Merge branch 'master' into staging

126 files changed, 4034 insertions, 1041 deletions

diff --git a/gnu/packages/ada.scm b/gnu/packages/ada.scm
new file mode 100644
index 0000000000..d60723edfa
--- /dev/null
+++ b/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
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 7623693722..8f48e42fec 100644
--- a/gnu/packages/admin.scm
+++ b/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"))
@@ -2463,8 +2468,8 @@ on systems running the Linux kernel.")
 open ports, and also complete the TCP connection and interact with the remote
 application, collecting the information received.")
     (home-page "https://github.com/robertdavidgraham/masscan")
-        ;; 'src/siphash24.c' is the SipHash reference implementation, which
-        ;; bears a CC0 Public Domain Dedication.
+    ;; 'src/siphash24.c' is the SipHash reference implementation, which
+    ;; bears a CC0 Public Domain Dedication.
     (license license:agpl3+)))
 
 (define-public hungrycat
diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index 6baefbca96..637cda0205 100644
--- a/gnu/packages/android.scm
+++ b/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/")
diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm
index 846e318aa1..0f4ecc4ab6 100644
--- a/gnu/packages/autotools.scm
+++ b/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))
-  "Return an wrapper around AUTOCONF that generates `configure' scripts that
+(define (make-autoconf-wrapper autoconf)
+  "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.
diff --git a/gnu/packages/avahi.scm b/gnu/packages/avahi.scm
index 480b5e8d97..7734028dc3 100644
--- a/gnu/packages/avahi.scm
+++ b/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
-     ;; "$(localstatedir)/run/avahi-daemon/socket", so set $(localstatedir)
-     ;; appropriately.
-     '(#:configure-flags '("--localstatedir=/var")))
+     '(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'set-avahi-socket-name
+                    (lambda _
+                      ;; The Avahi daemon socket is expected by
+                      ;; src/Makefile.am to be at
+                      ;; "$(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
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 73765dafe7..78754793a5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/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+)))
diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 9ea8748a5b..582c71cc4a 100644
--- a/gnu/packages/bootloaders.scm
+++ b/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
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 6a759f2b71..b1534e09a4 100644
--- a/gnu/packages/build-tools.scm
+++ b/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")
diff --git a/gnu/packages/calcurse.scm b/gnu/packages/calcurse.scm
index 93eeaf0ee6..8ee5d86e3c 100644
--- a/gnu/packages/calcurse.scm
+++ b/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)))
diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm
index 672064db12..2e51544b05 100644
--- a/gnu/packages/cdrom.scm
+++ b/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 the read filesystem image.
+to produce new complete file system images or add-on images to be appended
+to the read file system image.
 Supported extensions to ISO 9660 are Rock Ridge, Joliet, AAIP, zisofs.")
     (license gpl2+)))
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index ed883072b4..f1359b2cf6 100644
--- a/gnu/packages/chemistry.scm
+++ b/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)
-       ("netcdf", netcdf)
+       ("python-scientific" ,python2-scientific)
+       ("netcdf" ,netcdf)
        ("gv" ,gv)))
     (propagated-inputs
      `(("python-mmtk" ,python2-mmtk)))
diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index 13a89c7bcc..15fdf9d66f 100644
--- a/gnu/packages/code.scm
+++ b/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)))
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index d44ae2d259..f92239d505 100644
--- a/gnu/packages/compression.scm
+++ b/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)))
diff --git a/gnu/packages/connman.scm b/gnu/packages/connman.scm
index 25756019fd..7e87cd8968 100644
--- a/gnu/packages/connman.scm
+++ b/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")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c4cf394e6e..717fa7fdfa 100644
--- a/gnu/packages/cran.scm
+++ b/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+)))
diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm
index 32509fc3fc..fbf177d9da 100644
--- a/gnu/packages/curl.scm
+++ b/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
-           (lambda* (#:key outputs import-path #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (readme (string-append "src/" import-path "/README.md"))
-                    (misc (string-append out "/share/kurly/misc/")))
-               (install-file readme misc)
+         (add-after 'install 'install-documentation
+           (lambda* (#:key import-path outputs #:allow-other-keys)
+             (let* ((source (string-append "src/" import-path))
+                    (out (assoc-ref outputs "out"))
+                    (doc (string-append out "/share/doc/" ,name "-" ,version))
+                    (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)
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 87f65404f8..bcf1864775 100644
--- a/gnu/packages/databases.scm
+++ b/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))
diff --git a/gnu/packages/datamash.scm b/gnu/packages/datamash.scm
index 60c9ba795b..e839a1d985 100644
--- a/gnu/packages/datamash.scm
+++ b/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
diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm
new file mode 100644
index 0000000000..3c3189e073
--- /dev/null
+++ b/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)))
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index c52c812f00..4501b5c745 100644
--- a/gnu/packages/django.scm
+++ b/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)))
diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index b0f6ddaec2..d093b0d9b5 100644
--- a/gnu/packages/dns.scm
+++ b/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
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index c2c162c75c..da366441bd 100644
--- a/gnu/packages/emacs.scm
+++ b/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)))
diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index 142603b082..9d8e7fa1ae 100644
--- a/gnu/packages/emulators.scm
+++ b/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)
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 449584f57e..4d45aab772 100644
--- a/gnu/packages/engineering.scm
+++ b/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")
diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index 8550a89640..a0bf841415 100644
--- a/gnu/packages/enlightenment.scm
+++ b/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.
-                 (("/sbin/shutdown -h now") "/run/current-system/profile/sbin/halt")
-                 (("/sbin/shutdown -r now") "/run/current-system/profile/sbin/reboot"))
+                 (("/etc/acpi/sleep.sh force") "/run/current-system/profile/bin/loginctl suspend")
+                 (("/etc/acpi/hibernate.sh force") "/run/current-system/profile/bin/loginctl hibernate")
+                 (("/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)
diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm
index 0e65213c72..6522662c4e 100644
--- a/gnu/packages/file-systems.scm
+++ b/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/")
diff --git a/gnu/packages/flashing-tools.scm b/gnu/packages/flashing-tools.scm
index 192f84c36c..36c8353ee0 100644
--- a/gnu/packages/flashing-tools.scm
+++ b/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")
-       #:tests? #f; no tests
+     `(#:build-type "Release"
+       #:tests? #f                      ; no tests
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-invocations
diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index a323778cab..202ccc2ba2 100644
--- a/gnu/packages/freedesktop.scm
+++ b/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)
diff --git a/gnu/packages/fvwm.scm b/gnu/packages/fvwm.scm
index 5ff3d5e4f2..a4c31aefc6 100644
--- a/gnu/packages/fvwm.scm
+++ b/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)
diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 3025a68ec1..03a70bea49 100644
--- a/gnu/packages/game-development.scm
+++ b/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)
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index a33da03ad5..a03e58b0ad 100644
--- a/gnu/packages/games.scm
+++ b/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)
-              ("fontconfig", fontconfig)
-              ("freetype", freetype)
-              ("jansson", jansson)
-              ("libpng", libpng)
-              ("libzip", libzip)
-              ("mesa", mesa)
-              ("openssl", openssl)
-              ("sdl2", sdl2)
-              ("speexdsp", speexdsp)
-              ("zlib", zlib)))
+    (inputs `(("curl" ,curl)
+              ("fontconfig" ,fontconfig)
+              ("freetype" ,freetype)
+              ("jansson" ,jansson)
+              ("libpng" ,libpng)
+              ("libzip" ,libzip)
+              ("mesa" ,mesa)
+              ("openssl" ,openssl)
+              ("sdl2" ,sdl2)
+              ("speexdsp" ,speexdsp)
+              ("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
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 9014cc3206..9c7c071db0 100644
--- a/gnu/packages/geo.scm
+++ b/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)))
diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm
index c98f686d41..2483885c95 100644
--- a/gnu/packages/gimp.scm
+++ b/gnu/packages/gimp.scm
@@ -175,12 +175,12 @@ buffers.")
        ("libjpeg" ,libjpeg-8)
        ("atk" ,atk)
        ("gtk+" ,gtk+-2)
-       ("exif" ,libexif)                         ;optional, EXIF + XMP support
-       ("lcms" ,lcms)                            ;optional, color management
-       ("librsvg" ,librsvg)                      ;optional, SVG support
-       ("poppler", poppler)             ; optional, PDF support
-       ("python" ,python-2)                      ;optional, Python support
-       ("python2-pygtk" ,python2-pygtk)          ;optional, Python support
+       ("exif" ,libexif)                ; optional, EXIF + XMP support
+       ("lcms" ,lcms)                   ; optional, color management
+       ("librsvg" ,librsvg)             ; optional, SVG support
+       ("poppler" ,poppler)             ; optional, PDF support
+       ("python" ,python-2)             ; optional, Python support
+       ("python2-pygtk" ,python2-pygtk) ; optional, Python support
        ("gegl" ,gegl)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm
index 2a674a9fb7..bee61cec22 100644
--- a/gnu/packages/gl.scm
+++ b/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")
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 60a7925ee5..164d705ca5 100644
--- a/gnu/packages/gnome.scm
+++ b/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+")
diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm
index 29bfc8199f..f4eacd3023 100644
--- a/gnu/packages/gnunet.scm
+++ b/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)))
diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index eeab5c5afd..2696e332de 100644
--- a/gnu/packages/gnupg.scm
+++ b/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+)))
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index c9c96c4746..c8cec6b422 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/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-bug-1433005.patch"        "a6a9e26688c1" "0cvizvilb4k422j2gzqcbakznvsffmk6n6xn1ayj5rgxfaizkkqk")
-        (mozilla-patch "icecat-bug-1434580.patch"        "198ad052621e" "1721zx8hifdlflrhvw6hmkdgjbvsmxl9n84iji5qywhlp2krdk9r")
+        (mozilla-patch "icecat-CVE-2018-5145.patch"      "f0ec180993d2" "0jiazxcwki83wr00fyh2g518ynsd33p7nk65zk4d1682gn22lc8v")
+        (mozilla-patch "icecat-CVE-2018-5130.patch"      "a6a9e26688c1" "0cvizvilb4k422j2gzqcbakznvsffmk6n6xn1ayj5rgxfaizkkqk")
+        (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-bug-1416529.patch"        "f87ef3774d5e" "0payf3az2w93nzl5qknqx290jbxk8v39rwhdgq7wyd5f245dywxk")
-        (mozilla-patch "icecat-bug-1324042.patch"        "ac743923f81d" "0msyr45xr1j5q4x6ah4r907pwjngyi0k6pp9y8ixk21cnwbzrdwx")
-        (mozilla-patch "icecat-bug-1428947.patch"        "456913d7e8b5" "0fx0s06kxxj7g4hllinaskgh41z3k48zml6yqqzxx485qk3hdh9x")
+        (mozilla-patch "icecat-CVE-2018-5127.patch"      "2c4d7a59041b" "178c6gid89cvw52yqs43i6x6s5w0hslj0rfa2r8b4762ij3civ92")
+        (mozilla-patch "icecat-CVE-2018-5125-pt2.patch"  "f87ef3774d5e" "0payf3az2w93nzl5qknqx290jbxk8v39rwhdgq7wyd5f245dywxk")
+        (mozilla-patch "icecat-CVE-2018-5125-pt3.patch"  "ac743923f81d" "0msyr45xr1j5q4x6ah4r907pwjngyi0k6pp9y8ixk21cnwbzrdwx")
+        (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-bug-1437507.patch"        "5b3a5de48912" "1ifya05rcd34ryp9zawdacihhkkf2m0xn2q8m8c6v78bvxj0mgig")
-        (mozilla-patch "icecat-bug-1440926.patch"        "1df9b4404acd" "1sd59vsarfsbh3vlrzrqv6n1ni7vxdzm83j6s6g0fygl1h8kwijg")
+        (mozilla-patch "icecat-CVE-2018-5125-pt4.patch"  "014877bf17ea" "0hk90pnf7h7kvidji6ydvva1zpyraipn03pjhvprdqr7k2fqzmsz")
+        (mozilla-patch "icecat-CVE-2018-5125-pt5.patch"  "5b3a5de48912" "1ifya05rcd34ryp9zawdacihhkkf2m0xn2q8m8c6v78bvxj0mgig")
+        (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
diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 20a8c538be..e0ce1032f7 100644
--- a/gnu/packages/golang.scm
+++ b/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))))
diff --git a/gnu/packages/gps.scm b/gnu/packages/gps.scm
index 211a33ef89..e07c9f4acb 100644
--- a/gnu/packages/gps.scm
+++ b/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"))))
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 19c9b2269b..38924e42b2 100644
--- a/gnu/packages/graph.scm
+++ b/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))
diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm
index d6feab1197..d2f1b3b0b8 100644
--- a/gnu/packages/graphics.scm
+++ b/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 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
+;;; 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")
-             ;; 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")))
+                            (assoc-ref %outputs "out") "/lib64"))))
     (native-inputs
      `(("unzip" ,unzip)))
     (inputs
-     `(("giflib", giflib)
-       ("jasper", jasper)
-       ("librsvg", librsvg)
-       ("pth", pth)
-       ("qtbase", qtbase)
-       ("ffmpeg", ffmpeg)
-       ("mesa", mesa)))
+     `(("giflib" ,giflib)
+       ("jasper" ,jasper)
+       ("librsvg" ,librsvg)
+       ("pth" ,pth)
+       ("qtbase" ,qtbase)
+       ("ffmpeg" ,ffmpeg)
+       ("mesa" ,mesa)))
     (synopsis "High performance real-time graphics toolkit")
     (description
      "The OpenSceneGraph is a high performance 3D graphics toolkit
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index f1c3d3d010..d7061adcc6 100644
--- a/gnu/packages/gtk.scm
+++ b/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
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 91a440d928..ddd34ae7dc 100644
--- a/gnu/packages/guile.scm
+++ b/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")
-        (commit "951a32c56cc4d80f8836e3c7394783e69c1fcbad"))
+  (let ((revision "5")
+        (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
@@ -2008,40 +2011,30 @@ 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 "."
-                              (string-take commit 7)))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "git://dthompson.us/guile-syntax-highlight.git")
-                      (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
-                (sha256
-                 (base32
-                  "1zjr6sg3n7xbdsliy45i39dqanxvcms58ayx36wxrz72zpq58vq3"))))
-      (build-system gnu-build-system)
-      (arguments
-       '(#:phases (modify-phases %standard-phases
-                    (add-after 'unpack 'bootstrap
-                      (lambda _
-                        (zero? (system* "sh" "bootstrap")))))))
-      (native-inputs
-       `(("autoconf" ,autoconf)
-         ("automake" ,automake)
-         ("pkg-config" ,pkg-config)))
-      (inputs
-       `(("guile" ,guile-2.2)))
+  (package
+    (name "guile-syntax-highlight")
+    (version "0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://files.dthompson.us/"
+                                  "guile-syntax-highlight/"
+                                  "guile-syntax-highlight-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1p771kq15x83483m23bhah1sz6vkalg3drm7x279f4j1cxligkzi"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("guile" ,guile-2.2)))
       (synopsis "General-purpose syntax highlighter for GNU Guile")
       (description "Guile-syntax-highlight is a general-purpose syntax
 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")
-      (license license:lgpl3+))))
+    (home-page "http://dthompson.us/projects/guile-syntax-highlight.html")
+    (license license:lgpl3+)))
 
 (define-public guile-sjson
   (package
diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index f1b50b29bd..1190bc63a5 100644
--- a/gnu/packages/haskell-web.scm
+++ b/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")
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e7401e5cf4..9c59f56139 100644
--- a/gnu/packages/haskell.scm
+++ b/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)))
diff --git a/gnu/packages/idris.scm b/gnu/packages/idris.scm
index 6eb940c9d5..79f89d6f54 100644
--- a/gnu/packages/idris.scm
+++ b/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-async" ,ghc-async)
+       ("ghc-aeson" ,ghc-aeson-1.1.2.0)
        ("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-zlib" ,ghc-zlib)))
+       ("ghc-vector-binary-instances" ,ghc-vector-binary-instances)
+       ("ghc-zip-archive" ,ghc-zip-archive)))
     (arguments
      `(#:tests? #f ; FIXME: Test suite doesn't run in a sandbox.
        #:configure-flags
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index a397189037..c20c34b918 100644
--- a/gnu/packages/image.scm
+++ b/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+)))
diff --git a/gnu/packages/inkscape.scm b/gnu/packages/inkscape.scm
index dc5a30b868..ffd5f60b38 100644
--- a/gnu/packages/inkscape.scm
+++ b/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")))))
               (sha256
                (base32
-                "1lyghk6yarcv9nwkh6k366p6hb7rfilqcvbyji09hki59khd0a56"))))
+                "1chng2yw8dsjxc9gf92aqv7plj11cav8ax321wmakmv5bb09cch6"))))
     (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)))
diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm
index e59b34417b..bad27dacb6 100644
--- a/gnu/packages/irc.scm
+++ b/gnu/packages/irc.scm
@@ -100,7 +100,7 @@
        ("qttools" ,qttools)))
     (inputs
      `(("qca" ,qca)
-       ("qtbase", qtbase)
+       ("qtbase" ,qtbase)
        ("qtscript" ,qtscript)
        ("snorenotify" ,snorenotify)
        ("zlib" ,zlib)))
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 5cc4a56f81..5771366f66 100644
--- a/gnu/packages/java.scm
+++ b/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"))
@@ -1600,97 +1601,122 @@ IcedTea build harness.")
                        "DIST_NAME=\"guix\""))
                     #t))))
       (arguments
-       (substitute-keyword-arguments (package-arguments icedtea-7)
-         ((#:configure-flags flags)
-          `(let ((jdk (assoc-ref %build-inputs "jdk")))
-             `(;;"--disable-bootstrap"
-               "--enable-bootstrap"
-               "--enable-nss"
-               "--disable-downloading"
-               "--disable-system-pcsc"
-               "--disable-system-sctp"
-               "--disable-tests"      ;they are run in the check phase instead
-               "--with-openjdk-src-dir=./openjdk.src"
-               ,(string-append "--with-jdk-home=" jdk))))
-         ((#:phases phases)
-          `(modify-phases ,phases
-             (delete 'fix-x11-extension-include-path)
-             (delete 'patch-paths)
-             (delete 'set-additional-paths)
-             (delete 'patch-patches)
-             (add-after 'unpack 'patch-jni-libs
-               ;; Hardcode dynamically loaded libraries.
-               (lambda _
-                 (let* ((library-path (search-path-as-string->list
-                                       (getenv "LIBRARY_PATH")))
-                        (find-library (lambda (name)
-                                        (search-path
-                                         library-path
-                                         (string-append "lib" name ".so")))))
-                   (for-each
-                    (lambda (file)
-                      (catch 'decoding-error
-                        (lambda ()
-                          (substitute* file
-                            (("VERSIONED_JNI_LIB_NAME\\(\"(.*)\", \"(.*)\"\\)"
-                              _ name version)
-                             (format #f "\"~a\""  (find-library name)))
-                            (("JNI_LIB_NAME\\(\"(.*)\"\\)" _ name)
-                             (format #f "\"~a\"" (find-library name)))))
-                        (lambda _
-                          ;; Those are safe to skip.
