlph5vzcqp3dpc83lg7nkg3l1l2hmqdf5382a567vkm4s"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-cpan-meta-check" ,perl-cpan-meta-check)
@@ -4042,7 +4042,7 @@ that reads or writes data from in-core strings.")
 (define-public perl-io-stringy
   (package
     (name "perl-io-stringy")
-    (version "2.110")
+    (version "2.111")
     (source
      (origin
        (method url-fetch)
@@ -4050,7 +4050,7 @@ that reads or writes data from in-core strings.")
                            "IO-stringy-" version ".tar.gz"))
        (sha256
         (base32
-         "1vh4n0k22hx20rwvf6h7lp25wb7spg0089shrf92d2lkncwg8g3y"))))
+         "178rpx0ym5l2m9mdmpnr92ziscvchm541w94fd7ygi6311kgsrwc"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/IO-stringy/")
     (synopsis "IO:: interface for reading/writing an array of lines")
@@ -4062,14 +4062,14 @@ filehandles; in particular, IO::Scalar, IO::ScalarArray, and IO::Lines.")
 (define-public perl-io-tty
   (package
     (name "perl-io-tty")
-    (version "1.11")
+    (version "1.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/T/TO/TODDR/IO-Tty-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0lgd9xcbi4gf4gw1ka6fj94my3w1f3k1zamb4pfln0qxz45zlxx4"))))
+                "0399anjy3bc0w8xzsc3qx5vcyqryc9gc52lc7wh7i49hsdq8gvx2"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/~toddr/IO-Tty//")
     (synopsis "Perl interface to pseudo ttys")
@@ -4249,15 +4249,15 @@ installed.")
 (define-public perl-json-maybexs
   (package
     (name "perl-json-maybexs")
-    (version "1.003003")
+    (version "1.003010")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/"
+       (uri (string-append "mirror://cpan/authors/id/H/HA/HAARG/"
                            "JSON-MaybeXS-" version ".tar.gz"))
        (sha256
         (base32
-         "0q21wzz87drrvblxcm2py8fcvkzwx1hxzfybynz8ln7wv66vbx3f"))))
+         "0hs504x5zsa2vl6r7b3rvbygsak1ly24m1lg636bqp3x7jirmb30"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-test-without-module" ,perl-test-without-module)))
@@ -5759,7 +5759,7 @@ most specific one) is instantiated.")
        ("perl-file-configdir" ,perl-file-configdir)
        ("perl-file-find-rule" ,perl-file-find-rule)
        ("perl-hash-merge" ,perl-hash-merge)
-       ("perl-moo", perl-moo)
+       ("perl-moo" ,perl-moo)
        ("perl-moox-file-configdir" ,perl-moox-file-configdir)
        ("perl-namespace-clean" ,perl-namespace-clean)))
     (home-page "http://search.cpan.org/dist/MooX-ConfigFromFile/")
@@ -6577,14 +6577,14 @@ directory specifications in a cross-platform manner.")
 (define-public perl-path-tiny
   (package
     (name "perl-path-tiny")
-    (version "0.096")
+    (version "0.104")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/D/DA/DAGOLDEN/"
                                   "Path-Tiny-" version ".tar.gz"))
               (sha256
                (base32
-                "08dmr6ijjg3dp7h9dxix0nmad0fw16c6qzs4qc0hdz500gd64sr2"))))
+                "1vxaczi44d2acfyyzwa7p6c5gx3rgm6c36zbdl40982axg7iv7y6"))))
     (build-system perl-build-system)
     (arguments
      `(#:tests? #f)) ; Tests require additional test modules to be packaged
@@ -6757,7 +6757,7 @@ variables that should not be changed.")
 (define-public perl-ref-util-xs
   (package
     (name "perl-ref-util-xs")
-    (version "0.116")
+    (version "0.117")
     (source
      (origin
        (method url-fetch)
@@ -6765,7 +6765,7 @@ variables that should not be changed.")
                            "Ref-Util-XS-" version ".tar.gz"))
        (sha256
         (base32
-         "0l5dzbd71iclv8fdjk7685rq6pbfiiydh0n70br6g9l9iy2smr6f"))))
+         "0g33cndhj353h5xjihvgjc2h6vxwkyyzw63r4l06czvq4flcar7v"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Ref-Util-XS/")
     (synopsis "XS implementation for Ref::Util")
@@ -6880,7 +6880,7 @@ safely on things that may not be objects.")
 (define-public perl-scope-guard
   (package
     (name "perl-scope-guard")
-    (version "0.20")
+    (version "0.21")
     (source
      (origin
        (method url-fetch)
@@ -6888,7 +6888,7 @@ safely on things that may not be objects.")
                            "Scope-Guard-" version ".tar.gz"))
        (sha256
         (base32
-         "1lsagnz6pli035zvx5c1x4qm9fabi773vns86yd8lzfpldhfv3sv"))))
+         "0y6jfzvxiz8h5yfz701shair0ilypq2mvimd7wn8wi2nbkm1p6wc"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Scope-Guard/")
     (synopsis "Lexically-scoped resource management")
@@ -7521,15 +7521,15 @@ of a system.")
 (define-public perl-task-weaken
   (package
     (name "perl-task-weaken")
-    (version "1.04")
+    (version "1.05")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/A/AD/ADAMK/"
+       (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/"
                            "Task-Weaken-" version ".tar.gz"))
        (sha256
         (base32
-         "1i7kd9v8fjsqyhr4rx4a1jv7n5vfjjm1v4agb24pizh0b72p3qk7"))))
+         "0p5ryr3421p5rqj6dk5dcvxsml5gl9skbn7gv4szk50fimrvzww5"))))
     (build-system perl-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases

