Merge branch 'master' into core-updates

author: Marius Bakke <mbakke@fastmail.com> 2018-11-14 21:20:46 +0100
committer: Marius Bakke <mbakke@fastmail.com> 2018-11-14 21:20:46 +0100
commit: 79ee97a144aaaa890be0724aaf796e2a771179d7 (patch)
tree: fddd2f20003d60e42eed7a614acea91a13d854d7 /gnu
parent: 7d9d521fbcf1423f66d6f33208c03d5dacb7ba50 (diff)
parent: e921993c25626541385f191f0463cad8e5e5c5c7 (diff)
download: guix-79ee97a144aaaa890be0724aaf796e2a771179d7.tar.gz
61 files changed, 2057 insertions, 916 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index 3e355ac9b3..c4299fcbe4 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -816,7 +816,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/hplip-remove-imageprocessor.patch	\
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
   %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
-  %D%/packages/patches/icecat-CVE-2018-12383.patch		\
   %D%/packages/patches/icecat-use-system-graphite2+harfbuzz.patch	\
   %D%/packages/patches/icecat-use-system-media-libs.patch	\
   %D%/packages/patches/icedtea-6-hotspot-gcc-segfault-workaround.patch  \
@@ -1048,6 +1047,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/plink-1.07-unclobber-i.patch		\
   %D%/packages/patches/plink-endian-detection.patch		\
   %D%/packages/patches/plotutils-libpng-jmpbuf.patch		\
+  %D%/packages/patches/poppler-CVE-2018-19149.patch		\
   %D%/packages/patches/portaudio-audacity-compat.patch		\
   %D%/packages/patches/portmidi-modular-build.patch		\
   %D%/packages/patches/potrace-tests.patch			\
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 3c65ce102c..0da35ea62e 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -981,7 +981,7 @@ system administrator.")
 (define-public sudo
   (package
     (name "sudo")
-    (version "1.8.25p1")
+    (version "1.8.26")
     (source (origin
               (method url-fetch)
               (uri
@@ -991,7 +991,7 @@ system administrator.")
                                     version ".tar.gz")))
               (sha256
                (base32
-                "0nqri46d4dpycj96zin2f2wszmhm7q9mr68hhj9sp81pgmx9rjcx"))
+                "1qpyyfga8rs02p3186sns8qvh2bzwa48ka845nrcqh83dyd23nj0"))
               (modules '((guix build utils)))
               (snippet
                '(begin
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 28447552f2..6dc0d82668 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -572,13 +572,14 @@ based on human speech recordings.")
     (name "infamous-plugins")
     (version "0.2.04")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/ssj71/infamousPlugins/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ssj71/infamousPlugins.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1n6rhqsmvad7692w2h01niw5gqg5yk7a09wxl5ivs77zyp93vf7z"))))
+                "0hmqk80w4qxq09iag7b7srf2g0wigkyhzq0ywxvhz2iz0hq9k0dh"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests
@@ -610,13 +611,14 @@ envelope follower, distortion effects, tape effects and more.")
     (name "swh-plugins-lv2")
     (version "1.0.16")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/swh/"
-                                  "lv2/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/swh/lv2.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0j1mih0lp4fds07knp5i32in515sh0df1qi6694pmyz2wqnm295w"))))
+                "0y7nnww864mm4k6ayy2lhcws3wlbhb2gkyjbrwk921fvc18qk9mz"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no check target
@@ -654,14 +656,14 @@ emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.")
     (name "csound")
     (version "6.11.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/csound/csound/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/csound/csound.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "072pk5h9w0vhw0ncc9dn90haw1yv18v04iwwjn8nsp6930w7dvxd"))))
+                "1hlkrnv3gghx4v382nl6v6k2k1dzm5ddk35m5g3q6pzc959726s7"))))
     (build-system cmake-build-system)
     (inputs
      `(("alsa-lib" ,alsa-lib)
@@ -1174,19 +1176,15 @@ PS, and DAB+.")
 (define-public faust-2
   (package
     (inherit faust)
-    (version "2.1.0")
+    (version "2.5.23")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/grame-cncm/faust.git")
-                    (commit (string-append "v"
-                                           (string-map (lambda (c)
-                                                         (if (char=? c #\.) #\- c))
-                                                       version)))))
-              (file-name (string-append "faust-" version "-checkout"))
+              (method url-fetch)
+              (uri (string-append "https://github.com/grame-cncm/faust/"
+                                  "releases/download/" version
+                                  "/faust-" version ".tar.gz"))
               (sha256
                (base32
-                "06km0ygwxxwgw1lqldccqidxhmjfz8ck0wnbd95qk5sg8sbpc068"))))
+                "1yz5jnr76hh7rmxkpdi7gyrw1wp4gyqfpq8zyl97qdi5ga5gjznq"))))
     (build-system gnu-build-system)
     (arguments
      (substitute-keyword-arguments (package-arguments faust)
@@ -1194,7 +1192,7 @@ PS, and DAB+.")
         `(list (string-append "prefix=" (assoc-ref %outputs "out"))
                "world"))))
     (native-inputs
-     `(("llvm" ,llvm-with-rtti)
+     `(("llvm" ,llvm-3.8-with-rtti)
        ("which" ,which)
        ("xxd" ,xxd)
        ("ctags" ,emacs-minimal)  ; for ctags
@@ -1881,14 +1879,14 @@ software.")