-                          (format (current-error-port)
-                                  "warning: failed to substitute: ~a~%"
-                                  file))))
-                    (find-files "openjdk.src/jdk/src/solaris/native"
-                                "\\.c|\\.h"))
-                   #t)))
-             (replace 'install
-               (lambda* (#:key outputs #:allow-other-keys)
-                 (let ((doc (string-append (assoc-ref outputs "doc")
-                                           "/share/doc/icedtea"))
-                       (jre (assoc-ref outputs "out"))
-                       (jdk (assoc-ref outputs "jdk")))
-                   (copy-recursively "openjdk.build/docs" doc)
-                   (copy-recursively "openjdk.build/images/j2re-image" jre)
-                   (copy-recursively "openjdk.build/images/j2sdk-image" jdk)
-                   ;; Install the nss.cfg file to JRE to enable SSL/TLS
-                   ;; support via NSS.
-                   (copy-file (string-append jdk "/jre/lib/security/nss.cfg")
-                              (string-append jre "/lib/security/nss.cfg"))
-                   #t)))))))
+       `(#: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"
+                   "--enable-bootstrap"
+                   "--enable-nss"
+                   "--disable-downloading"
+                   "--disable-system-pcsc"
+                   "--disable-system-sctp"
+                   "--disable-tests"  ;they are run in the check phase instead
+                   "--with-openjdk-src-dir=./openjdk.src"
+                   ,(string-append "--with-jdk-home=" jdk))))
+             ((#:phases phases)
+              `(modify-phases ,phases
+                 (delete 'fix-x11-extension-include-path)
+                 (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 _
+                     (let* ((library-path (search-path-as-string->list
+                                           (getenv "LIBRARY_PATH")))
+                            (find-library (lambda (name)
+                                            (search-path
+                                             library-path
+                                             (string-append "lib" name ".so")))))
+                       (for-each
+                        (lambda (file)
+                          (catch 'decoding-error
+                            (lambda ()
+                              (substitute* file
+                                (("VERSIONED_JNI_LIB_NAME\\(\"(.*)\", \"(.*)\"\\)"
+                                  _ name version)
+                                 (format #f "\"~a\""  (find-library name)))
+                                (("JNI_LIB_NAME\\(\"(.*)\"\\)" _ name)
+                                 (format #f "\"~a\"" (find-library name)))))
+                            (lambda _
+                              ;; Those are safe to skip.
+                              (format (current-error-port)
+                                      "warning: failed to substitute: ~a~%"
+                                      file))))
+                        (find-files "openjdk.src/jdk/src/solaris/native"
+                                    "\\.c|\\.h"))
+                       #t)))
+                 (replace 'install
+                   (lambda* (#:key outputs #:allow-other-keys)
+                     (let ((doc (string-append (assoc-ref outputs "doc")
+                                               "/share/doc/icedtea"))
+                           (jre (assoc-ref outputs "out"))
+                           (jdk (assoc-ref outputs "jdk")))
+                       (copy-recursively "openjdk.build/docs" doc)
+                       (copy-recursively "openjdk.build/images/j2re-image" jre)
+                       (copy-recursively "openjdk.build/images/j2sdk-image" jdk)
+                       ;; Install the nss.cfg file to JRE to enable SSL/TLS
+                       ;; support via NSS.
+                       (copy-file (string-append jdk "/jre/lib/security/nss.cfg")
+                                  (string-append jre "/lib/security/nss.cfg"))
+                       #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")))))))
@@ -3860,39 +3886,30 @@ The jMock library
   (package (inherit java-hamcrest-core)
     (name "java-hamcrest-all")
     (arguments
-     (substitute-keyword-arguments (package-arguments java-hamcrest-core)
-       ;; FIXME: a unit test fails because org.hamcrest.SelfDescribing is not
-       ;; 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
-           ;; Some build targets override the classpath, so we need to patch
-           ;; the build.xml to ensure that required dependencies are on the
-           ;; classpath.
-           (add-after 'unpack 'patch-classpath-for-integration
-             (lambda* (#:key inputs #:allow-other-keys)
-               (substitute* "build.xml"
-                 ((" build/hamcrest-library-\\$\\{version\\}.jar" line)
-                  (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))))))
+     `(#:jdk ,icedtea-8
+       ,@(substitute-keyword-arguments (package-arguments java-hamcrest-core)
+           ((#:build-target _) "bigjar")
+           ((#:phases phases)
+            `(modify-phases ,phases
+               ;; Some build targets override the classpath, so we need to patch
+               ;; the build.xml to ensure that required dependencies are on the
+               ;; classpath.
+               (add-after 'unpack 'patch-classpath-for-integration
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   (substitute* "build.xml"
+                     ((" build/hamcrest-library-\\$\\{version\\}.jar" line)
+                      (string-join
+                       (cons line
+                             (append
+                              (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)))))))
     (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
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index 41bbc66dd2..7a44abdec2 100644
--- a/gnu/packages/julia.scm
+++ b/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
diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 246860e3f3..b763a03476 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/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)
-       ("networkmanager-qt", networkmanager-qt)
-       ("openssl", openssl)
+       ("libsm" ,libsm)
+       ("networkmanager-qt" ,networkmanager-qt)
+       ("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)
-       ("libpng", libpng)
-       ("openssl", openssl)
-       ("phonon", phonon)
+       ("libjpeg" ,libjpeg)
+       ("libpng" ,libpng)
+       ("openssl" ,openssl)
+       ("phonon" ,phonon)
        ("qtbase" ,qtbase)
        ("qtx11extras" ,qtx11extras)
        ("sonnet" ,sonnet)))
diff --git a/gnu/packages/language.scm b/gnu/packages/language.scm
index 237c4bc18d..cf85c510f1 100644
--- a/gnu/packages/language.scm
+++ b/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)
diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm
index 9d96e651ac..d6b70a4f17 100644
--- a/gnu/packages/libevent.scm
+++ b/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)
 
diff --git a/gnu/packages/libusb.scm b/gnu/packages/libusb.scm
index 10a5a91db4..e5a63803d8 100644
--- a/gnu/packages/libusb.scm
+++ b/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"))))
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index c0c963ec55..d63d3ba925 100644
--- a/gnu/packages/linux.scm
+++ b/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-hash "1h17wc12lvva5vcm2z06cf57ywxb6i2snm9vxixw1lwibnksrb6l")
+(define %linux-libre-version "4.15.10")
+(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-hash "1i14djw3rmxb6syl6vfd5w76rjksbbaviynwj2dwwp9ki1h6p1hr")
+(define %linux-libre-4.14-version "4.14.27")
+(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"
-                    "0fqixx3yyvznianygk8bfxzfqj8zpnjcalifhpfyb7rm3dyvi3wd"
+  (make-linux-libre "4.9.87"
+                    "1p8phvmxp04npzqzqcfmv8k9l5l65s7vpjcakdm0fxfkzvnswsp6"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.120"
-                    "17zk5dbpa3kilf8m8i6r2jifjgi4yjim42gyk9j6n4218jjcszv6"
+  (make-linux-libre "4.4.121"
+                    "1d7djrhiib0ds9ssjkali6b5w6rzap4zgj5hf9jq1jmqpp54jkm4"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.1
-  (make-linux-libre "4.1.49"
-                    "0dklmqj6ayjlkz97b811zdvpgb3yppahinji9l9jmkz4ssi7a1gs"
+  (make-linux-libre "4.1.50"
+                    "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)
-              ("libarchive", libarchive)))
-    (native-inputs `(("pkg-config", pkg-config)))
+    (inputs `(("fuse" ,fuse)
+              ("libarchive" ,libarchive)))
+    (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"
-                               "-DCMAKE_BUILD_TYPE=Release")
+       #: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)
-              ("flex", flex)
-              ("gmp", gmp)
-              ("libmnl", libmnl)
-              ("libnftnl", libnftnl)
-              ("readline", readline)))
-    (native-inputs `(("pkg-config", pkg-config)))
+    (inputs `(("bison" ,bison)
+              ("flex" ,flex)
+              ("gmp" ,gmp)
+              ("libmnl" ,libmnl)
+              ("libnftnl" ,libnftnl)
+              ("readline" ,readline)))
+    (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
diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index a506566a05..1cda606c20 100644
--- a/gnu/packages/lisp.scm
+++ b/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"))))
diff --git a/gnu/packages/logging.scm b/gnu/packages/logging.scm
index 27557e1b1b..f50a2f1cbb 100644
--- a/gnu/packages/logging.scm
+++ b/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
diff --git a/gnu/packages/lua.scm b/gnu/packages/lua.scm
index 0d4bf12817..69180abeac 100644
--- a/gnu/packages/lua.scm
+++ b/gnu/packages/lua.scm
@@ -354,12 +354,12 @@ secure session between the peers.")
     (inputs
      `(("gobject-introspection" ,gobject-introspection)
        ("glib" ,glib)
-       ("pango", pango)
-       ("gtk", gtk+-2)
+       ("pango" ,pango)
+       ("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
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 7d85d5208a..1d52b35929 100644
--- a/gnu/packages/mail.scm
+++ b/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/")
diff --git a/gnu/packages/make-bootstrap.scm b/gnu/packages/make-bootstrap.scm
index 779b7ef5aa..99488fb4c4 100644
--- a/gnu/packages/make-bootstrap.scm
+++ b/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")))))
diff --git a/gnu/packages/man.scm b/gnu/packages/man.scm
index 6d1efcee01..257cabbbb6 100644
--- a/gnu/packages/man.scm
+++ b/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
diff --git a/gnu/packages/mate.scm b/gnu/packages/mate.scm
index b892a768d8..0281b02daa 100644
--- a/gnu/packages/mate.scm
+++ b/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)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 8d0c10697f..64fe13b9bc 100644
--- a/gnu/packages/maths.scm
+++ b/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/"
-                           version ".tar.gz"))
+       (uri (string-append home-page "/archive/" 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+)))
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index b6323c39b2..6ce8b258bb 100644
--- a/gnu/packages/messaging.scm
+++ b/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)
-            ("openssl", openssl)))
-  (native-inputs `(("pkg-config", pkg-config)))
+            ("check" ,check)
+            ("openssl" ,openssl)))
+  (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)
-         ("libgcrypt", libgcrypt)
+         ("libsignal-protocol-c" ,libsignal-protocol-c)
+         ("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)
diff --git a/gnu/packages/mingw.scm b/gnu/packages/mingw.scm
index c7bc5c025d..f7f34e9dc3 100644
--- a/gnu/packages/mingw.scm
+++ b/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
-suitable for the development of native MS-Windows applications, and which does
-not depend on any 3rd-party C-Runtime dlls.")
+    (description
+     "Minimalist GNU for Windows (@dfn{MinGW}) is a complete software
+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+)))
diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm
index c5a86d02c6..31ec88db81 100644
--- a/gnu/packages/monitoring.scm
+++ b/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))
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index f47749b380..7818cfcc0b 100644
--- a/gnu/packages/music.scm
+++ b/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"))))
@@ -1753,10 +1754,10 @@ projects.")
               (patches (list (search-patch "portmidi-modular-build.patch")))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f ; tests cannot be linked
+     `(#: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
diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index bf4bee2f87..999f0578d7 100644
--- a/gnu/packages/networking.scm
+++ b/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")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://gnu/"
-                                  name "/" name "-" version ".tar.gz"))
-              (sha256
-               (base32
-                "1xsiivjjyhqcs6dyjcshrnxlgypvyfzacjz7gcjgl88xiw9lylri"))))
+    (version "1.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/alobbs/macchanger/"
+                           "releases/download/" version "/"
+                           name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1gs5m0jxyprdp00w2qkbnaqm3ilkjz0q1gqdg4nzdm8g4xy73qns"))))
     (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)
-              ("libxml2", libxml2)
-              ("ncurses", ncurses)
-              ("zlib", zlib)))
-    (native-inputs `(("pkg-config", pkg-config)))
+    (inputs `(("gnutls" ,gnutls)
+              ("libxml2" ,libxml2)
+              ("ncurses" ,ncurses)
+              ("zlib" ,zlib)))
+    (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)
-                     ("perl",perl)
-                     ("dejagnu",dejagnu)))
-    (inputs `(("readline",readline)
-              ("c-ares",c-ares)))
+    (native-inputs `(("pkg-config" ,pkg-config)
+                     ("perl" ,perl)
+                     ("dejagnu" ,dejagnu)))
+    (inputs `(("readline" ,readline)
+              ("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.
diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm
index 982d3f905c..976d0c048a 100644
--- a/gnu/packages/node.scm
+++ b/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"
-                           "--shared-zlib"
-                           "--shared-libuv"
-                           "--shared-cares"
+     '(#:configure-flags '("--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-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"))
+                         "test/parallel/test-eslint-inspector-check.js"))
 
              ;; FIXME: These tests fail in the build container, but they don't
              ;; seem to be indicative of real problems in practice.
@@ -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")
diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 2ec67ba7be..9346012390 100644
--- a/gnu/packages/ocaml.scm
+++ b/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/"
-                                  "archive/v" version ".tar.gz"))
+              (uri (string-append "https://github.com/vincent-hugot/qtest/"
+                                  "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")
diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index f0147bab59..c1380a1af5 100644
--- a/gnu/packages/openstack.scm
+++ b/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)
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 6ec70b12fe..709cdfd0f7 100644
--- a/gnu/packages/package-management.scm
+++ b/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)
diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index 46b6e795ab..8810392530 100644
--- a/gnu/packages/password-utils.scm
+++ b/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)
diff --git a/gnu/packages/patches/java-jeromq-fix-tests.patch b/gnu/packages/patches/java-jeromq-fix-tests.patch
new file mode 100644
index 0000000000..5466b92707
--- /dev/null
+++ b/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);
diff --git a/gnu/packages/patches/java-simple-xml-fix-tests.patch b/gnu/packages/patches/java-simple-xml-fix-tests.patch
new file mode 100644
index 0000000000..6270b87009
--- /dev/null
+++ b/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
diff --git a/gnu/packages/patches/lrzip-CVE-2017-8842.patch b/gnu/packages/patches/lrzip-CVE-2017-8842.patch
new file mode 100644
index 0000000000..89b4f2f5d9
--- /dev/null
+++ b/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;
diff --git a/gnu/packages/patches/shadow-CVE-2018-7169.patch b/gnu/packages/patches/shadow-CVE-2018-7169.patch
new file mode 100644
index 0000000000..eeae5b9b71
--- /dev/null
+++ b/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
+
diff --git a/gnu/packages/patches/util-linux-CVE-2018-7738.patch b/gnu/packages/patches/util-linux-CVE-2018-7738.patch
new file mode 100644
index 0000000000..080e2f56ba
--- /dev/null
+++ b/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
diff --git a/gnu/packages/patches/zsh-CVE-2018-7548.patch b/gnu/packages/patches/zsh-CVE-2018-7548.patch
new file mode 100644
index 0000000000..1ee15fad73
--- /dev/null
+++ b/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
+
diff --git a/gnu/packages/patches/zsh-CVE-2018-7549.patch b/gnu/packages/patches/zsh-CVE-2018-7549.patch
new file mode 100644
index 0000000000..abefcdf2f9
--- /dev/null
+++ b/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
+
diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index badff6e4d1..0bc4697229 100644
--- a/gnu/packages/perl.scm
+++ b/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
diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm
index 758ed3f6f1..90bc365d05 100644
--- a/gnu/packages/photo.scm
+++ b/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.
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 17d3bacf02..877c9c9c84 100644
--- a/gnu/packages/protobuf.scm
+++ b/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)))
diff --git a/gnu/packages/pulseaudio.scm b/gnu/packages/pulseaudio.scm
index 2721c231c3..43816e09f8 100644
--- a/gnu/packages/pulseaudio.scm
+++ b/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"))))
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index b898f088be..3734b6ba10 100644
--- a/gnu/packages/python-crypto.scm
+++ b/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")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index dce651246c..7974c005c2 100644
--- a/gnu/packages/python-web.scm
+++ b/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.
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 79ceaa2195..76b5460f63 100644
--- a/gnu/packages/python.scm
+++ b/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"))))))
diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm
index a8c2729ee8..d6082bd7a4 100644
--- a/gnu/packages/qt.scm
+++ b/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)
diff --git a/gnu/packages/ratpoison.scm b/gnu/packages/ratpoison.scm
index d630c24fd4..19321872c5 100644
--- a/gnu/packages/ratpoison.scm
+++ b/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/")
diff --git a/gnu/packages/rdesktop.scm b/gnu/packages/rdesktop.scm
index 1a2d0412d1..bd2b5737e9 100644
--- a/gnu/packages/rdesktop.scm
+++ b/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
-         (list "-DCMAKE_BUILD_TYPE=RELEASE"
-               "-DWITH_JPEG=ON"
+       `(#:build-type "RELEASE"
+         #:configure-flags
+         (list "-DWITH_JPEG=ON"
                ,@(if (string-prefix? "x86_64"
                                      (or (%current-target-system)
                                          (%current-system)))
diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm
index 10b26c0ce9..3b1c2d4885 100644
--- a/gnu/packages/samba.scm
+++ b/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
diff --git a/gnu/packages/sawfish.scm b/gnu/packages/sawfish.scm
index 9f9264457d..ede725877d 100644
--- a/gnu/packages/sawfish.scm
+++ b/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
diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm
index 8947509cb1..657ca875d5 100644
--- a/gnu/packages/scheme.scm
+++ b/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
diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm
index 222fd5b6f1..30d18aa1c3 100644
--- a/gnu/packages/sdl.scm
+++ b/gnu/packages/sdl.scm
@@ -122,9 +122,9 @@ joystick, and graphics hardware.")
                ("fcitx" ,fcitx) ; helps with CJK input
                ("glib" ,glib)
                ("ibus" ,ibus)
-               ("libxkbcommon", libxkbcommon)
-               ("wayland", wayland)
-               ("wayland-protocols", wayland-protocols))
+               ("libxkbcommon" ,libxkbcommon)
+               ("wayland" ,wayland)
+               ("wayland-protocols" ,wayland-protocols))
              (package-inputs sdl)))
     (license bsd-3)))
 
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 8df4841eae..f721165751 100644
--- a/gnu/packages/serialization.scm
+++ b/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"))))))
-    (home-page "http://www.msgpack.org")
+             (invoke "autoreconf" "-vfi")
+             #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))
diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm
index f4a38b8779..685f6d2df4 100644
--- a/gnu/packages/shells.scm
+++ b/gnu/packages/shells.scm
@@ -300,6 +300,8 @@ history mechanism, job control and a C-like syntax.")
                          (string-append
                            "http://www.zsh.org/pub/old/zsh-" version
                            ".tar.gz")))
+              (patches (search-patches "zsh-CVE-2018-7548.patch"
+                                       "zsh-CVE-2018-7549.patch"))
               (sha256
                (base32
                 "1jdcfinzmki2w963msvsanv29vqqfmdfm4rncwpw0r3zqnrcsywm"))))
diff --git a/gnu/packages/sml.scm b/gnu/packages/sml.scm
index b9bd7a7e82..1d7fd3fb51 100644
--- a/gnu/packages/sml.scm
+++ b/gnu/packages/sml.scm
@@ -42,7 +42,7 @@
     (build-system gnu-build-system)
     (inputs
      `(("gmp" ,gmp)
-       ("lesstif",lesstif)
+       ("lesstif" ,lesstif)
        ("libffi" ,libffi)
        ("libx11" ,libx11)
        ("libxt" ,libxt)))
diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm
index 58450e6a3e..fb3b11ba2d 100644
--- a/gnu/packages/spice.scm
+++ b/gnu/packages/spice.scm
@@ -69,6 +69,7 @@
                 (uri (git-reference
                         (url "https://anongit.freedesktop.org/git/spice/usbredir.git")
                         (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "052fywgi72j68dr5ybldncg4vk8iqfrh58la7iazyxxpph9aag1g"))))
diff --git a/gnu/packages/sssd.scm b/gnu/packages/sssd.scm
index 70ea5fe9e2..28a364ebd5 100644
--- a/gnu/packages/sssd.scm
+++ b/gnu/packages/sssd.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 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.