gnu/packages/photo.scm

@@ -481,11 +481,11 @@ a complete panorama and stitch any series of overlapping pictures.")
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no test suite
+       #:build-type "release"
        #:configure-flags
        (list (string-append "-DLENSFUNDBDIR="
                             (assoc-ref %build-inputs "lensfun")
                             "/share/lensfun")
-             "-DCMAKE_BUILD_TYPE=release"
              ; Don't optimize the build for the host machine. See the file
              ; 'ProcessorTargets.cmake' in the source distribution for more
              ; information.

gnu/packages/protobuf.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2016 Daniel Pimentel <d4n1@d4n1.org>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -149,14 +149,14 @@ code.")
 (define-public python-protobuf
   (package
     (name "python-protobuf")
-    (version "3.4.0")
+    (version "3.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "protobuf" version))
        (sha256
         (base32
-         "0x33xz85cy5ilg1n2rn92l4qwlcw25vzysx2ldv7k625yjg600pg"))))
+         "1q4b1m55w4gvcbzklbk8iylaii98n4in41k27d94w8ypbwlrm1q9"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-six" ,python-six)))

gnu/packages/pulseaudio.scm

@@ -271,6 +271,7 @@ sinks.")
               (method url-fetch)
               (uri (string-append "https://github.com/GeorgeFilipkin/"
                                   "pulsemixer/archive/" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "1lpad90ifr2xfldyf39sbwx1v85rif2gm9w774gwwpjv53zfgk1g"))))

gnu/packages/python-crypto.scm

@@ -510,14 +510,14 @@ faster ones are not available.")
 (define-public python-pyaes
   (package
     (name "python-pyaes")
-    (version "1.6.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyaes" version))
        (sha256
         (base32
-         "0bp9bjqy1n6ij1zb86wz9lqa1dhla8qr1d7w2kxyn7jbj56sbmcw"))))
+         "13vdaff15k0jyfcss4b4xvfgm8xyv0nrbyw5n1qc7lrqbi0b3h82"))))
     (build-system python-build-system)
     (home-page "https://github.com/ricmoo/pyaes")
     (synopsis "Implementation of AES in Python")
@@ -538,6 +538,7 @@ ECB and OFB).")
         (method url-fetch)
         (uri (string-append "https://github.com/wbond/asn1crypto/archive/"
                             version ".tar.gz"))
+        (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
           "1kn910896l3knmilla1c9ly20q181s43w1ah08lzkbm1h3j6pcz0"))))
@@ -720,14 +721,14 @@ protocol (Javascript Object Signing and Encryption).")
 (define-public python-pycryptodome
   (package
     (name "python-pycryptodome")
-    (version "3.4.7")
+    (version "3.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pycryptodome" version))
        (sha256
         (base32
-         "1xrsd6ql4w0ypkxnsg3fivs3r3z6dd93x44lhvam7jzh3gixzn0q"))))
+         "15mc1h5ij1b6hcqvb048kb4k0ip64n2ky0zz0rml2s78ylv7g5dp"))))
     (build-system python-build-system)
     (home-page "https://www.pycryptodome.org")
     (synopsis "Cryptographic library for Python")