 ;;;
@@ -81,14 +81,14 @@ fundamental object types for C.")
 (define-public sssd
   (package
     (name "sssd")
-    (version "1.16.0")
+    (version "1.16.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://releases.pagure.org/SSSD/sssd/"
                                   "sssd-" version ".tar.gz"))
               (sha256
                (base32
-                "03wllgbxxz2zv14dcqr8d2xssppi7ibckh0rlky8gvsw6vjsd0f5"))))
+                "0vjh1c5960wh86zjsamdjhljls7bb5fz5jpcazgzrpmga5w6ggrd"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 0ae4dddb64..8afccb0737 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -39,6 +39,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
+  #:use-module (gnu packages bash)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cran)
@@ -172,21 +173,15 @@ be output in text, PostScript, PDF or HTML.")
              ;; queries the mtime of a given file and records it in an object.
              ;; This is acceptable at runtime to detect stale source files,
              ;; but it destroys reproducibility at build time.
-             ;;
-             ;; Instead of disabling this feature, which may have unexpected
-             ;; consequences, we reset the mtime of generated files before
-             ;; passing them to the "srcfile" procedure.
-             (substitute* "src/library/Makefile.in"
-               (("@\\(cd base && \\$\\(MAKE\\) mkdesc\\)" line)
-                (string-append line "\n	find $(top_builddir)/library/tools | xargs touch -d '1970-01-01'; \n"))
-               (("@\\$\\(MAKE\\) Rdobjects" line)
-                (string-append "@find $(srcdir)/tools | xargs touch -d '1970-01-01'; \n	"
-                               line)))
-             (substitute* "src/library/tools/Makefile.in"
-               (("@\\$\\(INSTALL_DATA\\) all.R \\$\\(top_builddir\\)/library/\\$\\(pkg\\)/R/\\$\\(pkg\\)" line)
-                (string-append
-                 line
-                 "\n	find $(srcdir)/$(pkg) $(top_builddir)/library/$(pkg) | xargs touch -d \"1970-01-01\"; \n")))
+
+             ;; Similarly, the "srcfilecopy" procedure records the current
+             ;; time.  We change both of them to respect SOURCE_DATE_EPOCH.
+             (substitute* "src/library/base/R/srcfile.R"
+               (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
+                (string-append "timestamp <- \
+as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
+  as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
+} else { " time "}, origin=\"1970-01-01\")\n")))
 
              ;; This library is installed using "install_package_description",
              ;; so we need to pass the "builtStamp" argument.
@@ -267,13 +262,16 @@ be output in text, PostScript, PDF or HTML.")
        ("libxt" ,libxt)
        ("pcre" ,pcre)
        ("readline" ,readline)
+       ;; This avoids a reference to the ungraftable static bash.  R uses the
+       ;; detected shell for the "system" procedure.
+       ("bash" ,bash-minimal)
        ("which" ,which)
        ("zlib" ,zlib)))
     (native-search-paths
      (list (search-path-specification
             (variable "R_LIBS_SITE")
             (files (list "site-library/")))))
-    (home-page "http://www.r-project.org/")
+    (home-page "https://www.r-project.org/")
     (synopsis "Environment for statistical computing and graphics")
     (description
      "R is a language and environment for statistical computing and graphics.
@@ -941,14 +939,14 @@ solution for sending email, including attachments, from within R.")
 (define-public r-stringi
   (package
     (name "r-stringi")
-    (version "1.1.6")
+    (version "1.1.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringi" version))
        (sha256
         (base32
-         "122im5m8x9bqpahc0hbxmvdq6hnsmgnxwwyjpvbihyv2jq5kd44m"))))
+         "0nck1s2iglmkrn15ay2chrrwsy5lngcylz2sc87fxy5skxaahxdl"))))
     (build-system r-build-system)
     (inputs `(("icu4c" ,icu4c)))
     (native-inputs `(("pkg-config" ,pkg-config)))
@@ -2235,14 +2233,14 @@ collation, and NAMESPACE files.")
 (define-public r-openssl
   (package
     (name "r-openssl")
-    (version "1.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openssl" version))
        (sha256
         (base32
-         "1j8smqrb79lnaf2n9icksjiy641fcazsbkhmgg916s3nnyjngjz3"))))
+         "1qyql5gpwf88bkm1qarjhbqbq4hn6w0d8j4pxb5x7i96is30ap30"))))
     (build-system r-build-system)
     (inputs
      `(("libressl" ,libressl)))
@@ -2598,7 +2596,11 @@ certain criterion, e.g., it contains a certain regular file.")
        ("r-rprojroot" ,r-rprojroot)
        ("r-stringr" ,r-stringr)
        ("r-yaml" ,r-yaml)
-       ("ghc-pandoc" ,ghc-pandoc)))
+       ;; rmarkdown works with the 2.x release of Pandoc, but with degraded
+       ;; functionality.  For example, tabbed plots do not currently work with
+       ;; Pandoc 2.  The authors of rmarkdown recommend the use of Pandoc 1
+       ;; for the time being.
+       ("ghc-pandoc" ,ghc-pandoc-1)))
     (home-page "http://rmarkdown.rstudio.com")
     (synopsis "Convert R Markdown documents into a variety of formats")
     (description
@@ -3331,20 +3333,20 @@ memory-mapped files.")
 (define-public r-nmf
   (package
     (name "r-nmf")
-    (version "0.20.6")
+    (version "0.21.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "NMF" version))
        (sha256
         (base32
-         "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z"))))
+         "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
     (properties `((upstream-name . "NMF")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
-       ("r-bigmemory" ,r-bigmemory)
-       ("r-synchronicity" ,r-synchronicity)
+       ("r-bigmemory" ,r-bigmemory) ; suggested
+       ("r-synchronicity" ,r-synchronicity) ; suggested
        ("r-colorspace" ,r-colorspace)
        ("r-digest" ,r-digest)
        ("r-doparallel" ,r-doparallel)
@@ -4027,14 +4029,14 @@ existing packages provide.")
 (define-public r-sfsmisc
   (package
     (name "r-sfsmisc")
-    (version "1.1-1")
+    (version "1.1-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sfsmisc" version))
        (sha256
         (base32
-         "0jzmbywlyzfxs7hlmyd0iynghfc9qp5sa5lnhr73y8r360yv1ahf"))))
+         "0cgq2h11ngkzd6p34k6mqjnvlvc5vj4lnqrl64k05lb391j391w0"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/sfsmisc")
     (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
@@ -4906,27 +4908,6 @@ functions apply.  The implementation can easily be added to functions where
 showing the progress is useful e.g. bootstrap.")
     (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 and related applications including KNN classification,
-regression and information measures.")
-    (license license:gpl2+)))
-
 (define-public r-minqa
   (package
     (name "r-minqa")
@@ -5037,7 +5018,7 @@ using modular prediction and response module classes.")
      `(("r-matrix" ,r-matrix)
        ("r-matrixmodels" ,r-matrixmodels)
        ("r-sparsem" ,r-sparsem)))
-    (home-page "http://www.r-project.org")
+    (home-page "https://www.r-project.org")
     (synopsis "Quantile regression")
     (description
      "This package provides an estimation and inference methods for models
@@ -5469,6 +5450,7 @@ manually \"recoding\").")
          (uri (hg-reference
                (url "https://bitbucket.org/tanaylab/tgstat")
                (changeset changeset)))
+         (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
            "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
@@ -5503,6 +5485,7 @@ tools.")
          (uri (hg-reference
                (url "https://bitbucket.org/tanaylab/tgconfig")
                (changeset changeset)))
+         (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
            "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
diff --git a/gnu/packages/suckless.scm b/gnu/packages/suckless.scm
index c343b42274..eadc8409c2 100644
--- a/gnu/packages/suckless.scm
+++ b/gnu/packages/suckless.scm
@@ -138,14 +138,14 @@ optimising the environment for the application in use and the task performed.")
 (define-public dmenu
   (package
     (name "dmenu")
-    (version "4.7")
+    (version "4.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://dl.suckless.org/tools/dmenu-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1fgph549i0yw62x02jhfc8qmqk2rnzcnm46bxq6jig1cvkw3amm7"))))
+                "0qfvfrj10xlwd9hkvb57wshryan65bl6423h0qhiw1h76rf5lqgy"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f ; no tests
diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 6c3792b92f..04f258481e 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1692,7 +1692,7 @@ using sh's word-splitting rules.")
        '(#:import-path "github.com/zillode/notify"))
       (propagated-inputs
        `(("go-golang-org-x-sys-unix" ,go-golang-org-x-sys-unix)))
-      (synopsis "Filesystem event notification library")
+      (synopsis "File system event notification library")
       (description "This package provides @code{notify}, a file system event
 notification library in Go.")
       (home-page "https://github.com/zillode/notify")
@@ -1871,8 +1871,8 @@ Prometheus metrics.")
       (arguments
        '(#:import-path "github.com/prometheus/procfs"))
       (synopsis "Go library for reading @file{/proc}")
-      (description "This Go package @code{procfs} provides functions to retrieve
-system, kernel and process metrics from the pseudo-filesystem @file{/proc}.")
+      (description "The @code{procfs} Go package provides functions to retrieve
+system, kernel, and process metrics from the @file{/proc} pseudo file system.")
       (home-page "https://github.com/prometheus/procfs")
       (license asl2.0))))
 
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index eeae8bea41..6540a9feaf 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -128,9 +128,9 @@ configurable through a graphical wizard.")
                            (string-append "DESTDIR="
                                           (assoc-ref %outputs "out")))))
     (inputs
-     `(("vte", vte-ng)
-       ("gtk+", gtk+)
-       ("ncurses", ncurses)))
+     `(("vte" ,vte-ng)
+       ("gtk+" ,gtk+)
+       ("ncurses" ,ncurses)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
 
@@ -292,10 +292,10 @@ multi-seat support, a replacement for @command{mingetty}, and more.")
        #:phases (modify-phases %standard-phases
                   (delete 'configure))
        #:test-target "test"))
-    (inputs `(("ncurses", ncurses)))
-    (native-inputs `(("libtool", libtool)
+    (inputs `(("ncurses" ,ncurses)))
+    (native-inputs `(("libtool" ,libtool)
                      ("perl-test-harness" ,perl-test-harness)
-                     ("pkg-config", pkg-config)))
+                     ("pkg-config" ,pkg-config)))
     (synopsis "Keyboard entry processing library for terminal-based programs")
     (description
      "Libtermkey handles all the necessary logic to recognise special keys, UTF-8
@@ -692,7 +692,7 @@ terminal or piped input.")
              (delete-file "tests/test_input_output.py")
              #t)))))
     (propagated-inputs
-     `(("python-wcwidth", python-wcwidth)))
+     `(("python-wcwidth" ,python-wcwidth)))
     (native-inputs
      `(("python-pytest-runner" ,python-pytest-runner)
        ("python-pytest" ,python-pytest)))
@@ -762,7 +762,7 @@ than a terminal.")
              (invoke "nosetests" "-v"))))))
     (propagated-inputs
      `(("python-blessings" ,python-blessings)
-       ("python-wcwidth", python-wcwidth)))
+       ("python-wcwidth" ,python-wcwidth)))
     (native-inputs
      `(("python-mock" ,python-mock)
        ("python-pyte" ,python-pyte)
diff --git a/gnu/packages/terraform.scm b/gnu/packages/terraform.scm
new file mode 100644
index 0000000000..71b214ed0a
--- /dev/null
+++ b/gnu/packages/terraform.scm
@@ -0,0 +1,52 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages terraform)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system go)
+  #:use-module (gnu packages golang))
+
+(define-public terraform-docs
+  (package
+    (name "terraform-docs")
+    (version "0.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/segmentio/terraform-docs")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0xchpik32ab8m89s6jv671vswg8xhprfvh6s5md0zd36482d2nmm"))))
+    (build-system go-build-system)
+    (native-inputs
+     `(("go-github-com-hashicorp-hcl" ,go-github-com-hashicorp-hcl)
+       ("go-github-com-tj-docopt" ,go-github-com-tj-docopt)))
+    (arguments
+     '(#:import-path "github.com/segmentio/terraform-docs"))
+    (synopsis "Generate documentation from Terraform modules")
+    (description
+     "The @code{terraform-docs} utility can generate documentation describing
+the inputs and outputs for modules of the Terraform infrastructure management
+tool.  These can be shown, or written to a file in JSON or Markdown formats.")
+    (home-page "https://github.com/segmentio/terraform-docs")
+    (license license:expat)))
diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 764f4fff15..1416a00251 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
@@ -214,6 +214,7 @@ This package contains the binaries.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/dvips"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0fcy2hpapbj01ncpjj3v39yhr0jjxb6rm13qaxjjw66s3vydxls1"))))
@@ -244,6 +245,7 @@ This package contains the binaries.")
                                      %texlive-tag "/Master/texmf-dist/"
                                      "/fonts/map/dvips/tetex"))
                  (revision %texlive-revision)))
+           (file-name (string-append "dvips-font-maps-" version "-checkout"))
            (sha256
             (base32
              "100208pg7q6lj7swiq9p9287nn6b64bl62bnlaxpjni9y2kdrqy5"))))
@@ -255,10 +257,11 @@ This package contains the binaries.")
                                      %texlive-tag "/Master/texmf-dist/"
                                      "/fonts/enc/dvips/base"))
                  (revision %texlive-revision)))
+           (file-name (string-append "dvips-base-enc-" version "-checkout"))
            (sha256
             (base32
              "1xnf6ms0h87r55kxik4vicwr1907scj789lhqflqns8svvsli5iy"))))))
-    (home-page "http://www.ctan.org/pkg/dvips")
+    (home-page "https://www.ctan.org/pkg/dvips")
     (synopsis "DVI to PostScript drivers")
     (description "This package provides files needed for converting DVI files
 to PostScript.")
@@ -278,6 +281,7 @@ to PostScript.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/generic/unicode-data"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0ivrhp6jz31pl4z841g4ws41lmvdiwz4sslmhf02inlib79gz6r2"))))
@@ -292,7 +296,7 @@ to PostScript.")
              (mkdir-p target)
              (copy-recursively (assoc-ref %build-inputs "source") target)
              #t))))
-    (home-page "http://www.ctan.org/pkg/unicode-data")
+    (home-page "https://www.ctan.org/pkg/unicode-data")
     (synopsis "Unicode data and loaders for TeX")
     (description "This bundle provides generic access to Unicode Consortium
 data for TeX use.  It contains a set of text files provided by the Unicode
@@ -316,6 +320,7 @@ out to date by @code{unicode-letters.tex}. ")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/generic/dehyph-exptl"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1l9wgv99qq0ysvlxqpj4g8bl0dywbzra4g8m2kmpg2fb0i0hczap"))))
@@ -351,6 +356,7 @@ bundle.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/generic/tex-ini-files"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1wh42n1lmzcvi3g6mm31nm3yd5ha5bl260xqc444jg1m9fdp3wz5"))))
@@ -365,7 +371,7 @@ bundle.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://ctan.org/pkg/tex-ini-files")
+    (home-page "https://www.ctan.org/pkg/tex-ini-files")
     (synopsis "Files for creating TeX formats")
     (description "This bundle provides a collection of model \".ini\" files
 for creating TeX formats.  These files are commonly used to introduced
@@ -385,6 +391,7 @@ to adapt the plain e-TeX source file to work with XeTeX and LuaTeX.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/generic/hyph-utf8"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0ghizcz7ps16dzfqf66wwg5i181assc6qsm0g7g5dbmp909931vi"))))
@@ -399,7 +406,7 @@ to adapt the plain e-TeX source file to work with XeTeX and LuaTeX.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://ctan.org/pkg/hyph-utf8")
+    (home-page "https://ctan.org/pkg/hyph-utf8")
     (synopsis "Hyphenation patterns expressed in UTF-8")
     (description "Modern native UTF-8 engines such as XeTeX and LuaTeX need
 hyphenation patterns in UTF-8 format, whereas older systems require
@@ -441,6 +448,7 @@ converters, will completely supplant the older patterns.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/metafont"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1yl4n8cn5xqk2nc22zgzq6ymd7bhm6xx1mz3azip7i3ki4bhb5q5"))))
@@ -475,7 +483,7 @@ converters, will completely supplant the older patterns.")
                #t))))))
     (native-inputs
      `(("texlive-bin" ,texlive-bin)))
-    (home-page "http://www.ctan.org/pkg/metafont")
+    (home-page "https://www.ctan.org/pkg/metafont")
     (synopsis "Metafont base files")
     (description "This package provides the Metafont base files needed to
 build fonts using the Metafont system.")
@@ -492,7 +500,7 @@ build fonts using the Metafont system.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/map/fontname"))
                     (revision %texlive-revision)))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0cssbzcx15221dynp5sii72qh4l18mwkr14n8w1xb19j8pbaqasz"))))
@@ -526,6 +534,7 @@ documents.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/source/public/cm"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "045k5b9rdmbxpy1a3006l1x96z1rd18vg3cwrvnld9bqybw5qz44"))))
@@ -575,7 +584,7 @@ documents.")
     (native-inputs
      `(("texlive-bin" ,texlive-bin)
        ("texlive-metafont-base" ,texlive-metafont-base)))
-    (home-page "http://www.ctan.org/pkg/cm")
+    (home-page "https://www.ctan.org/pkg/cm")
     (synopsis "Computer Modern fonts for TeX")
     (description "This package provides the Computer Modern fonts by Donald
 Knuth.  The Computer Modern font family is a large collection of text,
@@ -594,6 +603,7 @@ display, and mathematical fonts in a range of styles, based on Monotype Modern
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/source/public/knuth-lib"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0in9aqyi8jkyf9d16z0li50z5fpwj1iwgwm83gmvwqcf7chfs04y"))))
@@ -657,6 +667,7 @@ fonts.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/source/public/latex-fonts"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0ypsm4xv9cw0jckk2qc7gi9hcmhf31mrg56pz3llyx3yd9vq2lps"))))
@@ -712,7 +723,7 @@ fonts.")
      `(("texlive-bin" ,texlive-bin)
        ("texlive-metafont-base" ,texlive-metafont-base)
        ("texlive-fonts-cm" ,texlive-fonts-cm)))
-    (home-page "http://www.ctan.org/pkg/latex-fonts")
+    (home-page "https://www.ctan.org/pkg/latex-fonts")
     (synopsis "Collection of fonts used in LaTeX distributions")
     (description "This is a collection of fonts for use with standard LaTeX
 packages and classes. It includes invisible fonts (for use with the slides
@@ -731,6 +742,7 @@ symbol fonts.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/source/public/amsfonts"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "07h20rvpbdb4k72hzmjkyb29426zr9wxsfp6yd4ajbbpd3vx8grb"))))
@@ -790,7 +802,7 @@ symbol fonts.")
      `(("texlive-fonts-cm" ,texlive-fonts-cm)
        ("texlive-metafont-base" ,texlive-metafont-base)
        ("texlive-bin" ,texlive-bin)))
-    (home-page "http://www.ctan.org/pkg/amsfonts")
+    (home-page "https://www.ctan.org/pkg/amsfonts")
     (synopsis "TeX fonts from the American Mathematical Society")
     (description
      "This package provides an extended set of fonts for use in mathematics,
@@ -812,6 +824,7 @@ details can be found in the documentation.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "amsfonts"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0slzfv5h2m03b2xvm2sasznz4azh6rgi069z161dja3l8rln79hm"))))
@@ -820,7 +833,7 @@ details can be found in the documentation.")
     (native-inputs
      `(("texlive-fonts-cm" ,texlive-fonts-cm)
        ("texlive-metafont-base" ,texlive-metafont-base)))
-    (home-page "http://www.ctan.org/pkg/amsfonts")
+    (home-page "https://www.ctan.org/pkg/amsfonts")
     (synopsis "TeX fonts from the American Mathematical Society")
     (description
      "This package provides basic LaTeX support for the symbol fonts provides
@@ -841,6 +854,7 @@ individual symbols defined in @code{amssymb.sty}.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/plain"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0mjgl3gscn3ps29yjambz1j9fg81ynnncb96vpprwx4xsijhsns0"))))
@@ -873,6 +887,11 @@ book).")
                                        %texlive-tag "/Master/texmf-dist/"
                                        dir))
                    (revision %texlive-revision)))
+             (file-name (string-append "texlive-generic-"
+                                       (last (string-split
+                                               (string-drop-right dir 1) #\/))
+                                       "-" (number->string %texlive-revision)
+                                       "-checkout"))
              (sha256 (base32 hash))))))
     (package
       (name "texlive-latex-base")
@@ -880,6 +899,7 @@ book).")
       (source (origin
                 (method svn-fetch)
                 (uri (texlive-ref "latex" "base"))
+                (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
                   "1h9pir2hz6i9avc4lrl733p3zf4rpkg8537x1zdbhs91hvhikw9k"))))
@@ -926,12 +946,10 @@ book).")
 
                (mkdir "build")
                (mkdir "web2c")
-               (and (zero? (system* "luatex" "-ini" "-interaction=batchmode"
-                                    "-output-directory=build"
-                                    "unpack.ins"))
-                    (zero? (system* "tex" "-ini" "-interaction=batchmode"
-                                    "-output-directory=web2c"
-                                    "tex.ini"))
+               (and (invoke "luatex" "-ini" "-interaction=batchmode"
+                            "-output-directory=build" "unpack.ins")
+                    (invoke "tex" "-ini" "-interaction=batchmode"
+                            "-output-directory=web2c" "tex.ini")
                     ;; LaTeX, pdfetex/pdftex, and XeTeX require e-TeX, which
                     ;; is enabled only in extended mode (activated with a
                     ;; leading asterisk).  We should not use luatex here,
@@ -939,25 +957,25 @@ book).")
                     ;; incompatible with any other TeX engine.
                     (every
                      (lambda (format)
-                       (zero? (system* "latex" "-ini" "-interaction=batchmode"
-                                       "-output-directory=web2c"
-                                       "-translate-file=cp227.tcx"
-                                       (string-append "*" format ".ini"))))
+                       (invoke "latex" "-ini" "-interaction=batchmode"
+                               "-output-directory=web2c"
+                               "-translate-file=cp227.tcx"
+                               (string-append "*" format ".ini")))
                      '("latex"
                        "pdflatex"
                        "pdfetex"))
                     (every
                      (lambda (format)
-                       (zero? (system* format "-ini" "-interaction=batchmode"
-                                       "-output-directory=web2c"
-                                       (string-append "*" format ".ini"))))
+                       (invoke format "-ini" "-interaction=batchmode"
+                               "-output-directory=web2c"
+                               (string-append "*" format ".ini")))
                      '("xetex"
                        "xelatex"))
                     (every
                      (lambda (format)
-                       (zero? (system* "luatex" "-ini" "-interaction=batchmode"
-                                       "-output-directory=web2c"
-                                       (string-append format ".ini"))))
+                       (invoke "luatex" "-ini" "-interaction=batchmode"
+                               "-output-directory=web2c"
+                               (string-append format ".ini")))
                      '("dviluatex" "dvilualatex" "luatex" "lualatex")))))
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
@@ -1003,7 +1021,7 @@ book).")
          ("texlive-fonts-cm" ,texlive-fonts-cm)
          ("texlive-fonts-latex" ,texlive-fonts-latex)
          ("texlive-fonts-knuth-lib" ,texlive-fonts-knuth-lib)))
-      (home-page "http://www.ctan.org/pkg/latex-base")
+      (home-page "https://www.ctan.org/pkg/latex-base")
       (synopsis "Base sources of LaTeX")
       (description
        "This bundle comprises the source of LaTeX itself, together with several
@@ -1019,12 +1037,13 @@ contain.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "filecontents"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0swkbxv8vg0yizadfnvrwjb4cj0pn34v9wm6v7wqq903fdav7k7q"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/filecontents"))
-    (home-page "http://www.ctan.org/pkg/filecontents")
+    (home-page "https://www.ctan.org/pkg/filecontents")
     (synopsis "Extended filecontents and filecontents* environments")
     (description
      "LaTeX2e's @code{filecontents} and @code{filecontents*} environments
@@ -1043,6 +1062,7 @@ overwrite existing files and letting you use @code{filecontents} /
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "generic" "ifxetex"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0w2xj7n0szavj329kds09q626szkc378p3w0sk022q0ln4ksz86d"))))
@@ -1052,7 +1072,7 @@ overwrite existing files and letting you use @code{filecontents} /
        #:tex-format "xelatex"))
     (inputs
      `(("texlive-latex-filecontents" ,texlive-latex-filecontents)))
-    (home-page "http://www.ctan.org/pkg/ifxetex")
+    (home-page "https://www.ctan.org/pkg/ifxetex")
     (synopsis "Am I running under XeTeX?")
     (description
      "This is a simple package which provides an @code{\\ifxetex} conditional,
@@ -1071,6 +1091,7 @@ requires the e-TeX extensions to the TeX primitive set.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/generic/epsf"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "14w3j81ympyvg8hkk9i1xgr8a0gfnfsb2ki8qqsk5pa051za1xcy"))))
@@ -1085,7 +1106,7 @@ requires the e-TeX extensions to the TeX primitive set.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/epsf")
+    (home-page "https://www.ctan.org/pkg/epsf")
     (synopsis "Simple macros for EPS inclusion")
     (description
      "This package provides the original (and now obsolescent) graphics
@@ -1103,6 +1124,7 @@ users, via its Plain TeX version.)")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "fancyvrb"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "03l7140y031rr14h02i4z9zqsfvrbn7wzwxbjsrjcgrk6sdr71wv"))))
@@ -1112,7 +1134,7 @@ users, via its Plain TeX version.)")
        ;; We exclude "fvrb-ex" to avoid a dependency on texlive-luaotfload and
        ;; thus texlive-luatex-lualibs.
        #:build-targets '("fancyvrb.ins")))
-    (home-page "http://www.ctan.org/pkg/fancyvrb")
+    (home-page "https://www.ctan.org/pkg/fancyvrb")
     (synopsis "Sophisticated verbatim text")
     (description
      "This package provides tools for the flexible handling of verbatim text
@@ -1130,6 +1152,7 @@ verbatim source).")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "graphics"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "07azyn0b1s49vbdlr6dmygrminxp72ndl24j1091hiiccvrjq3xc"))))
@@ -1162,6 +1185,9 @@ verbatim source).")
            (uri (git-reference
                  (url "https://github.com/latex3/graphics-cfg.git")
                  (commit "19d1238af17df376cd46333b229579b0f7f3a41f")))
+           (file-name (string-append "graphics-cfg-"
+                                     (number->string %texlive-revision)
+                                     "-checkout"))
            (sha256
             (base32
              "12kbgbm52gmmgn8zajb74s8n5rvnxcfdvs3iyj8vcw5vrsw5i6mh"))))
@@ -1173,10 +1199,13 @@ verbatim source).")
                                      %texlive-tag "/Master/texmf-dist/"
                                      "/tex/latex/graphics-def"))
                  (revision %texlive-revision)))
+           (file-name (string-append "graphics-def-"
+                                     (number->string %texlive-revision)
+                                     "-checkout"))
            (sha256
             (base32
              "0gi4qv6378nl84s8n1yx3hjqvv7r4lza7hpbymbl5rzwgw8qrnyb"))))))
-    (home-page "http://www.ctan.org/pkg/latex-graphics")
+    (home-page "https://www.ctan.org/pkg/latex-graphics")
     (synopsis "LaTeX standard graphics bundle")
     (description
      "This is a collection of LaTeX packages for producing color, including
@@ -1194,12 +1223,13 @@ keyval, and lscape.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "xcolor"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "01n613s7bcrd2n4jfawm0k4nn2ny3aaifp2jjfif3lz4sbv31494"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/xcolor"))
-    (home-page "http://www.ctan.org/pkg/xcolor")
+    (home-page "https://www.ctan.org/pkg/xcolor")
     (synopsis "Driver-independent color extensions for LaTeX and pdfLaTeX")
     (description
      "The package starts from the basic facilities of the colorcolor package,
@@ -1227,7 +1257,7 @@ tables.")
                 "1d3rmjgzh0025a1dza55zb6nzzlgd1y9snwx45wq1c1vf42m79h2"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/hyperref"))
-    (home-page "http://www.ctan.org/pkg/hyperref")
+    (home-page "https://www.ctan.org/pkg/hyperref")
     (synopsis "Extensive support for hypertext in LaTeX")
     (description
      "The @code{hyperref} package is used to handle cross-referencing commands
@@ -1247,6 +1277,7 @@ pdf and HTML backends.  The package is distributed with the @code{backref} and
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "oberdiek"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0aswvsxgsn709xmvpcg50d2xl7vcy1ckdxb9c1cligqqfjjvviqf"))))
@@ -1262,7 +1293,7 @@ pdf and HTML backends.  The package is distributed with the @code{backref} and
              (substitute* "oberdiek.ins"
                (("ifpdf.ins") "ifpdf.dtx"))
              #t)))))
-    (home-page "http://www.ctan.org/pkg/oberdiek")
+    (home-page "https://www.ctan.org/pkg/oberdiek")
     (synopsis "Bundle of packages submitted by Heiko Oberdiek")
     (description
      "The bundle comprises various LaTeX packages, providing among others:
@@ -1277,6 +1308,7 @@ arrows; record information about document class(es) used; and many more.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "tools"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "052a0pch2k5zls5jlay9xxcf93rw3i60a2x28y3ip3rhbsv3xgiz"))))
@@ -1284,7 +1316,7 @@ arrows; record information about document class(es) used; and many more.")
     (arguments
      '(#:tex-directory "latex/tools"
        #:build-targets '("tools.ins")))
-    (home-page "http://www.ctan.org/pkg/latex-tools")
+    (home-page "https://www.ctan.org/pkg/latex-tools")
     (synopsis "LaTeX standard tools bundle")
     (description
      "This package is a collection of (variously) simple tools provided as
@@ -1306,6 +1338,7 @@ xr, and xspace.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/latex/url"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "184s2543cwia5l7iibhlkl1ffbncfhjpv5p56zq0c15by5sghlac"))))
@@ -1341,13 +1374,14 @@ of file names.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "l3kernel"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0r0wfk594j8wkdqhh21haimwsfq8x5jch4ldm21hkzk5dnmvpbg6"))))
     (build-system texlive-build-system)
     (arguments
      '(#:tex-directory "latex/l3kernel"))
-    (home-page "http://www.ctan.org/pkg/l3kernel")
+    (home-page "https://www.ctan.org/pkg/l3kernel")
     (synopsis "LaTeX3 programmers’ interface")
     (description
      "The l3kernel bundle provides an implementation of the LaTeX3
@@ -1364,6 +1398,7 @@ that the LaTeX3 conventions can be used with regular LaTeX 2e packages.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "l3packages"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "16jplkvzdysfssijq9l051nsks65c2nrarsl17k8gjhc28yznj8y"))))
@@ -1386,7 +1421,7 @@ that the LaTeX3 conventions can be used with regular LaTeX 2e packages.")
              #t)))))
     (inputs
      `(("texlive-latex-l3kernel" ,texlive-latex-l3kernel)))
-    (home-page "http://www.ctan.org/pkg/l3packages")
+    (home-page "https://www.ctan.org/pkg/l3packages")
     (synopsis "High-level LaTeX3 concepts")
     (description
      "This bundle holds prototype implementations of concepts for a LaTeX
@@ -1411,6 +1446,7 @@ programming tools and kernel sup­port.  Packages provided in this release are:
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "fontspec"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1rx43y5xmjqvc27pjdnmqwp4pcw3czcfd6nfpmzc1gnqfl1hlc0q"))))
@@ -1420,7 +1456,7 @@ programming tools and kernel sup­port.  Packages provided in this release are:
        #:build-targets '("fontspec.dtx")))
     (inputs
      `(("texlive-latex-l3kernel" ,texlive-latex-l3kernel)))
-    (home-page "http://www.ctan.org/pkg/fontspec")
+    (home-page "https://www.ctan.org/pkg/fontspec")
     (synopsis "Advanced font selection in XeLaTeX and LuaLaTeX")
     (description
      "Fontspec is a package for XeLaTeX and LuaLaTeX.  It provides an
@@ -1441,6 +1477,7 @@ the l3kernel and xparse bundles from the LaTeX 3 development team.")
               (uri (string-append "https://github.com/lualatex/lualibs/"
                                   "releases/download/v"
                                   version "/lualibs.zip"))
+              (file-name (string-append name "-" version ".zip"))
               (sha256
                (base32
                 "1xx9blvrmx9hyhrl345lpai9m6xxnw997261a1ahn1bm5r2j5fqy"))))
@@ -1473,12 +1510,13 @@ this bundle for use independent of ConTeXt.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "amsmath"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "178ywjpdlv78qmfzqdyn6gy14620zjsn2q9wap76fbr9s4hw6dba"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/amsmath"))
-    (home-page "http://www.ctan.org/pkg/amsmath")
+    (home-page "https://www.ctan.org/pkg/amsmath")
     (synopsis "AMS mathematical facilities for LaTeX")
     (description
      "This is the principal package in the AMS-LaTeX distribution.  It adapts
@@ -1501,13 +1539,14 @@ definitions.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "amscls"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0jmcr37mcdi7drczppvr6lmz5d5yd9m67ii79gp2nglg1xpw934j"))))
     (build-system texlive-build-system)
     (arguments
      `(#:tex-directory "latex/amscls"))
-    (home-page "http://www.ctan.org/pkg/amscls")
+    (home-page "https://www.ctan.org/pkg/amscls")
     (synopsis "AMS document classes for LaTeX")
     (description
      "This bundle contains three AMS classes: @code{amsartamsart} (for writing
@@ -1524,6 +1563,7 @@ distribution.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "babel"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1n3i5adsyy7jw0imnzrm2i8wkf73i3mjk9h3ic8cb9cd19i4r9r3"))))
@@ -1539,7 +1579,7 @@ distribution.")
              (substitute* "babel.ins"
                (("askonceonly") "askforoverwritefalse"))
              #t)))))
-    (home-page "http://www.ctan.org/pkg/babel")
+    (home-page "https://www.ctan.org/pkg/babel")
     (synopsis "Multilingual support for Plain TeX or LaTeX")
     (description
      "The package manages culturally-determined typographical (and other)
@@ -1564,7 +1604,7 @@ polyglossia package rather than Babel.")
                 "1s404wbx91z5w65hm024kyl4h56zsa096irx18vsx8jvlmwsr5wc"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "generic/babel-english"))
-    (home-page "http://www.ctan.org/pkg/babel-english")
+    (home-page "https://www.ctan.org/pkg/babel-english")
     (synopsis "Babel support for English")
     (description
      "This package provides the language definition file for support of
@@ -1580,13 +1620,14 @@ for Canadian and USA text.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "cyrillic"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1mdhl35hwas68ki56qqngzar37dwv4mm64l2canihr255bz34lbv"))))
     (build-system texlive-build-system)
     (arguments
      '(#:tex-directory "latex/cyrillic"))
-    (home-page "http://www.ctan.org/pkg/latex-cyrillic")
+    (home-page "https://www.ctan.org/pkg/latex-cyrillic")
     (synopsis "Support for Cyrillic fonts in LaTeX")
     (description
      "This bundle of macros files provides macro support (including font
@@ -1602,12 +1643,13 @@ language that is written in a Cyrillic alphabet.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "psnfss"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1920dcq8613yzprasbg80fh4fcjcidvvl54wkx438nimyxcri7qz"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/psnfss"))
-    (home-page "http://www.ctan.org/pkg/psnfss")
+    (home-page "https://www.ctan.org/pkg/psnfss")
     (synopsis "Font support for common PostScript fonts")
     (description
      "The PSNFSS collection includes a set of files that provide a complete
@@ -1727,7 +1769,7 @@ It includes little more than the required set of LaTeX packages.")))
                 "15i4k479dwrpr0kspmm70g1yn4p3dkh0whyzmr93hph9bggnh1i1"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/amsrefs"))
-    (home-page "http://www.ctan.org/pkg/amsrefs")
+    (home-page "https://www.ctan.org/pkg/amsrefs")
     (synopsis "LaTeX-based replacement for BibTeX")
     (description
      "Amsrefs is a LaTeX package for bibliographies that provides an archival
@@ -1756,7 +1798,7 @@ conjunction with BibTeX or as a replacement for BibTeX.")
            (lambda _
              (for-each delete-file (find-files "." "\\.drv$"))
              #t)))))
-    (home-page "http://www.ctan.org/pkg/bigfoot")
+    (home-page "https://www.ctan.org/pkg/bigfoot")
     (synopsis "Footnotes for critical editions")
     (description
      "This package aims to provide a one-stop solution to requirements for
@@ -1784,7 +1826,7 @@ documentation.  The bigfoot bundle also provides the @code{perpage} and
                 "1jrja9b1pzdh9zgv1jh807w4xijqja58n2mqny6dkwicv8qfgbfg"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/blindtext"))
-    (home-page "http://www.ctan.org/pkg/blindtext")
+    (home-page "https://www.ctan.org/pkg/blindtext")
     (synopsis "Producing 'blind' text for testing")
     (description
      "The package provides the commands @code{\\blindtext} and
@@ -1816,7 +1858,7 @@ ipsum\" text, see the @code{lipsum} package).")
            (lambda _
              (delete-file "dinbrief.drv")
              #t)))))
-    (home-page "http://www.ctan.org/pkg/dinbrief")
+    (home-page "https://www.ctan.org/pkg/dinbrief")
     (synopsis "German letter DIN style")
     (description
      "This package implements a document layout for writing letters according
@@ -1842,7 +1884,7 @@ package.")
                 "1zyl2pcz2x529gzj5m93a1s4ipymdabf7qdjl3l1673pizd4hfyv"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/draftwatermark"))
-    (home-page "http://www.ctan.org/pkg/draftwatermark")
+    (home-page "https://www.ctan.org/pkg/draftwatermark")
     (synopsis "Put a grey textual watermark on document pages")
     (description
      "This package provides a means to add a textual, light grey watermark on
@@ -1866,7 +1908,7 @@ on everypage.")
                 "06h28b26dyjkj9shksphgqfv4130jfkwhbw737hxn7d3yvdfffyd"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/environ"))
-    (home-page "http://www.ctan.org/pkg/environ")
+    (home-page "https://www.ctan.org/pkg/environ")
     (synopsis "New interface for environments in LaTeX")
     (description
      "This package provides the @code{\\collect@@body} command (as in
@@ -1888,7 +1930,7 @@ define a new author interface to creating new environments.")
                 "0pvmhsd4xmpil0m3c7qcgwilbk266mlkzv03g0jr8r3zd8jxlyzq"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/eqparbox"))
-    (home-page "http://www.ctan.org/pkg/eqparbox")
+    (home-page "https://www.ctan.org/pkg/eqparbox")
     (synopsis "Create equal-widthed parboxes")
     (description
      "LaTeX users sometimes need to ensure that two or more blocks of text
@@ -1924,7 +1966,7 @@ also provided.")