gnu/packages/python-web.scm

@@ -823,7 +823,7 @@ internationalized messages within program source text.")
      '(#:tests? #f)) ; FIXME: Tests can't find zope.event.
     (propagated-inputs
      `(("python-zope-event" ,python-zope-event)
-       ("python-zope-exceptions", python-zope-exceptions)
+       ("python-zope-exceptions" ,python-zope-exceptions)
        ("python-zope-interface" ,python-zope-interface)))
     (native-inputs
      `(("python-zope-testing" ,python-zope-testing)
@@ -1693,14 +1693,14 @@ provide an easy-to-use Python interface for building OAuth1 and OAuth2 clients."
 (define-public python-betamax
   (package
     (name "python-betamax")
-    (version "0.8.0")
+    (version "0.8.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "betamax" version))
         (sha256
          (base32
-          "18f8v5gng3j773jlbbzx4rg1i4y2zw3m2l1zpmbvp8bh5a2q1i42"))))
+          "1hki1c2vs7adq7zr56wi6i5bhrkia4s2ywpv2c98ibnczz709w2v"))))
     (build-system python-build-system)
     (arguments
      '(;; Many tests fail because they require networking.

gnu/packages/python.scm

@@ -1164,14 +1164,14 @@ after Andy Lester’s Perl module WWW::Mechanize.")
 (define-public python-simplejson
   (package
     (name "python-simplejson")
-    (version "3.10.0")
+    (version "3.13.2")
     (source
      (origin
       (method url-fetch)
       (uri (pypi-uri "simplejson" version))
       (sha256
        (base32
-        "1qhwsykjlb85igb4cfl6v6gkprzbbg8gyqdd7zscc8w3x0ifcfwm"))))
+        "02jg5nixffqyicfqdl4dil82fh1z9p2as758wp0nqwalw0hcykjc"))))
     (build-system python-build-system)
     (home-page "http://simplejson.readthedocs.org/en/latest/")
     (synopsis
@@ -1857,7 +1857,7 @@ version numbers.")
 (define-public python-jsonschema
   (package
     (name "python-jsonschema")
-    (version "2.5.1")
+    (version "2.6.0")
     (source (origin
              (method url-fetch)
              (uri
@@ -1866,7 +1866,7 @@ version numbers.")
                version ".tar.gz"))
              (sha256
               (base32
-               "0hddbqjm4jq63y8jf44nswina1crjs16l9snb6m3vvgyg31klrrn"))))
+               "00kf3zmpp9ya4sydffpifn0j0mzm342a2vzh82p6r0vh10cg7xbg"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
@@ -1935,14 +1935,14 @@ something else) to Python data-types.")
 (define-public python-kitchen
   (package
     (name "python-kitchen")
-    (version "1.2.4")
+    (version "1.2.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "kitchen" version))
        (sha256
         (base32
-         "0ggv3p4x8jvmmzhp0xm00h6pvh1g0gmycw71rjwagnrj8n23vxrq"))))
+         "1zakh6l0yjvwic9p0nkvmbidpnkygkxbigh2skmb5gccyrhbp7xg"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-chardet" ,python-chardet)))
@@ -3806,6 +3806,7 @@ Python's distutils.")
        (uri (git-reference
              (url "https://github.com/dieterv/elib.intl.git")
              (commit "d09997cfef")))
+       (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
          "0y7vzff9xgbnaay7m0va1arl6g68ncwrvbgwl7jqlclsahzzb09d"))))
@@ -4055,13 +4056,13 @@ PNG, PostScript, PDF, and SVG file output.")
 (define-public python-decorator
   (package
     (name "python-decorator")
-    (version "4.1.2")
+    (version "4.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "decorator" version))
        (sha256
-        (base32 "1d8npb11kxyi36mrvjdpcjij76l5zfyrz2f820brf0l0rcw4vdkw"))))
+        (base32 "03iaf116rm3w8b4agb8hzf6z9331mrvi4khfxq35zkx17sgxsikx"))))
     (build-system python-build-system)
     (arguments '(#:tests? #f)) ; no test target
     (home-page "https://pypi.python.org/pypi/decorator/")
@@ -4427,14 +4428,14 @@ without using the configuration machinery.")
 (define-public python-jupyter-core
   (package
     (name "python-jupyter-core")
-    (version "4.2.1")
+    (version "4.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append (pypi-uri "jupyter_core" version)))
        (sha256
         (base32
-         "1cy7inv218dgh4m1fbzbsiqpz733ylgjrj62jxqpfzs3r2cm7ic9"))))
+         "1dy083rarba8prn9f9srxq3c7n7vyql02ycrqq306c40lr57aw5s"))))
     (build-system python-build-system)
     ;; FIXME: not sure how to run the tests
     (arguments `(#:tests? #f))
@@ -5066,6 +5067,17 @@ more advanced mathematics.")
        (sha256
         (base32 "190n29sppw7g8ihilc5451y7jlfcaw56crqiqbf1jff43dlmfnxc"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Run the core tests after installation.  By default it would run
+         ;; *all* tests, which take a very long time to complete and are known
+         ;; to be flaky.
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key outputs #:allow-other-keys)
+             (invoke "python3" "-c" "import sympy; sympy.test(\"/core\")")
+             #t)))))
     (propagated-inputs
      `(("python-mpmath" ,python-mpmath)))
     (home-page "http://www.sympy.org/")
@@ -5077,7 +5089,19 @@ as possible in order to be comprehensible and easily extensible.")
     (license license:bsd-3)))
 