              (for-each delete-file
                        (find-files "." "\\.drv$"))
              #t)))))
-    (home-page "http://www.ctan.org/pkg/expdlist")
+    (home-page "https://www.ctan.org/pkg/expdlist")
     (synopsis "Expanded description environments")
     (description
      "The package provides additional features for the LaTeX
@@ -1945,6 +1987,7 @@ without affecting the structure of the list (this works for @code{itemize} and
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/latex/filemod"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0vpxilfw69xv78f03g0j0zw0bw4qcn36whqp8phcq48qk1ax2kr2"))))
@@ -1959,7 +2002,7 @@ without affecting the structure of the list (this works for @code{itemize} and
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/filemod")
+    (home-page "https://www.ctan.org/pkg/filemod")
     (synopsis "Provide file modification times, and compare them")
     (description
      "This package provides macros to read and compare the modification dates
@@ -1985,7 +2028,7 @@ but non-expandable ones.")
                 "11gvvjvmdfs9b7mm19yf80zwkx49jqcbq6g8qb9y5ns1r1qvnixp"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/ifplatform"))
-    (home-page "http://www.ctan.org/pkg/ifplatform")
+    (home-page "https://www.ctan.org/pkg/ifplatform")
     (synopsis "Conditionals to test which platform is being used")
     (description
      "This package uses the (La)TeX extension @code{-shell-escape} to
@@ -2004,12 +2047,13 @@ classes of systems.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "natbib"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0aqliq0nwblxyrzhwhv77pnmk7qh2y3prgq7z7qhwcbgz5kisld7"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/natbib"))
-    (home-page "http://www.ctan.org/pkg/natbib")
+    (home-page "https://www.ctan.org/pkg/natbib")
     (synopsis "Flexible bibliography support")
     (description
      "This bundle provides a package that implements both author-year and
@@ -2033,7 +2077,7 @@ designed from the start to be compatible with @code{natbib}.")
                 "1dxbl5il7wbbsp0v45vk884xi1192wxw03849pb1g5q4x808n352"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/psfrag"))
-    (home-page "http://www.ctan.org/pkg/psfrag")
+    (home-page "https://www.ctan.org/pkg/psfrag")
     (synopsis "Replace strings in encapsulated PostScript figures")
     (description
      "This package allows LaTeX constructions (equations, picture
@@ -2071,7 +2115,7 @@ rotated.")
        ("texlive-latex-oberdiek" ,texlive-latex-oberdiek)
        ("texlive-latex-psfrag" ,texlive-latex-psfrag)
        ("texlive-latex-trimspaces" ,texlive-latex-trimspaces)))
-    (home-page "http://www.ctan.org/pkg/pstool")
+    (home-page "https://www.ctan.org/pkg/pstool")
     (synopsis "Process PostScript graphisc within pdfLaTeX documents")
     (description
      "This is a package for processing PostScript graphics with @code{psfrag}
@@ -2091,12 +2135,13 @@ re-processing.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/latex/seminar"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0y4i651b75y6006n03x8n86bsqvjsailvvz9bhzy51dzsznqidq0"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/seminar"))
-    (home-page "http://www.ctan.org/pkg/seminar")
+    (home-page "https://www.ctan.org/pkg/seminar")
     (synopsis "Make overhead slides")
     ;; TODO: This package may need fancybox and xcomment at runtime.
     (description
@@ -2114,6 +2159,7 @@ recent classes such as powerdot or beamer, both of which are tuned to
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "trimspaces"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0da00lb32am4g63mn96625wg48p3pj3spx79lajrk17d549apwqa"))))
@@ -2131,7 +2177,7 @@ recent classes such as powerdot or beamer, both of which are tuned to
              #t)))))
     (inputs
      `(("texlive-latex-filecontents" ,texlive-latex-filecontents)))
-    (home-page "http://www.ctan.org/pkg/trimspaces")
+    (home-page "https://www.ctan.org/pkg/trimspaces")
     (synopsis "Trim spaces around an argument or within a macro")
     (description
      "This very short package allows you to expandably remove spaces around a
@@ -2166,7 +2212,7 @@ space-stripped macros.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/capt-of")
+    (home-page "https://www.ctan.org/pkg/capt-of")
     (synopsis "Captions on more than floats")
     (description
      "This package defines a command @code{\\captionof} for putting a caption
@@ -2199,7 +2245,7 @@ to something that's not a float.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/etoolbox")
+    (home-page "https://www.ctan.org/pkg/etoolbox")
     (synopsis "e-TeX tools for LaTeX")
     (description
      "This package is a toolbox of programming facilities geared primarily
@@ -2237,7 +2283,7 @@ of the LaTeX kernel.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/fncychap")
+    (home-page "https://www.ctan.org/pkg/fncychap")
     (synopsis "Seven predefined chapter heading styles")
     (description
      "This package provides seven predefined chapter heading styles.  Each
@@ -2272,7 +2318,7 @@ headings.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/framed")
+    (home-page "https://www.ctan.org/pkg/framed")
     (synopsis "Framed or shaded regions that can break across pages")
     (description
      "The package creates three environments: @code{framed}, which puts an
@@ -2306,7 +2352,7 @@ course of the framed/shaded matter.  There is also a command
            (lambda _
              (delete-file "g-brief.drv")
              #t)))))
-    (home-page "http://www.ctan.org/pkg/g-brief")
+    (home-page "https://www.ctan.org/pkg/g-brief")
     (synopsis "Letter document class")
     (description
      "This package is designed for formatting formless letters in German; it
@@ -2328,7 +2374,7 @@ are LaTeX 2.09 @code{documentstyle} and LaTeX 2e class files for both an
                 "0d4l0msk8j5pi95xnmm9wygv1vbpkwkv5amx9l0km86cs79jpp1h"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/galois"))
-    (home-page "http://www.ctan.org/pkg/galois")
+    (home-page "https://www.ctan.org/pkg/galois")
     (synopsis "Typeset Galois connections")
     (description
      "The package deals with connections in two-dimensional style, optionally
@@ -2348,7 +2394,7 @@ in colour.")
                 "03g9by54yrypn599y98r1xh7qw0bbbmpzq0bfwpj6j5q5rkl1mfa"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/gcite"))
-    (home-page "http://www.ctan.org/pkg/gcite")
+    (home-page "https://www.ctan.org/pkg/gcite")
     (synopsis "Citations in a reader-friendly style")
     (description
      "The package allows citations in the German style, which is considered by
@@ -2372,7 +2418,7 @@ BibLaTeX, and is considered experimental.")
                 "1r2kfcwclg33yk5z8mvlagwxj7nr1mc3w4bdpmhrwv6dn8mrbvw8"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/geometry"))
-    (home-page "http://www.ctan.org/pkg/geometry")
+    (home-page "https://www.ctan.org/pkg/geometry")
     (synopsis "Flexible and complete interface to document dimensions")
     (description
      "This package provides an easy and flexible user interface to customize
@@ -2397,7 +2443,7 @@ ability to communicate the paper size it's set up to the output.")
                 "0caxs74hla28hc67csf5i5ahadx97w8vxh3mdmsprxbpd1mr7ssg"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/mdwtools"))
-    (home-page "http://www.ctan.org/pkg/mdwtools")
+    (home-page "https://www.ctan.org/pkg/mdwtools")
     (synopsis "Miscellaneous tools by Mark Wooding")
     (description
      "This collection of tools includes: @code{atsupport} for short commands
@@ -2421,7 +2467,7 @@ array environments; verbatim handling; and syntax diagrams.")
                 "09mvszd5qgqg4cfglpj5qxyzjz190ppb9p8gnsnjydwp1akvhayf"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/polyglossia"))
-    (home-page "http://www.ctan.org/pkg/polyglossia")
+    (home-page "https://www.ctan.org/pkg/polyglossia")
     (synopsis "Alternative to babel for XeLaTeX and LuaLaTeX")
     (description
      "This package provides a complete Babel replacement for users of LuaLaTeX
@@ -2441,7 +2487,7 @@ and XeLaTeX; it relies on the @code{fontspec} package, version 2.0 at least.")
                 "14b2bc7cqz4ckxxycim9sw6jkrr1pahivm1rdbpz5k6hl967w1s3"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/supertabular"))
-    (home-page "http://www.ctan.org/pkg/supertabular")
+    (home-page "https://www.ctan.org/pkg/supertabular")
     (synopsis "Multi-page tables package")
     (description
      "This package was a predecessor of @code{longtable}; the newer
@@ -2461,6 +2507,7 @@ situations where longtable has problems.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/texinfo"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "09zj2w3lx0y6i2syfjjgizahf86z301dw8p37ln6syfhqhzqdz46"))))
@@ -2475,7 +2522,7 @@ situations where longtable has problems.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/texinfo")
+    (home-page "https://www.ctan.org/pkg/texinfo")
     (synopsis "TeX macros to handle Texinfo files")
     (description
      "Texinfo is the preferred format for documentation in the GNU project;
@@ -2498,7 +2545,7 @@ hypertext linkages in some cases).")
                 "0d1050i973wnxigy0xpky5l7vn4ff7ldhkjpdqsw5s653gagwixp"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/upquote"))
-    (home-page "http://www.ctan.org/pkg/upquote")
+    (home-page "https://www.ctan.org/pkg/upquote")
     (synopsis "Show \"realistic\" quotes in verbatim")
     (description
      "Typewriter-style fonts are best for program listings, but Computer
@@ -2524,6 +2571,7 @@ does not affect @code{\\tt}, @code{\\texttt}, etc.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/latex/anysize"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "19khwqjlvznc955sijhww3c4zbb0053rvzwv9nz738qknq7y18vb"))))
@@ -2538,7 +2586,7 @@ does not affect @code{\\tt}, @code{\\texttt}, etc.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/anysize")
+    (home-page "https://www.ctan.org/pkg/anysize")
     (synopsis "Simple package to set up document margins")
     (description
      "This is a simple package to set up document margins.  This package is
@@ -2553,12 +2601,13 @@ considered obsolete; alternatives are the @code{typearea} package from the
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "appendix"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0rxfpr8vq3brwx5rc7qn91ixlp9zva4zrms8a579fqa1g5yva7vg"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/appendix"))
-    (home-page "http://www.ctan.org/pkg/appendix")
+    (home-page "https://www.ctan.org/pkg/appendix")
     (synopsis "Extra control of appendices")
     (description
      "The appendix package provides various ways of formatting the titles of
@@ -2575,12 +2624,13 @@ command.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "changebar"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1ik4m8pzfsn1grlda6fniqqfwmgj7rfxwg63jdw0p0qv002vc7ik"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/changebar"))
-    (home-page "http://www.ctan.org/pkg/changebar")
+    (home-page "https://www.ctan.org/pkg/changebar")
     (synopsis "Generate changebars in LaTeX documents")
     (description
      "Identify areas of text to be marked with changebars with the
@@ -2631,12 +2681,13 @@ copy-and-paste functions work properly.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "colortbl"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "190pmq8la2rq07xry8bn8z8yywzxv6fqyqaj7yjfj5rgw6x0mas8"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/colortbl"))
-    (home-page "http://www.ctan.org/pkg/colortbl")
+    (home-page "https://www.ctan.org/pkg/colortbl")
     (synopsis "Add colour to LaTeX tables")
     (description
      "This package allows rows, columns, and even individual cells in LaTeX
@@ -2654,6 +2705,7 @@ tables to be coloured.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/latex/fancybox"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0smmnaad2q8qwicay1frri990lv65l0k8cwzsvdsyp3jk8kp042w"))))
@@ -2668,7 +2720,7 @@ tables to be coloured.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/fancybox")
+    (home-page "https://www.ctan.org/pkg/fancybox")
     (synopsis "Variants of \\fbox and other games with boxes")
     (description
      "This package provides variants of @code{\\fbox}: @code{\\shadowbox},
@@ -2688,6 +2740,7 @@ floats, center, flushleft, and flushright, lists, and pages.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/latex/fancyhdr"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "04h430agf8aj7ziwyb46xpk95c605rjk1wzhr63m6ylipihidlgw"))))
@@ -2702,7 +2755,7 @@ floats, center, flushleft, and flushright, lists, and pages.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/fancyhdr")
+    (home-page "https://www.ctan.org/pkg/fancyhdr")
     (synopsis "Extensive control of page headers and footers in LaTeX2e")
     (description
      "The package provides extensive facilities, both for constructing headers
@@ -2717,12 +2770,13 @@ would automatically change the heading style in use).")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "float"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0nbl7wylkv22fcdv4p8byhhj575fli6jnqjpkhrkbv8dzwah84nq"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/float"))
-    (home-page "http://www.ctan.org/pkg/float")
+    (home-page "https://www.ctan.org/pkg/float")
     (synopsis "Improved interface for floating objects")
     (description
      "This package improves the interface for defining floating objects such
@@ -2740,12 +2794,13 @@ with @code{\\floatplacement{figure}{H}}.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "footmisc"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "03x61wwql8nh6zrqiiiq3rb0x7m3pn48c606zapy19y21fybwdxs"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/footmisc"))
-    (home-page "http://www.ctan.org/pkg/footmisc")
+    (home-page "https://www.ctan.org/pkg/footmisc")
     (synopsis "Range of footnote options")
     (description
      "This is a collection of ways to change the typesetting of footnotes.
@@ -2763,6 +2818,7 @@ footnotes with symbols rather than numbers.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "listings"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1nsn9wp3wl12b36c0sqrim33lf33cr5wky0h4ncnw8lvqgm7h8wf"))))
@@ -2770,7 +2826,7 @@ footnotes with symbols rather than numbers.")
     (arguments
      '(#:tex-directory "latex/listings"
        #:build-targets '("listings.ins")))
-    (home-page "http://www.ctan.org/pkg/listings")
+    (home-page "https://www.ctan.org/pkg/listings")
     (synopsis "Typeset source code listings using LaTeX")
     (description
      "The package enables the user to typeset programs (programming code)
@@ -2790,6 +2846,7 @@ styles.  Support for @code{hyperref} is provided.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/latex/jknapltx"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0m034x72f2g07icr50gacyxfb9g1lz2rmqh4kqr1qjb421x2kds9"))))
@@ -2804,7 +2861,7 @@ styles.  Support for @code{hyperref} is provided.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/jknappen")
+    (home-page "https://www.ctan.org/pkg/jknappen")
     (synopsis "Miscellaneous packages by Joerg Knappen")
     (description
      "This package provides miscellaneous macros by Joerg Knappen, including:
@@ -2828,6 +2885,7 @@ in SGML; use maths minus in text as appropriate; simple Young tableaux.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/source/jknappen/ec/"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "12av65fbz9xiashm09c9m1fj1mijxls5xspd7652ry1n5s0nixy4"))))
@@ -2855,13 +2913,13 @@ in SGML; use maths minus in text as appropriate; simple Young tableaux.")
              (mkdir "build")
              (every (lambda (font)
                       (format #t "building font ~a\n" font)
-                      (zero? (system* "mf" "-progname=mf"
-                                      "-output-directory=build"
-                                      (string-append "\\"
-                                                     "mode:=ljfour; "
-                                                     "mag:=1; "
-                                                     "batchmode; "
-                                                     "input " (basename font ".mf")))))
+                      (invoke "mf" "-progname=mf"
+                              "-output-directory=build"
+                              (string-append "\\"
+                                             "mode:=ljfour; "
+                                             "mag:=1; "
+                                             "batchmode; "
+                                             "input " (basename font ".mf"))))
                     (find-files "." "[0-9]+\\.mf$"))))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
@@ -2879,7 +2937,7 @@ in SGML; use maths minus in text as appropriate; simple Young tableaux.")
      `(("texlive-bin" ,texlive-bin)
        ("texlive-metafont-base" ,texlive-metafont-base)
        ("texlive-fonts-cm" ,texlive-fonts-cm)))
-    (home-page "http://www.ctan.org/pkg/ec")
+    (home-page "https://www.ctan.org/pkg/ec")
     (synopsis "Computer modern fonts in T1 and TS1 encodings")
     (description
      "The EC fonts are European Computer Modern Fonts, supporting the complete
@@ -2909,6 +2967,7 @@ texlive-2017.1/Master/texmf-dist/doc/fonts/ec/copyrite.txt"))))
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/source/public/rsfs/"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0r12pn02r4a955prcvq0048nifh86ihlcgvw3pppqqvfngv34l5h"))))
@@ -2936,13 +2995,13 @@ texlive-2017.1/Master/texmf-dist/doc/fonts/ec/copyrite.txt"))))
              (mkdir "build")
              (every (lambda (font)
                       (format #t "building font ~a\n" font)
-                      (zero? (system* "mf" "-progname=mf"
-                                      "-output-directory=build"
-                                      (string-append "\\"
-                                                     "mode:=ljfour; "
-                                                     "mag:=1; "
-                                                     "batchmode; "
-                                                     "input " (basename font ".mf")))))
+                      (invoke "mf" "-progname=mf"
+                              "-output-directory=build"
+                              (string-append "\\"
+                                             "mode:=ljfour; "
+                                             "mag:=1; "
+                                             "batchmode; "
+                                             "input " (basename font ".mf"))))
                     (find-files "." "[0-9]+\\.mf$"))))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
@@ -2960,7 +3019,7 @@ texlive-2017.1/Master/texmf-dist/doc/fonts/ec/copyrite.txt"))))
      `(("texlive-bin" ,texlive-bin)
        ("texlive-metafont-base" ,texlive-metafont-base)
        ("texlive-fonts-cm" ,texlive-fonts-cm)))
-    (home-page "http://www.ctan.org/pkg/rsfs")
+    (home-page "https://www.ctan.org/pkg/rsfs")
     (synopsis "Ralph Smith's Formal Script font")
     (description
      "The fonts provide uppercase formal script letters for use as symbols in
@@ -2978,12 +3037,13 @@ one of the packages @code{calrsfs} and @code{mathrsfs}.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "eso-pic"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1xvmms28mvvfpks9x7lfya2xhh5k8jy3qnlih1mzcnf156xnb89z"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/eso-pic"))
-    (home-page "http://www.ctan.org/pkg/eso-pic")
+    (home-page "https://www.ctan.org/pkg/eso-pic")
     (synopsis "Add picture commands (or backgrounds) to every page")
     (description
      "The package adds one or more user commands to LaTeX's @code{shipout}
@@ -3002,6 +3062,7 @@ routine, which may be used to place the output at fixed positions.  The
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/latex/eepic"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1c68gvh021pvybg07apsd2xhq2ljbg80kq94wh71drdga3c2zqjw"))))
@@ -3016,7 +3077,7 @@ routine, which may be used to place the output at fixed positions.  The
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/eepic")
+    (home-page "https://www.ctan.org/pkg/eepic")
     (synopsis "Extensions to epic and the LaTeX drawing tools")
     (description
      "Extensions to @code{epic} and the LaTeX picture drawing environment,
@@ -3053,7 +3114,7 @@ splines, and filled circles and ellipses.  The package uses @code{tpic}
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/enumitem")
+    (home-page "https://www.ctan.org/pkg/enumitem")
     (synopsis "Customize basic list environments")
     (description
      "This package is intended to ease customizing the three basic list
@@ -3070,12 +3131,13 @@ in the form @code{key=value} are available, for example:
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "multirow"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0qlxy47f1f8plgch3jqfsnrdgpyz20sz46yp33i2jwvf9hvfczf0"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/multirow"))
-    (home-page "http://www.ctan.org/pkg/multirow")
+    (home-page "https://www.ctan.org/pkg/multirow")
     (synopsis "Create tabular cells spanning multiple rows")
     (description
      "The package provides tools for creating tabular cells spanning multiple
@@ -3094,6 +3156,7 @@ entry at the \"natural\" width of its text.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/latex/overpic"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0m29q9qdb00558b7g2i7iw6w62n5s46yx81j8m99qkv77magk4fm"))))
@@ -3108,7 +3171,7 @@ entry at the \"natural\" width of its text.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/overpic")
+    (home-page "https://www.ctan.org/pkg/overpic")
     (synopsis "Combine LaTeX commands over included graphics")
     (description
      "The @code{overpic} environment is a cross between the LaTeX
@@ -3144,7 +3207,7 @@ positions; a grid for orientation is available.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/parskip")
+    (home-page "https://www.ctan.org/pkg/parskip")
     (synopsis "Layout with zero \\parindent, non-zero \\parskip")
     (description
      "Simply changing @code{\\parskip} and @code{\\parindent} leaves a layout
@@ -3159,12 +3222,13 @@ designed class) helps alleviate this untidiness.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "pdfpages"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "06p5smfq66559ppdnmkl3hp8534x84ywbscimsiir4gllpya3i9h"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/pdfpages"))
-    (home-page "http://www.ctan.org/pkg/pdfpages")
+    (home-page "https://www.ctan.org/pkg/pdfpages")
     (synopsis "Include PDF documents in LaTeX")
     (description
      "This package simplifies the inclusion of external multi-page PDF
@@ -3182,6 +3246,7 @@ use this package to insert PostScript files, in addition to PDF files.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "fonts" "stmaryrd"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "08pn4ca3vl6qm9l3wm5h5iyjsrg411kkm1yana329xwg2j14s9n6"))))
@@ -3197,7 +3262,7 @@ use this package to insert PostScript files, in addition to PDF files.")
                (("fontdef\\}\\}" line)
                 (string-append line "\n\\endbatchfile")))
              #t)))))
-    (home-page "http://www.ctan.org/pkg/stmaryrd")
+    (home-page "https://www.ctan.org/pkg/stmaryrd")
     (synopsis "St Mary Road symbols for theoretical computer science")
     (description
      "The fonts were originally distributed as Metafont sources only, but
@@ -3214,12 +3279,13 @@ the whole font.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "subfigure"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "15spcl5wb7w269qd6y596vp4yi8sa5ppcx8w4z2i9kyp02r3a0yb"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/subfigure"))
-    (home-page "http://www.ctan.org/pkg/subfigure")
+    (home-page "https://www.ctan.org/pkg/subfigure")
     (synopsis "Figures divided into subfigures")
     (description
      "This (deprecated) package provides support for the manipulation and
@@ -3246,7 +3312,7 @@ the more recent @code{subcaption} package more satisfactory.")
                 "1adkdx2zkk42g82nqf57lv1nc1z7kwl13jmy8vpcsizsa0xdnx9n"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/tabulary"))
-    (home-page "http://www.ctan.org/pkg/tabulary")
+    (home-page "https://www.ctan.org/pkg/tabulary")
     (synopsis "Tabular with variable width columns balanced")
     (description
      "The package defines a @code{tabular*}-like environment, @code{tabulary},
@@ -3269,6 +3335,7 @@ according to the natural width of the widest cell in the column.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/latex/threeparttable"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "10vy9k150w2lviw8h22s2mcykff38xci653m5823s2vv44pwbmzq"))))
@@ -3283,7 +3350,7 @@ according to the natural width of the widest cell in the column.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/threeparttable")
+    (home-page "https://www.ctan.org/pkg/threeparttable")
     (synopsis "Tables with captions and notes all the same width")
     (description
      "This package facilitates tables with titles (captions) and notes.  The
@@ -3406,7 +3473,7 @@ environment.")
            (sha256
             (base32
              "1bal5fhw0xlhl37ayv8vlnqnsn1y82kadzfjhbgr223blspp4zsj"))))))
-    (home-page "http://www.ctan.org/pkg/threeparttable")
+    (home-page "https://www.ctan.org/pkg/threeparttable")
     (synopsis "Times-like fonts in support of mathematics")
     (description
      "Txfonts supplies virtual text roman fonts using Adobe Times (or URW
@@ -3476,6 +3543,7 @@ of ink traps which typify the Kurier font.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/latex/titlesec"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "04nmkhqx6jxcxx9a30zbcd5smxi5fd0cbp132bki7fnvhspnhg21"))))
@@ -3490,7 +3558,7 @@ of ink traps which typify the Kurier font.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/titlesec")
+    (home-page "https://www.ctan.org/pkg/titlesec")
     (synopsis "Select alternative section titles")
     (description
      "This package provides an interface to sectioning commands for selection
@@ -3513,7 +3581,7 @@ floats in a page.  You may assign headers/footers to individual floats, too.")
                 "1lvxrqfwcwa4p31zyfm80gr05v8c28xybv5ri79zi2ngz6834z12"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/type1cm"))
-    (home-page "http://www.ctan.org/pkg/type1cm")
+    (home-page "https://www.ctan.org/pkg/type1cm")
     (synopsis "Arbitrary size font selection in LaTeX")
     (description
      "LaTeX, by default, restricts the sizes at which you can use its default
@@ -3523,7 +3591,7 @@ this is particularly useful when using scalable versions of the CM
 fonts (Bakoma, or the versions from BSR/Y&Y, or True Type versions from Kinch,
 PCTeX, etc.).  In fact, since modern distributions will automatically generate
 any bitmap font you might need, @code{type1cm} has wider application than just
-those using scaleable versions of the fonts.  Note that the LaTeX distribution
+those using scalable versions of the fonts.  Note that the LaTeX distribution
 now contains a package @code{fix-cm},f which performs the task of
 @code{type1cm}, as well as doing the same job for T1- and TS1-encoded
 @code{ec} fonts.")
@@ -3536,12 +3604,13 @@ now contains a package @code{fix-cm},f which performs the task of
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "lh"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "00gdiwh3sfhh1iimjhpja7lm7k4vzqzql2irgwnpz94qvh25zwi5"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/lh"))
-    (home-page "http://www.ctan.org/pkg/lh")
+    (home-page "https://www.ctan.org/pkg/lh")
     (synopsis "Cyrillic fonts that support LaTeX standard encodings")
     (description
      "The LH fonts address the problem of the wide variety of alphabets that
@@ -3566,6 +3635,7 @@ OT2 encoded fonts, CM bright shaped fonts and Concrete shaped fonts.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/metapost"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "03nvjddffiz796wll6axzmgfvynyciy2mqamv20qx252w71vwkwd"))))
@@ -3580,7 +3650,7 @@ OT2 encoded fonts, CM bright shaped fonts and Concrete shaped fonts.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/metapost")
+    (home-page "https://www.ctan.org/pkg/metapost")
     (synopsis "Create scalable illustrations")
     (description
      "MetaPost uses a language based on that of Metafont to produce precise
@@ -3601,7 +3671,7 @@ than the bitmaps Metafont creates.")
               (file-name (string-append name "-" version "-checkout"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/acmart"))
-    (home-page "http://www.ctan.org/pkg/acmart")
+    (home-page "https://www.ctan.org/pkg/acmart")
     (synopsis "Class for typesetting publications of ACM")
     (description
      "This package provides a class for typesetting publications of the
@@ -3634,7 +3704,7 @@ Association for Computing Machinery (ACM).")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/varwidth")
+    (home-page "https://www.ctan.org/pkg/varwidth")
     (synopsis "Variable-width minipage")
     (description
      "The @code{varwidth} environment is superficially similar to
@@ -3649,12 +3719,13 @@ get a narrower “natural” width.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "wasysym"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1sgwbfwjjf70g54hh93gsd9jp9nm67w6n74x9d72a56n07jbk5hv"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/wasysym"))
-    (home-page "http://www.ctan.org/pkg/wasysym")
+    (home-page "https://www.ctan.org/pkg/wasysym")
     (synopsis "LaTeX support file to use the WASY2 fonts")
     (description
      "The wasy2WASY2 (Waldi Symbol) font by Roland Waldi provides many glyphs
@@ -3689,7 +3760,7 @@ to use interface for these symbols.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/wrapfig")
+    (home-page "https://www.ctan.org/pkg/wrapfig")
     (synopsis "Produces figures which text can flow around")
     (description
      "This package allows figures or tables to have text wrapped around them.
@@ -3723,7 +3794,7 @@ It does not work in combination with list environments, but can be used in a
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/ucs")
+    (home-page "https://www.ctan.org/pkg/ucs")
     (synopsis "Extended UTF-8 input encoding support for LaTeX")
     (description
      "The bundle provides the @code{ucs} package, and @code{utf8x.def},
@@ -3757,7 +3828,7 @@ package of that name now exists.")
            (lambda _
              (delete-file "preview.drv")
              #t)))))
-    (home-page "http://www.ctan.org/pkg/preview")
+    (home-page "https://www.ctan.org/pkg/preview")
     (synopsis "Extract bits of a LaTeX source for output")
     (description
      "The main purpose of the preview package is the extraction of selected
@@ -3782,7 +3853,7 @@ files.")
                 "0jmasg40bk53zdd2jc8nc18jvdai3p2wmamy7hwli8gls4nf25qp"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/acronym"))
-    (home-page "http://www.ctan.org/pkg/acronym")
+    (home-page "https://www.ctan.org/pkg/acronym")
     (synopsis "Expand acronyms at least once")
     (description
      "This package ensures that all acronyms used in the text are spelled out
@@ -3803,6 +3874,7 @@ e-TeX.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/generic/pdftex"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0k68zmqzs4qvrqxdwsrawbjb14hxqjfamq649azvai0jjxdpkljd"))))
@@ -3817,7 +3889,7 @@ e-TeX.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/pdftex")
+    (home-page "https://www.ctan.org/pkg/pdftex")
     (synopsis "TeX extension for direct creation of PDF")
     (description
      "This package provides an extension of TeX which can be configured to
diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm
index f1ccab9af9..cbf077cea3 100644
--- a/gnu/packages/text-editors.scm
+++ b/gnu/packages/text-editors.scm
@@ -81,10 +81,10 @@
      (list (search-path-specification
             (variable "VIS_PATH")
             (files '("share/vis")))))
-    (inputs `(("lua", lua)
-              ("ncurses", ncurses)
-              ("libtermkey", libtermkey)
-              ("lua-lpeg", lua-lpeg)
+    (inputs `(("lua" ,lua)
+              ("ncurses" ,ncurses)
+              ("libtermkey" ,libtermkey)
+              ("lua-lpeg" ,lua-lpeg)
               ("tre" ,tre)))
     (synopsis "Vim-like text editor")
     (description
diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index d75ba7766e..2d8a104d54 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -632,6 +632,7 @@ source code.")
          (uri (git-reference
                (url "https://github.com/aflc/editdistance.git")
                (commit commit)))
+         (file-name (git-file-name name version))
          (sha256
           (base32
            "1l43svsv12crvzphrgi6x435z6xg8m086c64armp8wzb4l8ccm7g"))))
@@ -643,7 +644,7 @@ source code.")
              (lambda _
                (with-directory-excursion "editdistance"
                  (delete-file "bycython.cpp")
-                 (zero? (system* "cython" "--cplus" "bycython.pyx"))))))))
+                 (invoke "cython" "--cplus" "bycython.pyx")))))))
       (native-inputs
        `(("python-cython" ,python-cython)))
       (home-page "https://www.github.com/aflc/editdistance")
diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index 59414f6d7c..c7a285079c 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2013, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2015 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2015, 2017 Cyril Roelandt <tipecaml@gmail.com>
 ;;; Copyright © 2016 Sou Bunnbu <iyzsong@gmail.com>
@@ -43,7 +43,7 @@
 (define-public time
   (package
     (name "time")
-    (version "1.8")
+    (version "1.9")
     (source
      (origin
       (method url-fetch)
@@ -51,7 +51,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "06rfg8dn0q2r8pdq8i6brrs6rqrsgvkwbbl4kfx3a6lnal0m8bwa"))))
+        "07jj7cz6lc13iqrpgn81ivqh8rkm73p4rnivwgrrshk23v4g1b7v"))))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/time/")
     (synopsis "Run a command, then display its resource usage")
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 45f5255665..bd86b2e0d9 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -512,13 +512,13 @@ netcat implementation that supports TLS.")
   (package
     (name "python-acme")
     ;; Remember to update the hash of certbot when updating python-acme.
-    (version "0.21.1")
+    (version "0.22.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "acme" version))
               (sha256
                (base32
-                "02x6f37ddldaxrxzh2wjw8wmzqchxb7gl5i4i4daysas9yzqlvi9"))))
+                "1s2zamyb99zdyga3c75xxgnj0z2hixw8wv24v1l4p49fncnxab2a"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -567,7 +567,7 @@ netcat implementation that supports TLS.")
               (uri (pypi-uri name version))
               (sha256
                (base32
-                "1sn4wqkp6kjj9p8maf4jnjwwvb083hgakm9i10rk9273nnqfkj76"))))
+                "1cyb3lhxrw7ghyhrl2wc95vqhdaxz6n4pai66c573gcly7c7sc7f"))))
     (build-system python-build-system)
     (arguments
      `(,@(substitute-keyword-arguments (package-arguments python-acme)
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 209df2bb12..a3f4a4dd4b 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -473,7 +473,7 @@ to lock down your entire repository.")
 (define-public git-remote-gcrypt
   (package
    (name "git-remote-gcrypt")
-   (version "1.0.2")
+   (version "1.0.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -482,7 +482,7 @@ to lock down your entire repository.")
              (file-name (string-append name "-" version "-checkout"))
              (sha256
               (base32
-               "0kc6qi5gavziqlwnzpy7v4ah7yw860v3i8pyna6way0cfr0qnpr2"))))
+               "1vay3204729c7wajgn3nxf0s0hzwpdrw14pl6kd8w2ss25gvw2k1"))))
    (build-system trivial-build-system)
    (arguments
     `(#:modules ((guix build utils))
@@ -785,6 +785,7 @@ will work.")
               (uri (git-reference
                     (url "https://github.com/nvie/gitflow/")
                     (commit "15aab26490facf285acef56cb5d61025eacb3a69")))
+              (file-name (git-file-name name version))
               (sha256
                (base32
                 "01fs97q76fdfnvmrh2cyjhywcs3pykf1dg58sy0frflnsdzs6prx"))))
@@ -902,6 +903,7 @@ though this can be overridden.")
                       ;; are interested in just one for this package.
                       (url "https://github.com/dustin/bindir")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1dcq0y16yznbv4k9h8gg90kv1gkn8r8dbvl4m2rpfd7q5nqhn617"))))
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index baedb2a522..f66bfa2435 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1062,7 +1062,7 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.")
        ("waf" ,python-waf)
        ("wayland" ,wayland)
        ("wayland-protocols" ,wayland-protocols)
-       ("libxkbcommon", libxkbcommon)
+       ("libxkbcommon" ,libxkbcommon)
        ("youtube-dl" ,youtube-dl)
        ("zlib" ,zlib)))
     (arguments
@@ -1158,7 +1158,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2018.02.26")
+    (version "2018.03.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1166,7 +1166,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0ijjnx8qjxk07v5dbz3n5z3cvz8dlkmh7jkyvgng7inl74c29zq5"))))
+                "1ibmz91anli1vzkgw2i3h4wf1i8arzd74730ylwcwyg3375xryjb"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
@@ -1276,7 +1276,7 @@ other site that youtube-dl supports.")
 (define-public you-get
   (package
     (name "you-get")
-    (version "0.4.1025")
+    (version "0.4.1040")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1285,7 +1285,7 @@ other site that youtube-dl supports.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "10103jw1gzar85jlajzl9wslk08vw21n26hkhfcz5bvkm9lxxs2c"))))
+                "0257p9bn426rv0cjk2j5hsx6cg7dz5gpjwlqq0sy1axa47phis46"))))
     (build-system python-build-system)
     (inputs
      `(("ffmpeg" ,ffmpeg)))             ; for multi-part and >=1080p videos
@@ -2038,7 +2038,7 @@ making @dfn{screencasts}.")
 (define-public simplescreenrecorder
   (package
     (name "simplescreenrecorder")
-    (version "0.3.9")
+    (version "0.3.10")
     (source
      (origin
        (method url-fetch)
@@ -2047,7 +2047,7 @@ making @dfn{screencasts}.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1gnf9wbiq2fcbqcn1a5nfmp8r0nxrrlgh2wly2mfkkwymynhx0pk"))))
+         "02rl9yyx3hlz9fqvgzv7ipmvx2qahj7ws5wx2m7zs3lssq3qag3g"))))
     (build-system cmake-build-system)
     ;; Although libx11, libxfixes, libxext are listed as build dependencies in
     ;; README.md, the program builds and functions properly without them.
@@ -2461,7 +2461,7 @@ MPEG-2, MPEG-4, DVD (VOB)...
        ("libtool" ,libtool)
        ("pkg-config" ,pkg-config)
        ("zlib" ,zlib)
-       ("libmediainfo", libmediainfo)
+       ("libmediainfo" ,libmediainfo)
        ("libzen" ,libzen)))
     (build-system gnu-build-system)
     (arguments
@@ -2761,7 +2761,7 @@ It counts more than 100 plugins.")
               (file-name (string-append name "-" version ".tar.gz"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("autoconf" ,(autoconf-wrapper))
+     `(("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
        ("pkg-config" ,pkg-config)))
     (inputs
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index f8f9de16fc..55a92eca0d 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -613,14 +613,14 @@ domains, their live performance and resource utilization statistics.")
 (define-public criu
   (package
     (name "criu")
-    (version "3.5")
+    (version "3.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://download.openvz.org/criu/criu-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "1w0ybla7ac0ql0jzh0vxdf2w9amqp88jcg0na3b33r3hq8acry6x"))))
+                "0qrpz7pvnks34v7d8lb73flz3mb7qwnib94pdwaxh0mskn8470fq"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
@@ -747,7 +747,7 @@ Machine Protocol.")
              ("sdl2" ,sdl2)
              ("sdl2-ttf" ,sdl2-ttf)
              ("spice-protocol" ,spice-protocol)))
-   (native-inputs `(("pkg-config", pkg-config)))
+   (native-inputs `(("pkg-config" ,pkg-config)))
    (arguments
     `(#:tests? #f ;; No tests are available.
       #:phases (modify-phases %standard-phases
diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 642ca1c044..0fc3197077 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -128,6 +128,7 @@ Only \"Universal TUN/TAP device driver support\" is needed in the kernel.")
                  (git-reference
                   (url "git://git.infradead.org/users/dwmw2/vpnc-scripts.git")
                   (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "0pa36w4wlyyvfb66cayhans99wsr2j5si2fvfr7ldfm512ajwn8h"))))
diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm
index 478de6a444..12b1f93015 100644
--- a/gnu/packages/vulkan.scm
+++ b/gnu/packages/vulkan.scm
@@ -1,5 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -102,7 +104,7 @@ and for the GLSL.std.450 extended instruction set.
                                                (assoc-ref %build-inputs
                                                           "spirv-headers")))))
      (inputs `(("spirv-headers" ,spirv-headers)))
-     (native-inputs `(("pkg-config", pkg-config)
+     (native-inputs `(("pkg-config" ,pkg-config)
                       ("python" ,python)))
      (home-page "https://github.com/KhronosGroup/SPIRV-Tools")
      (synopsis "API and commands for processing SPIR-V modules")
@@ -189,7 +191,7 @@ interpretation of the specifications for these languages.")