 (define-public python2-sympy
-  (package-with-python2 python-sympy))
+  (package
+    (inherit (package-with-python2 python-sympy))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Run the core tests after installation.  By default it would run
+         ;; *all* tests, which take a very long time to complete and are known
+         ;; to be flaky.
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key outputs #:allow-other-keys)
+             (invoke "python" "-c" "import sympy; sympy.test(\"/core\")")
+             #t)))))))
 
 (define-public python-q
   (package
@@ -5557,14 +5581,14 @@ Python.")
 (define-public python-markdown
   (package
     (name "python-markdown")
-    (version "2.6.8")
+    (version "2.6.11")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Markdown" version))
        (sha256
         (base32
-         "0cqfhr1km2s5d8jm6hbwgkrrj9hvkjf2gab3s2axlrw1clgaij0a"))))
+         "108g80ryzykh8bj0i7jfp71510wrcixdi771lf2asyghgyf8cmm8"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -5590,7 +5614,7 @@ markdown_py is also provided to convert Markdown files to HTML.")
 (define-public python-ptyprocess
   (package
     (name "python-ptyprocess")
-    (version "0.5.1")
+    (version "0.5.2")
     (source
      (origin
        (method url-fetch)
@@ -5599,7 +5623,7 @@ markdown_py is also provided to convert Markdown files to HTML.")
              version ".tar.gz"))
        (sha256
         (base32
-         "19l1xrjn4l9gjz01s3vg92gn2dd9d8mw1v86ppkzlnr9m5iwwc05"))))
+         "0ra31k10v3629xq0kdn8lwmfbi97anmk48r03yvh7mks0kq96hg6"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-nose" ,python-nose)))
@@ -5743,7 +5767,7 @@ from an XML-based format.")
 (define-public python-ly
   (package
     (name "python-ly")
-    (version "0.9.4")
+    (version "0.9.5")
     (source
      (origin
        (method url-fetch)
@@ -5752,7 +5776,7 @@ from an XML-based format.")
                            "/python-ly-" version ".tar.gz"))
        (sha256
         (base32
-         "0g6n288l83sfwavxh1aryi0aqvsr3sp7v6f903mckwqa4scpky62"))))
+         "0x98dv7p8mg26p4816yy8hz4f34zf6hpnnfmr56msgh9jnsm2qfl"))))
     (build-system python-build-system)
     (arguments
      ;; FIXME: Some tests need network access.
@@ -6109,13 +6133,13 @@ implementations of ASN.1-based codecs and protocols.")
 (define-public python-ipaddress
   (package
     (name "python-ipaddress")
-    (version "1.0.18")
+    (version "1.0.19")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ipaddress" version))
               (sha256
                (base32
-                "1q8klj9d84cmxgz66073x1j35cplr3r77vx1znhxiwl5w74391ax"))))
+                "10agaa1cys1bk1ycpl2w8lky9vjx8h1xh1z29mg0niqx0638c390"))))
     (build-system python-build-system)
     (home-page "https://github.com/phihag/ipaddress")
     (synopsis "IP address manipulation library")
@@ -6409,14 +6433,14 @@ Debian-related files, such as:
 (define-public python-nbformat
   (package
     (name "python-nbformat")
-    (version "4.3.0")
+    (version "4.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "nbformat" version))
        (sha256
         (base32
-         "12s7j4qja8b5bs1kyw5dzmrqbjxxj8wk52cyasbiqbv7fblcrssz"))))
+         "00nlf08h8yc4q73nphfvfhxrcnilaqanb8z0mdy6nxk0vzq4wjgp"))))
     (build-system python-build-system)
     (arguments `(#:tests? #f)) ; no test target
     (propagated-inputs
@@ -6461,7 +6485,7 @@ Jupyter Notebook format and Python APIs for working with notebooks.")
 (define-public python-entrypoints
   (package
     (name "python-entrypoints")
-    (version "0.2.2")
+    (version "0.2.3")
     (source
      (origin
        (method url-fetch)
@@ -6470,7 +6494,7 @@ Jupyter Notebook format and Python APIs for working with notebooks.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0azqlkh3j0za080lsf5crnhaxx3c93k9dpv5ihkhf5cppgw5sjz5"))))
+         "1pdvgfr5bxyvnfvxbsd3zi0dh3il71pc4k6rinx6zpps91b84a56"))))
     (build-system python-build-system)
     ;; The package does not come with a setup.py file, so we have to generate
     ;; one ourselves.
@@ -6667,14 +6691,14 @@ in the data.")
 (define-public python-jupyter-console
   (package
     (name "python-jupyter-console")
-    (version "5.0.0")
+    (version "5.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "jupyter_console" version))
        (sha256
         (base32
-         "04acmkwsi99rcg3vb54c6n492zv35s92h2ahabc0w6wj976cipvx"))))
+         "1kam1qzgwr7srhm5r6aj90di5sws4bq0jmiw15452ddamb9yspal"))))
     (build-system python-build-system)
     ;; FIXME: it's not clear how to run the tests.
     (arguments `(#:tests? #f))
@@ -7208,13 +7232,13 @@ Abstract Syntax Tree.")
 (define-public python-rply
   (package
     (name "python-rply")
-    (version "0.7.4")
+    (version "0.7.5")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "rply" version))
               (sha256
                (base32
-                "12rp1d9ba7nvd5rhaxi6xzx1rm67r1k1ylsrkzhpwnphqpb06cvj"))))
+                "0lv428895zxsz43968qx0q9bimwqnfykndz4dpjbq515w2gvzhjh"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-appdirs" ,python-appdirs)))
@@ -7384,14 +7408,14 @@ concurrent.futures package from Python 3.2")
 (define-public python-colorama
   (package
    (name "python-colorama")
-   (version "0.3.7")
+   (version "0.3.9")
    (source
     (origin
      (method url-fetch)
      (uri (pypi-uri "colorama" version))
      (sha256
       (base32
-       "0avqkn6362v7k2kg3afb35g4sfdvixjgy890clip4q174p9whhz0"))))
+       "1wd1szk0z3073ghx26ynw43gnc140ibln1safgsis6s6z3s25ss8"))))
    (build-system python-build-system)
    (synopsis "Colored terminal text rendering for Python")
    (description "Colorama is a Python library for rendering colored terminal
@@ -7487,14 +7511,14 @@ servers.")
 (define-public python-jmespath
   (package
    (name "python-jmespath")
-   (version "0.9.0")
+   (version "0.9.3")
    (source
     (origin
      (method url-fetch)
      (uri (pypi-uri "jmespath" version))
      (sha256
       (base32
-       "0g9xvl69y7nr3w7ag4fsp6sm4fqf6vrqjw7504x2hzrrsh3ampq8"))))
+       "0r7wc7fsxmlwzxx9j1j7rms06c6xs6d4sysirdhz1jk2mb4x90ba"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-nose" ,python-nose)))
@@ -8586,12 +8610,12 @@ own code, responding to click events and updating clock every second.")
 (define-public python-tblib
   (package
     (name "python-tblib")
-    (version "1.3.0")
+    (version "1.3.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "tblib" version))
               (sha256 (base32
-                       "02iahfkfa927hb4jq2bak36ldihwapzacfiq5lyxg8llwn98a1yi"))))
+                       "1rsg8h069kqgncyv8fgzyj6qflk6j10cb78pa5jk34ixwq044vj3"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -8861,14 +8885,14 @@ data in Python.")
 (define-public python-kazoo
   (package
     (name "python-kazoo")
-    (version "2.2.1")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "kazoo" version))
        (sha256
         (base32
-         "10pb864if9qi2pq9lfb9m8f7z7ss6rml80gf1d9h64lap5crjnjj"))))
+         "16y213k7r8shyn2zw1k6lkzjgcrvm441pqv8scvcjixhvpbx3hm7"))))
     (build-system python-build-system)
     (arguments '(#:tests? #f)) ; XXX: needs zookeeper
     (propagated-inputs
@@ -8968,13 +8992,13 @@ etc.")
 (define-public python-chai
   (package
     (name "python-chai")
-    (version "1.1.1")
+    (version "1.1.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "chai" version))
               (sha256
                (base32
-                "016kf3irrclpkpvcm7q0gmkfibq7jgy30a9v73pp42bq9h9a32bl"))))
+                "1k6n6zbgrrs83crp6mr3yqj9zlv40b8rpisyrliwsq7naml2p3gz"))))
     (build-system python-build-system)
     (home-page "https://github.com/agoragames/chai")
     (synopsis "Mocking framework for Python")
@@ -10992,6 +11016,7 @@ exception message with a traceback that points to the culprit.")
        ;; The PyPI version wouldn't contain tests.
        (uri (string-append "https://github.com/mwclient/mwclient/archive/"
                            "v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
          "1jj0yhilkjir00719fc7w133x7hdyhkxhk6xblla4asig45klsfv"))))
@@ -11950,7 +11975,7 @@ library.")
        "08if5yax1xn5yfp8p3765ccjmfcv9di7i4m5jckgnwvdsgznwkbj"))))
    (build-system python-build-system)
    (native-inputs `(("pkg-config" ,pkg-config)
-                    ("python-cython", python-cython)))
+                    ("python-cython" ,python-cython)))
    (home-page "https://github.com/aresch/rencode")
    (synopsis "Serialization of heterogeneous data structures")
    (description
@@ -12057,14 +12082,14 @@ ignoring formatting changes.")
 (define-public python-tqdm
   (package
     (name "python-tqdm")
-    (version "4.19.5")
+    (version "4.19.6")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "tqdm" version))
          (sha256
            (base32
-             "0xvkffm77nqckk29xjy5fkqvig5b97vk7nzafp3cn36w4zqyccnz"))))
+             "1pw0ngm0zn9papdmkwipi3yih5c3di6d0w849bdmrraq4d2d9h2y"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-flake8" ,python-flake8)
@@ -12084,14 +12109,14 @@ design and layout.")
 (define-public python-pkginfo
   (package
     (name "python-pkginfo")
-    (version "1.4.1")
+    (version "1.4.2")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pkginfo" version))
         (sha256
           (base32
-            "17pqjfpq3c6xzdmk8pski6jcjgjv78q00zjf2bgzb668pzm6l6mv"))))
+            "0x6lm17p1ks031mj6pajyp4rkq74vpqq8qwjb7ikgwmkli1day2q"))))
     (build-system python-build-system)
     (arguments
      ;; The tests are broken upstream.
@@ -12125,7 +12150,7 @@ created by running @code{python setup.py develop}).")
     (build-system python-build-system)
     (propagated-inputs
      `(("python-tqdm" ,python-tqdm)
-       ("python-pkginfo", python-pkginfo)
+       ("python-pkginfo" ,python-pkginfo)
        ("python-requests" ,python-requests)
        ("python-requests-toolbelt" ,python-requests-toolbelt)))
     (home-page "https://github.com/pypa/twine")
@@ -12232,6 +12257,7 @@ executed more than a given number of times during a given period.")
        (method url-fetch)
        (uri (string-append "https://github.com/kovidgoyal/dukpy/archive/v"
                            version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
          "0pj39rfwlzivqm5hkrsza7gssg6ggpxlq5ivc8f3h7x5pfgc6y6c"))))
@@ -12534,7 +12560,7 @@ is the new Pyro version that is actively developed.")
      `(("netcdf" ,netcdf)))
     (propagated-inputs
      `(("python-numpy" ,python2-numpy-1.8)
-       ("python-pyro", python2-pyro)))
+       ("python-pyro" ,python2-pyro)))
     (arguments
      ;; ScientificPython is not compatible with Python 3
      `(#:python ,python-2
@@ -12599,14 +12625,14 @@ and works only with Python 2 and NumPy < 1.9.")
 (define-public python-phonenumbers
   (package
     (name "python-phonenumbers")
-    (version "8.8.9")
+    (version "8.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "phonenumbers" version))
        (sha256
         (base32
-         "1lhhxmx3hk0b5891nc0p82dl5bq2w9cqbawmh8j5zy587af2j6fq"))))
+         "03fmrgb4r8x3ykmddjs9i3zhs703in8smikj3a6447blqpimwyh1"))))
     (build-system python-build-system)
     (home-page
      "https://github.com/daviddrysdale/python-phonenumbers")
@@ -12881,7 +12907,7 @@ and other tools.")
              #t)))))
     (propagated-inputs
      `(("python-pygments" ,python-pygments)
-       ("python-requests", python-requests)
+       ("python-requests" ,python-requests)
        ("python-babel" ,python-babel) ; optional, for internationalization
        ("python-curtsies" ,python-curtsies) ; >= 0.1.18
        ("python-greenlet" ,python-greenlet)
@@ -12954,8 +12980,64 @@ interpreter. bpython's main features are
     (synopsis "Python library for monitoring inotify events")
     (description
      "@code{pyinotify} provides a Python interface for monitoring
-filesystem events on Linux.")
+file system events on Linux.")
     (license license:expat)))
 