               ("mesa" ,mesa)
               ("spirv-tools" ,spirv-tools)
               ("wayland" ,wayland)))
-    (native-inputs `(("pkg-config", pkg-config)
+    (native-inputs `(("pkg-config" ,pkg-config)
                      ("python" ,python)))
     (home-page
      "https://github.com/KhronosGroup/Vulkan-LoaderAndValidationLayers")
@@ -210,74 +212,68 @@ and the ICD.")
   (let ((commit "773ec22d49f40b7161820f29d953be4a7e40190d")
         (revision "1"))
     (package
-     (name "shaderc")
-     (version (string-append "0.0-" revision "." (string-take commit 9)))
-     (source
-      (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/google/shaderc")
-             (commit commit)))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "0b41inb1czxv3mciip0lfdxv19ccx2ys31fivfywjn2q8va1gd1f"))))
-     (build-system meson-build-system)
-     (arguments
-      `(#:tests? #f ;; Tests don't work yet.
-        #:phases
-        (modify-phases %standard-phases
-          (replace 'configure
-                   (lambda* (#:key outputs #:allow-other-keys)
-                     (let ((out (assoc-ref outputs "out")))
-                     ;; Remove various lines and touch build-version.inc or
-                     ;; configuring won't work.
-                     (invoke "touch" "glslc/src/build-version.inc")
-                     (substitute* "CMakeLists.txt" (("..PYTHON_EXE..*") ""))
-                     (substitute* "CMakeLists.txt"
-                                  ((".*update_build_version.py..*") ""))
-                     (substitute* "CMakeLists.txt"
-                                  ((".*add_custom_target.build-version.*") ""))
-                     (substitute* "CMakeLists.txt"
-                                  ((".*spirv-tools_SOURCE_DIR.*glslang_SOURCE_DIR.*")
-                                   ""))
-                     (substitute* "CMakeLists.txt"
-                                  ((".*Update build-version.inc.*") ""))
-                     (substitute* "CMakeLists.txt" ((".*--check.*") ""))
-                     (substitute* "glslc/src/main.cc" ((".*build-version.inc.*")
-                                                       "\"1\""))
-                     (invoke "cmake" "-GNinja" "-DCMAKE_BUILD_TYPE=Release"
-                                     "-DSHADERC_SKIP_TESTS=ON"
-                                     "-DCMAKE_INSTALL_LIBDIR=lib"
-                                     (string-append "-DCMAKE_INSTALL_PREFIX="
-                                                    out)))))
-          (add-after 'unpack 'unpack-sources
-                     (lambda* (#:key inputs #:allow-other-keys)
-                       (let ((spirv-tools-source (assoc-ref %build-inputs
-                                                            "spirv-tools-source"))
-                             (spirv-headers-source (assoc-ref %build-inputs
-                                                              "spirv-headers-source"))
-                             (glslang-source (assoc-ref %build-inputs
-                                                        "glslang-source")))
-                         (mkdir-p "third-party/spirv-tools")
-                         (copy-recursively spirv-tools-source
-                                           "third_party/spirv-tools")
-                         (mkdir-p "third-party/spirv-tools/external/spirv-headers")
-                         (copy-recursively spirv-headers-source
-                                           (string-append "third_party/spirv-tools"
-                                                          "/external/spirv-headers"))
-                         (mkdir-p "third-party/glslang")
-                         (copy-recursively glslang-source
-                                           "third_party/glslang")
-                         #t))))))
-     (inputs `(("python" ,python)))
-     (native-inputs `(("cmake" ,cmake)
-                      ("glslang-source", (package-source glslang))
-                      ("pkg-config", pkg-config)
-                      ("spirv-headers-source", (package-source spirv-headers))
-                      ("spirv-tools-source", (package-source spirv-tools))))
-     (home-page "https://github.com/google/shaderc")
-     (synopsis "Tools for shader compilation")
-     (description "Shaderc is a collection of tools, libraries and tests for
+      (name "shaderc")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/google/shaderc")
+               (commit commit)))
+         (file-name (string-append name "-" version ".tar.gz"))
+         (sha256
+          (base32
+           "0b41inb1czxv3mciip0lfdxv19ccx2ys31fivfywjn2q8va1gd1f"))))
+      (build-system meson-build-system)
+      (arguments
+       `(#:tests? #f                    ; tests don't work yet.
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'configure
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out")))
+                 ;; Remove various lines and touch build-version.inc or
+                 ;; configuring won't work.
+                 (invoke "touch" "glslc/src/build-version.inc")
+                 (substitute* "CMakeLists.txt" (("..PYTHON_EXE..*") ""))
+                 (substitute* "CMakeLists.txt"
+                   ((".*update_build_version.py..*") ""))
+                 (substitute* "CMakeLists.txt"
+                   ((".*add_custom_target.build-version.*") ""))
+                 (substitute* "CMakeLists.txt"
+                   ((".*spirv-tools_SOURCE_DIR.*glslang_SOURCE_DIR.*")
+                    ""))
+                 (substitute* "CMakeLists.txt"
+                   ((".*Update build-version.inc.*") ""))
+                 (substitute* "CMakeLists.txt" ((".*--check.*") ""))
+                 (substitute* "glslc/src/main.cc" ((".*build-version.inc.*")
+                                                   "\"1\""))
+                 (invoke "cmake" "-GNinja" "-DCMAKE_BUILD_TYPE=Release"
+                         "-DSHADERC_SKIP_TESTS=ON"
+                         "-DCMAKE_INSTALL_LIBDIR=lib"
+                         (string-append "-DCMAKE_INSTALL_PREFIX="
+                                        out)))))
+           (add-after 'unpack 'unpack-sources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((spirv-tools-source (assoc-ref inputs "spirv-tools-source"))
+                     (spirv-headers-source (assoc-ref inputs "spirv-headers-source"))
+                     (glslang-source (assoc-ref inputs "glslang-source")))
+                 (copy-recursively spirv-tools-source "third_party/spirv-tools")
+                 (copy-recursively spirv-headers-source
+                                   (string-append "third_party/spirv-tools"
+                                                  "/external/spirv-headers"))
+                 (copy-recursively glslang-source "third_party/glslang")
+                 #t))))))
+      (inputs
+       `(("python" ,python)))
+      (native-inputs
+       `(("cmake" ,cmake)
+         ("glslang-source" ,(package-source glslang))
+         ("pkg-config" ,pkg-config)
+         ("spirv-headers-source" ,(package-source spirv-headers))
+         ("spirv-tools-source" ,(package-source spirv-tools))))
+      (home-page "https://github.com/google/shaderc")
+      (synopsis "Tools for shader compilation")
+      (description "Shaderc is a collection of tools, libraries, and tests for
 shader compilation.")
-     (license license:asl2.0))))
+      (license license:asl2.0))))
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 2b1f1bdadb..fc8e380a5b 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -159,6 +159,7 @@ and its related documentation.")
               (uri (string-append
                     "https://github.com/GrahamDumpleton/mod_wsgi/archive/"
                     version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "0n1yhmrfp8mjbsngmyjl937c6rc0069p6wdi1lknrbn1q42hzw6q"))))
@@ -845,6 +846,7 @@ UTS#46.")
                      ":pserver:anonymous@tidy.cvs.sourceforge.net:/cvsroot/tidy")
                     (module "tidy")
                     (revision "2009-12-23")))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "14dsnmirjcrvwsffqp3as70qr6bbfaig2fv3zvs5g7005jrsbvpb"))
@@ -958,9 +960,9 @@ of people.")
      ; named 'stubout'". The tests can be run by replacing the check phase with
      ; the command "python setup.py nosetests --verbosity=3".
     (native-inputs `(; Required for tests:
-                     ("python-mox3", python-mox3)
-                     ("python-nose", python-nose)))
-    (propagated-inputs `(("python-numpy", python-numpy)))
+                     ("python-mox3" ,python-mox3)
+                     ("python-nose" ,python-nose)))
+    (propagated-inputs `(("python-numpy" ,python-numpy)))
     (home-page "https://github.com/novnc/websockify")
     (synopsis "WebSockets support for any application/server")
     (description "Websockify translates WebSockets traffic to normal socket
@@ -987,7 +989,7 @@ directions.")
        #:tests? #f))                         ; no test target
     (native-inputs `(("flex" ,flex)))
     (inputs `(("gnutls" ,gnutls)
-              ("libcrypt", libgcrypt)))
+              ("libcrypt" ,libgcrypt)))
     (home-page "https://www.gedanken.org.uk/software/wwwoffle/")
     (synopsis "Caching web proxy optimized for intermittent internet links")
     (description "WWWOFFLE is a proxy web server that is especially good for
@@ -4972,10 +4974,10 @@ used to start services with both privileged and non-privileged port numbers.")
          "0n29wcgw32rhnraj9j21ibhwi0xagmmcskhbaz8ihxly7nx3p9h8"))))
     (build-system cmake-build-system)
     (outputs '("out"
-               "static")) ; 1.0MiB of .a files
+               "static"))               ; 1.0MiB of .a files
     (arguments
-     `(#:tests? #f ; No tests available
-       #:configure-flags (list "-DCMAKE_BUILD_TYPE=Release")
+     `(#:tests? #f                      ; no tests available
+       #:build-type "Release"
        #:phases
        (modify-phases %standard-phases
          (add-after 'install 'move-static-libraries
@@ -6275,7 +6277,7 @@ in Perl but is not nearly as capable as @code{HTML::Tidy}.")
 (define-public geomyidae
   (package
     (name "geomyidae")
-    (version "0.29")
+    (version "0.31")
     (source
      (origin
        (method url-fetch)
@@ -6283,7 +6285,7 @@ in Perl but is not nearly as capable as @code{HTML::Tidy}.")
                            "geomyidae-" version ".tar.bz2"))
        (sha256
         (base32
-         "0qxgxp6psfrgfqhndyq2z54nb1qrmvvljddnxdwp207jbz366bja"))))
+         "1ih7220c6mgq4r7blm4kx3pxbl53sph58lqgwci6cmi3c0sq5c3x"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags (list "CC=gcc"
diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm
index 340221640c..df049e15a3 100644
--- a/gnu/packages/webkit.scm
+++ b/gnu/packages/webkit.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2015 David Hashe <david.hashe@dhashe.com>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017, 2018 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -54,14 +55,14 @@
 (define-public webkitgtk
   (package
     (name "webkitgtk")
-    (version "2.18.6")
+    (version "2.20.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.webkitgtk.org/releases/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0g5cpdijjv5hlrbi4i4dh97yrh5apnyvm90wpr9f84hgyk12r4ck"))))
+                "0g0an3pc2yz13gzpaysfgch2yp510gw1qcpk0xr8m6mx43vl1xjp"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no tests
@@ -79,7 +80,12 @@
                           ;; included.  More investigation is needed.  For
                           ;; now, we explicitly disable it to prevent an error
                           ;; at configuration time.
-                          "-DUSE_GSTREAMER_GL=OFF")
+                          "-DUSE_GSTREAMER_GL=OFF"
+
+                          ;; XXX Disable WOFF2 ‘web fonts’.  These were never
+                          ;; supported in our previous builds.  Enabling them
+                          ;; requires building libwoff2 and possibly woff2dec.
+                          "-DUSE_WOFF2=OFF")
        #:phases
        (modify-phases %standard-phases
          (add-after
@@ -130,7 +136,7 @@
        ("libxt" ,libxt)
        ("mesa" ,mesa)
        ("sqlite" ,sqlite)))
-    (home-page "http://www.webkitgtk.org/")
+    (home-page "https://www.webkitgtk.org/")
     (synopsis "Web content engine for GTK+")
     (description
      "WebKitGTK+ is a full-featured port of the WebKit rendering engine,
diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm
index c6a319965a..585b8a0342 100644
--- a/gnu/packages/wget.scm
+++ b/gnu/packages/wget.scm
@@ -152,21 +152,21 @@ online pastebin services.")
           (zero? (system* "sh" "./bootstrap"
                           "--gnulib-srcdir=gnulib"
                           "--no-git")))))))
-   (inputs `(("autoconf", autoconf)
-             ("automake", automake)
-             ("doxygen", doxygen)
-             ("flex", flex)
-             ("gettext", gettext-minimal)
-             ("gnutls", gnutls/dane)
-             ("libiconv", libiconv)
-             ("libidn2", libidn2)
-             ("libmicrohttpd", libmicrohttpd)
-             ("libpsl", libpsl)
-             ("libtool", libtool)
-             ("pcre2", pcre2)
-             ("python", python)))
+   (inputs `(("autoconf" ,autoconf)
+             ("automake" ,automake)
+             ("doxygen" ,doxygen)
+             ("flex" ,flex)
+             ("gettext" ,gettext-minimal)
+             ("gnutls" ,gnutls/dane)
+             ("libiconv" ,libiconv)
+             ("libidn2" ,libidn2)
+             ("libmicrohttpd" ,libmicrohttpd)
+             ("libpsl" ,libpsl)
+             ("libtool" ,libtool)
+             ("pcre2" ,pcre2)
+             ("python" ,python)))
    ;; TODO: Add libbrotlidec, libnghttp2.
-   (native-inputs `(("pkg-config", pkg-config)))
+   (native-inputs `(("pkg-config" ,pkg-config)))
    (home-page "https://gitlab.com/gnuwget/wget2")
    (synopsis "Successor of GNU Wget")
    (description "GNU Wget2 is the successor of GNU Wget, a file and recursive
diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index e71538f1b0..8496eb3365 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -26,9 +26,13 @@
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
   #:use-module (gnu packages admin)
   #:use-module (gnu packages audio)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cups)
@@ -47,11 +51,13 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages mp3)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages photo)
   #:use-module (gnu packages samba)
   #:use-module (gnu packages scanner)
+  #:use-module (gnu packages sdl)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages video)
   #:use-module (gnu packages vulkan)
@@ -212,34 +218,84 @@ integrate Windows applications into your desktop.")
     (synopsis "Implementation of the Windows API (WoW64 version)")
     (supported-systems '("x86_64-linux" "aarch64-linux"))))
 
+(define-public wine-staging-patchset-data
+  (package
+   (name "wine-staging-patchset-data")
+   (version "3.4")
+   (source
+    (origin
+     (method url-fetch)
+     (uri (string-append "https://github.com/wine-staging/wine-staging/archive/v"
+                         version ".zip"))
+     (file-name (string-append name "-" version ".zip"))
+     (sha256
+      (base32
+       "00yzh9bqs2rjgvk78xv3gfkbv4f2bkch9vb1ii4xh883f7wvkz93"))))
+   (build-system trivial-build-system)
+   (native-inputs
+    `(("bash" ,bash)
+      ("coreutils" ,coreutils)
+      ("unzip" ,unzip)))
+   (arguments
+    `(#:modules ((guix build utils))
+      #:builder
+      (begin
+        (use-modules (guix build utils))
+        (let* ((out (assoc-ref %outputs "out"))
+               (wine-staging (string-append out "/share/wine-staging"))
+               (source (assoc-ref %build-inputs "source"))
+               (sh (string-append (assoc-ref %build-inputs "bash") "/bin/bash"))
+               (env (string-append (assoc-ref %build-inputs "coreutils") "/bin/env"))
+               (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")))
+          (copy-file source (string-append ,name "-" ,version ".zip"))
+          (invoke unzip (string-append ,name "-" ,version ".zip"))
+          (substitute* (string-append "wine-staging-" ,version
+                                      "/patches/patchinstall.sh") (("/bin/sh") sh))
+          (substitute* (string-append "wine-staging-" ,version
+                                      "/patches/gitapply.sh") (("/usr/bin/env") env))
+          (mkdir-p wine-staging)
+          (copy-recursively (string-append "wine-staging-" ,version)
+                            wine-staging)))))
+   (home-page "https://github.com/wine-staging")
+   (synopsis "Patchset for Wine")
+   (description
+    "wine-staging-patchset-data contains the patchset to build Wine-Staging.")
+   (license license:lgpl2.1+)))
+
 (define-public wine-staging
   (package
     (inherit wine)
     (name "wine-staging")
-    (version "2.21")
+    (version (package-version wine-staging-patchset-data))
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "https://github.com/wine-compholio/wine-patched/archive/"
-                    "staging-" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+                    "https://dl.winehq.org/wine/source/"
+                    (version-major version) ".x"
+                    "/wine-" version ".tar.xz"))
+              (file-name (string-append name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1pjaxj7h3q6y356np908fvsx0bf7yx5crqvgl4hza6gfssdmsr5r"))))
-    (inputs `(("gtk+", gtk+)
-              ("libva", libva)
+                "14wf7536rkmhav9ibbvhqqkfqmbk1dckhd2679i5scizr5x290x4"))))
+    (inputs `(("autoconf" ,autoconf) ; for autoreconf
+              ("gtk+" ,gtk+)
+              ("libva" ,libva)
+              ("python" ,python)
+              ("sdl2" ,sdl2)
+              ("util-linux" ,util-linux) ; for hexdump
               ("vulkan-icd-loader" ,vulkan-icd-loader)
+              ("wine-staging-patchset-data" ,wine-staging-patchset-data)
               ,@(package-inputs wine)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'hardcode-libvulkan-path
+         (add-before 'configure 'patch-source-wine-staging
            (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((libvulkan (string-append (assoc-ref %build-inputs
-                               "vulkan-icd-loader") "/lib/libvulkan.so")))
-               ;; Hard-code the path to libvulkan.so.
-               (substitute* "dlls/vulkan/vulkan_thunks.c" (("libvulkan.so")
-                            libvulkan))
+             (let* ((source (assoc-ref %build-inputs "source"))
+                    (script (string-append (assoc-ref %build-inputs
+                            "wine-staging-patchset-data")
+                            "/share/wine-staging/patches/patchinstall.sh")))
+               (invoke script (string-append "DESTDIR=" ".") "--all")
                #t)))
          (add-after 'configure 'patch-dlopen-paths
            ;; Hardcode dlopened sonames to absolute paths.
@@ -261,7 +317,7 @@ the development branch yet.  The idea of Wine-Staging is to provide
 experimental features faster to end users and to give developers the
 possibility to discuss and improve their patches before they are
 integrated into the main branch.")
-    (home-page "https://wine-staging.com")
+    (home-page "https://github.com/wine-staging")
     ;; In addition to the regular Wine license (lgpl2.1+), Wine-Staging
     ;; provides Liberation and WenQuanYi Micro Hei fonts.  Those use
     ;; different licenses.  In particular, the latter is licensed under
@@ -281,13 +337,13 @@ integrated into the main branch.")
              (string-append "libdir=" %output "/lib/wine64"))
        #:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'hardcore-libvulkan-path
+         (add-before 'configure 'patch-source-wine-staging
            (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((libvulkan (string-append (assoc-ref %build-inputs
-                               "vulkan-icd-loader") "/lib/libvulkan.so")))
-               ;; Hard-code the path to libvulkan.so.
-               (substitute* "dlls/vulkan/vulkan_thunks.c" (("libvulkan.so")
-                            libvulkan))
+             (let* ((source (assoc-ref %build-inputs "source"))
+                    (script (string-append (assoc-ref %build-inputs
+                            "wine-staging-patchset-data")
+                            "/share/wine-staging/patches/patchinstall.sh")))
+               (invoke script (string-append "DESTDIR=" ".") "--all")
                #t)))
          (add-after 'install 'copy-wine32-binaries
            (lambda* (#:key outputs #:allow-other-keys)
diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 888173313b..9bd3492413 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -175,14 +175,14 @@ commands would.")
 (define-public i3-wm
   (package
     (name "i3-wm")
-    (version "4.14.1")
+    (version "4.15")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://i3wm.org/downloads/i3-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "1cazmfbbx6n8c81h6x6pdayq3mxs2ml3adz165z8vapkc72kl1nh"))))
+                "09jk70hsdxab24lqvj2f30ijrkbv3f6q9xi5dcsax1dw3x6m4z91"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
@@ -710,7 +710,7 @@ experience.")