 (define-public python2-pyinotify
   (package-with-python2 python-pyinotify))
+
+;; Ada parser uses this version.
+(define-public python2-quex-0.67.3
+  (package
+    (name "python2-quex")
+    (version "0.67.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/quex/HISTORY/"
+                           (version-major+minor version)
+                           "/quex-" version ".zip"))
+       (sha256
+        (base32
+         "14gv8ll3ipqv4kyc2xiy891nrmjl4ic823zfyx8hassagyclyppw"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (share/quex (string-append out "/share/quex"))
+                    (bin (string-append out "/bin")))
+               (copy-recursively "." share/quex)
+               (mkdir-p bin)
+               (symlink (string-append share/quex "/quex-exe.py")
+                        (string-append bin "/quex"))
+               #t))))))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "QUEX_PATH")
+            (files '("share/quex")))))
+    (home-page "http://quex.sourceforge.net/")
+    (synopsis "Lexical analyzer generator in Python")
+    (description "@code{quex} is a lexical analyzer generator in Python.")
+    (license license:lgpl2.1+)))        ; Non-military
+
+(define-public python2-quex
+  (package (inherit python2-quex-0.67.3)
+    (name "python2-quex")
+    (version "0.68.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/quex/DOWNLOAD/quex-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0svc9nla3b9145d6b7fb9dizx412l3difzqw0ilh9lz52nsixw8j"))
+       (file-name (string-append name "-" version ".tar.gz"))))))