               ("libxdg-basedir" ,libxdg-basedir)
               ("libxkbcommon" ,libxkbcommon)
               ("lua" ,lua)
-              ("lua-lgi",lua-lgi)
+              ("lua-lgi" ,lua-lgi)
               ("pango" ,pango)
               ("startup-notification" ,startup-notification)
               ("xcb-util" ,xcb-util)
diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index 407f2f80df..de832d5368 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -1101,7 +1101,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
 (define-public rofi
   (package
     (name "rofi")
-    (version "1.4.2")
+    (version "1.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/DaveDavenport/rofi/"
@@ -1109,7 +1109,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
                                   version "/rofi-" version ".tar.xz"))
               (sha256
                (base32
-                "1129cbg76g56c6ckzj5y5haf92jxhx3b71cr3qmhrb0n8g4gi38s"))))
+                "0li2hl55sxzdpbxxiwgxsvkhyy6bh8qd2j1r8xh8y6q8a318zsz9"))))
     (build-system gnu-build-system)
     (inputs
      `(("pango" ,pango)
@@ -1126,6 +1126,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
      `(("bison" ,bison)
        ("check" ,check)
        ("flex" ,flex)
+       ("glib:bin" ,glib "bin")
        ("pkg-config" ,pkg-config)))
     (arguments
      `(#:parallel-tests? #f ; May fail in some circumstances.
@@ -1136,8 +1137,30 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
              (substitute* '("test/helper-expand.c")
                (("~root") "/root")
                (("~") "")
-               (("g_get_home_dir \\(\\)") "\"/\"")))))))
-    (home-page "https://davedavenport.github.io/rofi/")
+               (("g_get_home_dir \\(\\)") "\"/\""))
+             #t))
+         (add-before 'check 'add-missing-configuration-files
+           (lambda _
+             ;; These files are missing in the 1.5.0 release, causing a test
+             ;; failure: <https://github.com/DaveDavenport/rofi/issues/782>.
+             (with-directory-excursion "subprojects/libnkutils/tests"
+               (mkdir "gtk-3.0")
+               (call-with-output-file "gtk-3.0/settings.ini"
+                 (lambda (port)
+                   (format port "[Settings]
+gtk-double-click-time = 300
+gtk-cursor-theme-name = gnome
+")))
+               (mkdir "gtk-4.0")
+               (call-with-output-file "gtk-4.0/settings.ini"
+                 (lambda (port)
+                   (format port "[Settings]
+gtk-double-click-time = 300
+gtk-icon-theme-name = nothing-like-this-theme
+gtk-enable-primary-paste = true
+")))
+               #t))))))
+    (home-page "https://github.com/DaveDavenport/rofi")
     (synopsis "Application launcher")
     (description "Rofi is a minimalist application launcher.  It memorizes which
 applications you regularly use and also allows you to search for an application
@@ -1309,9 +1332,9 @@ XCB util-xrm module provides the following libraries:
                         (install-file "README" doc)
                         ;; Avoid unspecified return value.
                         #t))))))
-    (inputs `(("libx11", libx11)
-              ("libxext", libxext)
-              ("libxxf86vm", libxxf86vm)))
+    (inputs `(("libx11" ,libx11)
+              ("libxext" ,libxext)
+              ("libxxf86vm" ,libxxf86vm)))
     (synopsis "Tiny monitor calibration loader for XFree86 (or X.org)")
     (description "xcalib is a tiny tool to load the content of vcgt-Tags in ICC
 profiles to the video card's gamma ramp.  It does work with most video card
diff --git a/gnu/packages/xiph.scm b/gnu/packages/xiph.scm
index f9caea4192..d3a590bc58 100644
--- a/gnu/packages/xiph.scm
+++ b/gnu/packages/xiph.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2014 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 © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -81,6 +81,7 @@ periodic timestamps for seeking.")
   (package
    (name "libvorbis")
    (version "1.3.5")
+   (replacement libvorbis-1.3.6)
    (source (origin
             (method url-fetch)
             (uri (string-append "http://downloads.xiph.org/releases/vorbis/"
@@ -105,6 +106,18 @@ polyphonic) audio and music at fixed and variable bitrates from 16 to
                                "See COPYING in the distribution."))
    (home-page "https://xiph.org/vorbis/")))
 
+;; For CVE-2018-5146.
+(define-public libvorbis-1.3.6
+  (package/inherit libvorbis
+    (version "1.3.6")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://downloads.xiph.org/releases/vorbis/"
+                                  "libvorbis-" version ".tar.xz"))
+              (sha256
+               (base32
+                "05dlzjkdpv46zb837wysxqyn8l636x3dw8v8ymlrwz2fg1dbn05g"))))))
+
 (define libtheora
   (package
     (name "libtheora")
diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 5f7a95463a..212b1c8e8a 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Raimon Grau <raimonster@gmail.com>
 ;;; Copyright © 2016 Mathieu Lirzin <mthl@gnu.org>
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
@@ -993,6 +993,7 @@ UTF-8 and UTF-16 encoding.")
                                   version "/tinyxml_"
                                   (string-join (string-split version #\.) "_")
                                   ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "14smciid19lvkxqznfig77jxn5s4iq3jpb47vh5a6zcaqp7gvg8m"))
@@ -1006,12 +1007,12 @@ UTF-8 and UTF-16 encoding.")
          (delete 'configure)
          (add-after 'build 'build-shared-library
            (lambda _
-             (zero? (system* "g++" "-Wall" "-O2" "-shared" "-fpic"
-                             "tinyxml.cpp" "tinyxmlerror.cpp"
-                             "tinyxmlparser.cpp" "tinystr.cpp"
-                             "-o" "libtinyxml.so"))))
+             (invoke "g++" "-Wall" "-O2" "-shared" "-fpic"
+                     "tinyxml.cpp" "tinyxmlerror.cpp"
+                     "tinyxmlparser.cpp" "tinystr.cpp"
+                     "-o" "libtinyxml.so")))
          (replace 'check
-           (lambda _ (zero? (system "./xmltest"))))
+           (lambda _ (invoke "./xmltest")))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -1060,9 +1061,10 @@ C++ programming language.")
        (method url-fetch)
        (uri (string-append "https://github.com/leethomason/tinyxml2/archive/"
                            version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-       (base32
-        "083z4r4khcndxi9k840lcr48sqxvar4gpsnf749xfdn1bkr8xcql"))))
+        (base32
+         "083z4r4khcndxi9k840lcr48sqxvar4gpsnf749xfdn1bkr8xcql"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))    ; no tests
@@ -1307,7 +1309,8 @@ SAX2 APIs.")
                                   version ".zip"))
               (sha256
                (base32
-                "0w19k1awslmihpwsxwjbg89hv0vjhk4k3i0vrfchy3mqknd988y5"))))
+                "0w19k1awslmihpwsxwjbg89hv0vjhk4k3i0vrfchy3mqknd988y5"))
+              (patches (search-patches "java-simple-xml-fix-tests.patch"))))
     (build-system ant-build-system)
     (arguments
      `(#:build-target "build"
@@ -1413,7 +1416,7 @@ characters into a single event.")
     (propagated-inputs
      `(("perl-libxml" ,perl-libxml)
        ("perl-xml-filter-buffertext" ,perl-xml-filter-buffertext)
-       ("perl-xml-namespacesupport", perl-xml-namespacesupport)
+       ("perl-xml-namespacesupport" ,perl-xml-namespacesupport)
        ("perl-xml-sax-base" ,perl-xml-sax-base)))
     (home-page "http://search.cpan.org/dist/XML-SAX-Writer/")
     (synopsis "SAX2 XML Writer")
@@ -1470,7 +1473,7 @@ It provides a flexible escaping technique and pretty printing.")
        ("perl-xml-sax-writer" ,perl-xml-sax-writer)
        ("perl-xml-simple" ,perl-xml-simple)
        ("perl-xml-xpathengine" ,perl-xml-xpathengine)
-       ("perl-test-pod", perl-test-pod)
+       ("perl-test-pod" ,perl-test-pod)
        ("perl-tree-xpathengine" ,perl-tree-xpathengine)))
     (home-page "http://search.cpan.org/dist/XML-Twig/")
     (synopsis "Perl module for processing huge XML documents in tree mode")
diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index b258f446b9..871fae29d7 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -2000,7 +2000,7 @@ information used in connecting to the X server.")
 (define-public xbacklight
   (package
     (name "xbacklight")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
       (origin
         (method url-fetch)
@@ -2010,7 +2010,7 @@ information used in connecting to the X server.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0arnd1j8vzhzmw72mqhjjcb2qwcbs9qphsy3ps593ajyld8wzxhp"))))
+            "0pmzaz4kp38qv2lqiw5rnqhwzmwrq65m1x5j001mmv99wh9isnk1"))))
     (build-system gnu-build-system)
     (inputs
      `(("libxcb" ,libxcb)
@@ -2030,7 +2030,7 @@ the same way.")
 (define-public xbitmaps
   (package
     (name "xbitmaps")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
       (origin
         (method url-fetch)
@@ -2040,7 +2040,7 @@ the same way.")
                ".tar.bz2"))
         (sha256
           (base32
-            "178ym90kwidia6nas4qr5n5yqh698vv8r02js0r4vg3b6lsb0w9n"))))
+            "1vh73sc13s7w5r6gnc6irca56s7998bja7wgdivkfn8jccawgw5r"))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)))
     (home-page "https://www.x.org/wiki/")
@@ -2177,7 +2177,7 @@ X11 Inter-Client Communication Conventions Manual (ICCCM).")
 (define-public xcursor-themes
   (package
     (name "xcursor-themes")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
       (origin
         (method url-fetch)
@@ -2187,7 +2187,7 @@ X11 Inter-Client Communication Conventions Manual (ICCCM).")
                ".tar.bz2"))
         (sha256
           (base32
-            "11mv661nj1p22sqkv87ryj2lcx4m68a04b0rs6iqh3fzp42jrzg3"))))
+            "0whjiq6d5z4z75zh37pji6llfcyrg6q3mg9zx5zqyncnj39q30xf"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxcursor" ,libxcursor)
@@ -3853,7 +3853,7 @@ can be combined together using the 'rules' component of this database.")
 (define-public xkill
   (package
     (name "xkill")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
       (origin
         (method url-fetch)
@@ -3863,7 +3863,7 @@ can be combined together using the 'rules' component of this database.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0bl1ky8ps9jg842j4mnmf4zbx8nkvk0h77w7bqjlpwij9wq2mvw8"))))
+            "0szzd9nzn0ybkhnfyizb876irwnjsnb78rcaxx6prb71jmmbpw65"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxmu" ,libxmu)
@@ -3908,7 +3908,7 @@ programs that have displayed undesired windows on a user's screen.")
 (define-public xlsclients
   (package
     (name "xlsclients")
-    (version "1.1.3")
+    (version "1.1.4")
     (source
       (origin
         (method url-fetch)
@@ -3918,7 +3918,7 @@ programs that have displayed undesired windows on a user's screen.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0g9x7rrggs741x9xwvv1k9qayma980d88nhdqw7j3pn3qvy6d5jx"))))
+            "1h8931sn34mcip6vpi4v7hdmr1r58gkbw4s2p97w98kykks2lgvp"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxcb" ,libxcb)))
@@ -3935,7 +3935,7 @@ running on X server.")
 (define-public xlsfonts
   (package
     (name "xlsfonts")
-    (version "1.0.5")
+    (version "1.0.6")
     (source
      (origin
        (method url-fetch)
@@ -3945,7 +3945,7 @@ running on X server.")
              ".tar.bz2"))
        (sha256
         (base32
-         "1yi774g6r1kafsbnxbkrwyndd3i60362ck1fps9ywz076pn5naa0"))))
+         "0s6kxgv78chkwsqmhw929f4pf91gq63f4yvixxnan1h00cx0pf49"))))
     (build-system gnu-build-system)
     (inputs
      `(("xproto" ,xproto)
@@ -3962,7 +3962,7 @@ protocol.")
 (define-public xfontsel
   (package
     (name "xfontsel")
-    (version "1.0.5")
+    (version "1.0.6")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3970,7 +3970,7 @@ protocol.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1grir464hy52a71r3mpm9mzvkf7nwr3vk0b1vc27pd3gp588a38p"))))
+                "0700lf6hx7dg88wq1yll7zjvf9gbwh06xff20yffkxb289y0pai5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -4094,7 +4094,7 @@ refers to the included common xorg.css stylesheet.")
 (define-public xpr
   (package
     (name "xpr")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
       (origin
         (method url-fetch)
@@ -4104,7 +4104,7 @@ refers to the included common xorg.css stylesheet.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1dbcv26w2yand2qy7b3h5rbvw1mdmdd57jw88v53sgdr3vrqvngy"))))
+            "07qy9lwjvxighcmg6qvjkgagad3wwvidrfx0jz85lgynz3qy0dmr"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
@@ -4123,7 +4123,7 @@ it for output on various types of printers.")
 (define-public xprop
   (package
     (name "xprop")
-    (version "1.2.2")
+    (version "1.2.3")
     (source
       (origin
         (method url-fetch)
@@ -4133,7 +4133,7 @@ it for output on various types of printers.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1ilvhqfjcg6f1hqahjkp8qaay9rhvmv2blvj3w9asraq0aqqivlv"))))
+            "06sjgahjiz85v0k0pmv5x05chc591xynl5ah1bqzz1bdr0lgnanj"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
@@ -4180,7 +4180,7 @@ and Reflect (RandR) extension.")
 (define-public xrdb
   (package
     (name "xrdb")
-    (version "1.1.0")
+    (version "1.1.1")
     (source
       (origin
         (method url-fetch)
@@ -4190,7 +4190,7 @@ and Reflect (RandR) extension.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0nsnr90wazcdd50nc5dqswy0bmq6qcj14nnrhyi7rln9pxmpp0kk"))))
+            "1dqp486nd5sagbg572kl0k839nwvpqnb7jvppyb7jj5vrpkss8rd"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxmu" ,libxmu)
@@ -4211,7 +4211,7 @@ file.")
 (define-public xrefresh
   (package
     (name "xrefresh")
-    (version "1.0.5")
+    (version "1.0.6")
     (source
       (origin
         (method url-fetch)
@@ -4221,7 +4221,7 @@ file.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1mlinwgvql6s1rbf46yckbfr9j22d3c3z7jx3n6ix7ca18dnf4rj"))))
+            "0lv3rlshh7s0z3aqx5ahnnf8cl082m934bk7gv881mz8nydznz98"))))
     (build-system gnu-build-system)
     (inputs
       `(("libx11" ,libx11)))
@@ -4239,7 +4239,7 @@ up your screen.")
 (define-public xset
   (package
     (name "xset")
-    (version "1.2.3")
+    (version "1.2.4")
     (source
       (origin
         (method url-fetch)
@@ -4249,7 +4249,7 @@ up your screen.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0qw0iic27bz3yz2wynf1gxs70hhkcf9c4jrv7zhlg1mq57xz90j3"))))
+            "0my987wjvra7l92ry6q44ky383yg3phzxhdbn3lqhapm1ll9bzg4"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
@@ -4268,7 +4268,7 @@ up your screen.")
 (define-public xsetroot
   (package
     (name "xsetroot")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
       (origin
         (method url-fetch)
@@ -4278,7 +4278,7 @@ up your screen.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1nf3ii31m1knimbidaaym8p61fq3blv8rrdr2775yhcclym5s8ds"))))
+            "0z21mqvmdl6rl63q77479wgkfygnll57liza1i3va7sr4fx45i0h"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxmu" ,libxmu)
@@ -4353,7 +4353,7 @@ extension.")
 (define-public xwd
   (package
     (name "xwd")
-    (version "1.0.6")
+    (version "1.0.7")
     (source
       (origin
         (method url-fetch)
@@ -4363,7 +4363,7 @@ extension.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0ybx48agdvjp9lgwvcw79r1x6jbqbyl3fliy3i5xwy4d4si9dcrv"))))
+            "1537i8q8pgf0sjklakzfvjwrq5b246qjywrx9ll8xfg0p6w1as6d"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxt" ,libxt)
@@ -4386,7 +4386,7 @@ dump and twice whenthe dump is completed.")
 (define-public xwininfo
   (package
     (name "xwininfo")
-    (version "1.1.3")
+    (version "1.1.4")
     (source
       (origin
         (method url-fetch)
@@ -4396,7 +4396,7 @@ dump and twice whenthe dump is completed.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1y1zn8ijqslb5lfpbq4bb78kllhch8in98ps7n8fg3dxjpmb13i1"))))
+            "00avrpw4h5mr1klp41lv2j4dmq465v6l5kb5bhm4k5ml8sm9i543"))))
     (build-system gnu-build-system)
     (inputs
       `(("libx11" ,libx11)
@@ -4414,7 +4414,7 @@ Various information is displayed depending on which options are selected.")
 (define-public xwud
   (package
     (name "xwud")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
       (origin
         (method url-fetch)
@@ -4424,7 +4424,7 @@ Various information is displayed depending on which options are selected.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1ggql6maivah58kwsh3z9x1hvzxm1a8888xx4s78cl77ryfa1cyn"))))
+            "1a8hdgy40smvblnh3s9f0vkqckl68nmivx7d48zk34m8z18p16cr"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
@@ -5650,14 +5650,14 @@ The XCB util-wm module provides the following libraries:
 (define-public xinit
   (package
     (name "xinit")
-    (version "1.3.4")
+    (version "1.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://xorg/individual/app/xinit-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "1cq2g469mb2cfgr8k57960yrn90bl33vfqri4pdh2zm0jxrqvn3m"))))
+                "1vw2wlg74ig52naw0cha3pgzcwwk25l834j42cg8m5zmybp3a213"))))
     (build-system gnu-build-system)
     (inputs
      `(("xproto" ,xproto)
@@ -5739,7 +5739,7 @@ of an X11 screen.")
 (define-public xmessage
   (package
     (name "xmessage")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
      (origin
        (method url-fetch)
@@ -5749,7 +5749,7 @@ of an X11 screen.")
              ".tar.gz"))
        (sha256
         (base32
-         "1jmcac1xbwplbxfl75sr6w3zqhx1khpdzlqippjsr31cjp1rjc48"))))
+         "0sw0b0cbrjl44brw7qi1jkm61xd7a1lpj04418c6iqk6mf83llwr"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -5983,7 +5983,7 @@ basic eye-candy effects.")
               ("python2-rencode" ,python2-rencode)
               ("xorg-server" ,xorg-server)))
     (native-inputs `(("pkg-config" ,pkg-config)
-                     ("python2-cython", python2-cython)))
+                     ("python2-cython" ,python2-cython)))
     (arguments
      `(#:python ,python-2 ;; no full Python 3 support yet
        #:configure-flags '("--with-tests"
diff --git a/gnu/packages/zile.scm b/gnu/packages/zile.scm
index c0bbafdd59..fd3d168b3d 100644
--- a/gnu/packages/zile.scm
+++ b/gnu/packages/zile.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
@@ -102,7 +102,7 @@ default Emacs configuration, but it carries a much lighter feature set.")
          ,@(package-inputs zile)))
       (native-inputs
        `(("m4" ,m4)                               ;for 'bootstrap'
-         ("autoconf" ,(autoconf-wrapper))
+         ("autoconf" ,autoconf-wrapper)
          ("automake" ,automake)
 
          ;; For some reason, 'bootstrap' insists on having these.