gnu/packages/qt.scm

@@ -1937,7 +1937,7 @@ different kinds of sliders, and much more.")
        ("libwebp" ,libwebp)
        ("sqlite" ,sqlite)
        ("fontconfig" ,fontconfig)
-       ("libxrender", libxrender)
+       ("libxrender" ,libxrender)
        ("qtbase" ,qtbase)
        ("qtdeclarative" ,qtdeclarative)
        ("qtmultimedia" ,qtmultimedia)

gnu/packages/ratpoison.scm

@@ -79,7 +79,7 @@
        ("readline" ,readline)
        ("xextproto" ,xextproto)))
     (native-inputs
-     `(("perl",perl)
+     `(("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("ratpoison.desktop" ,ratpoison.desktop)))
     (home-page "https://www.nongnu.org/ratpoison/")

gnu/packages/rdesktop.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -111,9 +112,9 @@ to remotely control a user's Windows desktop.")
          ("zlib" ,zlib)
          ("openssl" ,openssl)))
       (arguments
-       `(#:configure-flags
+       `(#:build-type "RELEASE"
-         (list "-DCMAKE_BUILD_TYPE=RELEASE"
+         #:configure-flags
-               "-DWITH_JPEG=ON"
+         (list "-DWITH_JPEG=ON"
                ,@(if (string-prefix? "x86_64"
                                      (or (%current-target-system)
                                          (%current-system)))

gnu/packages/samba.scm

@@ -50,14 +50,14 @@
 (define-public cifs-utils
   (package
     (name "cifs-utils")
-    (version "6.7")
+    (version "6.8")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://download.samba.org/pub/linux-cifs/"
                            name "/" name "-" version ".tar.bz2"))
        (sha256 (base32
-                "1ayghnkryy1n1zm5dyvyyr7n3807nsm6glfcbbki5c2a8w91dwmj"))))
+                "0ygz3pagjpaj5ky11hzh4byyymb7fpmqiqkprn11zwj31h2zdlg7"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -148,14 +148,14 @@ anywhere.")
 (define-public samba
   (package
     (name "samba")
-    (version "4.7.5")
+    (version "4.7.6")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://download.samba.org/pub/samba/stable/"
                                  "samba-" version ".tar.gz"))
              (sha256
               (base32
-               "13gyr0sk9vx6mccr2h35ca3g92kp50cqxrlzfgrddfmskzx08v9i"))))
+               "0vkxqp3wh7bpn1fd45lznmrpn2ma1fq75yq28vi08rggr07y7v8y"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/sawfish.scm

@@ -58,7 +58,7 @@
      `(("makeinfo"   ,texinfo)
        ("pkg-config" ,pkg-config)
 
-       ("autoconf" ,(autoconf-wrapper))
+       ("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
        ("libtool"  ,libtool)))
     (inputs

gnu/packages/scheme.scm

@@ -519,7 +519,7 @@ of libraries.")
 (define-public gambit-c
   (package
     (name "gambit-c")
-    (version "4.8.8")
+    (version "4.8.9")
     (source
      (origin
        (method url-fetch)
@@ -529,7 +529,7 @@ of libraries.")
              (string-map (lambda (c) (if (char=? c #\.) #\_ c)) version)
              ".tgz"))
        (sha256
-        (base32 "1plw1id94mpg2c4y6q9z39ndcz1hbxfnp3i08szsg6794rasmgkk"))))
+        (base32 "16sg1s8myzxqpimj5ry6lfza0qfs157zj28bvmxwwgy89jd9m5v7"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags

gnu/packages/sdl.scm

@@ -122,9 +122,9 @@ joystick, and graphics hardware.")
                ("fcitx" ,fcitx) ; helps with CJK input
                ("glib" ,glib)
                ("ibus" ,ibus)
-               ("libxkbcommon", libxkbcommon)
+               ("libxkbcommon" ,libxkbcommon)
-               ("wayland", wayland)
+               ("wayland" ,wayland)
-               ("wayland-protocols", wayland-protocols))
+               ("wayland-protocols" ,wayland-protocols))
              (package-inputs sdl)))
     (license bsd-3)))
 

gnu/packages/serialization.scm

@@ -8,7 +8,8 @@
 ;;; Copyright © 2017 Gregor Giesen <giesen@zaehlwerk.net>
 ;;; Copyright © 2017 Frederick M. Muriithi <fredmanglis@gmail.com>
 ;;; Copyright © 2017 ng0 <ng0@infotropique.org>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,17 +33,21 @@
   #:use-module (guix utils)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
+  #:use-module (guix build-system r)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages cran)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages lua)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages perl)
-  #:use-module (guix build-system python))
+  #:use-module (gnu packages statistics))
 
 (define-public cereal
   (package
@@ -70,7 +75,8 @@
           (lambda _
             (substitute* "doc/doxygen.in"
               (("@CMAKE_CURRENT_SOURCE_DIR@") "."))
-            (zero? (system* "doxygen" "doc/doxygen.in"))))
+            (invoke "doxygen" "doc/doxygen.in")
+            #t))
          ;; There is no "install" target, so we have to provide our own
          ;; "install" phase.
          (replace 'install
@@ -131,8 +137,9 @@ such as compact binary encodings, XML, or JSON.")
        (modify-phases %standard-phases
          (add-after 'unpack 'autoconf
            (lambda _
-             (system* "autoreconf" "-vfi"))))))
+             (invoke "autoreconf" "-vfi")
-    (home-page "http://www.msgpack.org")
+             #t)))))
+    (home-page "https://www.msgpack.org")
     (synopsis "Binary serialization library")
     (description "Msgpack is a library for C/C++ that implements binary
 serialization.")
@@ -409,3 +416,74 @@ JSON's ability, but serializes to a binary format which is smaller and faster
 to generate and parse.  The two primary functions are @code{cbor.loads} and
 @code{cbor.dumps}.")
     (license license:asl2.0)))
+
+(define-public flatbuffers
+  (package
+    (name "flatbuffers")
+    (version "1.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://github.com/google/flatbuffers/archive/v"
+                            version ".tar.gz"))
+        (sha256
+         (base32
+          "0blc978wc5h91662vai24xj92c3bx56y6hzid90qva7il302jl64"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:build-type "Release"
+       #:configure-flags
+       (list (string-append "-DCMAKE_INSTALL_LIBDIR="
+                            (assoc-ref %outputs "out") "/lib"))))
+    (home-page "https://google.github.io/flatbuffers/")
+    (synopsis "Memory-efficient serialization library")
+    (description "FlatBuffers is a cross platform serialization library for C++,
+C#, C, Go, Java, JavaScript, PHP, and Python.  It was originally created for
+game development and other performance-critical applications.")
+    (license license:asl2.0)))
+
+(define-public r-feather
+  (package
+    (name "r-feather")
+    (version "0.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "feather" version))
+        (sha256
+         (base32
+          "1q6dbkfnkpnabq8lb6bm9ma44cfcghx2lm23pyk3vg7943wrn1pi"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-hms" ,r-hms)
+       ("r-rcpp" ,r-rcpp)
+       ("r-tibble" ,r-tibble)))
+    (home-page "https://github.com/wesm/feather")
+    (synopsis "R Bindings to the Feather API")
+    (description "Read and write feather files, a lightweight binary columnar
+daa store designed for maximum speed.")
+    (license license:asl2.0)))
+
+(define-public python-feather-format
+  (package
+    (name "python-feather-format")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "feather-format" version))
+        (sha256
+         (base32
+          "1adivm5w5ji4qv7hq7942vqlk8l2wgw87bdlsia771z14z3zp857"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-pandas" ,python-pandas)
+       ("python-pyarrow" ,python-pyarrow)))
+    (home-page "https://github.com/wesm/feather")
+    (synopsis "Python wrapper to the Feather file format")
+    (description "This package provides a Python wrapper library to the
+Apache Arrow-based Feather binary columnar serialization data frame format.")
+    (license license:asl2.0)))
+
+(define-public python2-feather-format
+  (package-with-python2 python-feather-format))