     (name "lvtk")
     (version "1.2.0")
     (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/lvtk/lvtk/archive/"
-                                 version
-                                 ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/lvtk/lvtk.git")
+                   (commit version)))
+             (file-name (git-file-name name version))
              (sha256
               (base32
-               "03nbj2cqcklqwh50zj2gwm07crh5iwqbpxbpzwbg5hvgl4k4rnjd"))))
+               "1b01zvzl70ana6l1kn8fgyr7msnn3c7x61cgw7fdpp50322352p8"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f  ; no check target
@@ -2274,36 +2272,32 @@ tempo and pitch of an audio recording independently of one another.")
     (name "rtmidi")
     (version "2.1.0")
     (source (origin
-              (method url-fetch)
-              (uri
-               (string-append "https://github.com/powertab/rtmidi/archive/"
-                              version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/powertab/rtmidi.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0d49lapnmdgmjxh4vw57h6xk74nn5r0zwysv7jbd7m8kqhpq5rjj"))))
+                "106v177y3nrjv2l1yskch4phpqd8h97b67zj0jiq9pc3c69jr1ay"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
-       #:phases (modify-phases %standard-phases
-                  (add-after
-                   'unpack 'autoconf
-                   (lambda _ (invoke "autoreconf" "-vfi")))
-                  (add-before
-                   'build 'fix-makefile
-                   (lambda _
-                     (substitute* "Makefile"
-                       (("/bin/ln") "ln")
-                       (("RtMidi.h RtError.h") "RtMidi.h"))
-                     #t))
-                  (add-before
-                   'install 'make-target-dirs
-                   (lambda _
-                     (let ((out (assoc-ref %outputs "out")))
-                       (mkdir-p (string-append out "/bin"))
-                       (mkdir (string-append out "/lib"))
-                       (mkdir (string-append out "/include")))
-                     #t)))))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'fix-makefile
+           (lambda _
+             (substitute* "Makefile"
+               (("/bin/ln") "ln")
+               (("RtMidi.h RtError.h") "RtMidi.h"))
+             #t))
+         (add-before 'install 'make-target-dirs
+           (lambda _
+             (let ((out (assoc-ref %outputs "out")))
+               (mkdir-p (string-append out "/bin"))
+               (mkdir (string-append out "/lib"))
+               (mkdir (string-append out "/include")))
+             #t)))))
     (inputs
      `(("jack" ,jack-1)
        ("alsa-lib" ,alsa-lib)))
@@ -2754,20 +2748,14 @@ portions of LAME.")
      ;; TODO: Add ASIHPI.
      `(("alsa-lib" ,alsa-lib)
        ("jack" ,jack-1)))
+    ;; Autoreconf is necessary because the audacity-compat patch modifies .in
+    ;; files.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
        ("libtool" ,libtool)
        ("pkg-config" ,pkg-config)))
-    (arguments
-     '(#:phases
-       ;; Autoreconf is necessary because the audacity-compat patch modifies
-       ;; .in files.
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
-           (lambda _
-             (invoke "autoreconf" "-vif"))))
-       #:tests? #f))                    ;no 'check' target
+    (arguments '(#:tests? #f))                    ;no 'check' target
     (home-page "http://www.portaudio.com/")
     (synopsis "Audio I/O library")
     (description
@@ -2813,12 +2801,13 @@ synthesizer written in C++.")
     (version "1.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/Themaister/RSound/archive/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Themaister/RSound.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1wzs40c0k5zpkmm5ffl6c17xmr399sxli7ys0fbb9ib0fd334knx"))))
+        (base32 "0gspmr3klwnq98h17p5hc6ifygya4p80g4g8r7a1qavm3mv19waf"))))
     (build-system gnu-build-system)
     (inputs
      `(("alsa-lib" ,alsa-lib)
@@ -2851,14 +2840,14 @@ with a much different focus than most other audio daemons.")
     (name "xjackfreak")
     (version "1.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/johnhldavis/xjackfreak/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/johnhldavis/xjackfreak.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0xj6gpxfnw9jbdgwgm0x23xgfvj2kwmwb1nk0drw8lxgcchkq7d9"))))
+                "18c546qidbrj0f5wfiq5llii2192xpln0ab3r4vpr7i3wybxqjfz"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
@@ -3026,15 +3015,16 @@ point audio data.")
     (name "cuetools")
     (version "1.4.1")
     (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/svend/cuetools/archive/"
-                                 version ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/svend/cuetools.git")
+                   (commit version)))
+             (file-name (git-file-name name version))
              (sha256
               (base32
-               "01xi3rvdmil9nawsha04iagjylqr1l9v9vlzk99scs8c207l58i4"))))
+               "02ksv1ahf1v4cr2xbclsfv5x17m9ivzbssb5r8xjm97yh8a7spa3"))))
     (build-system gnu-build-system)
-    ;; The source tarball is not bootstrapped.
+    ;; The source checkout is not bootstrapped.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
@@ -3075,13 +3065,14 @@ use them split WAVE data into multiple files.")
     (name "dcadec")
     (version "0.2.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/foo86/dcadec/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/foo86/dcadec.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0i0dpypgqkhhi4v1fmsp2way6w9kbcix3c7q79pmg39yvrzj17gd"))))
+                "07nd0ajizrp1w02bsyfcv18431r8m8rq8gjfmz9wmckpg7cxj2hs"))))
     (build-system gnu-build-system)
     (arguments
      ;; Test files are missing: https://github.com/foo86/dcadec/issues/53
@@ -3386,13 +3377,14 @@ the following features:
     (version "1.6")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/dpayne/cli-visualizer/archive/"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dpayne/cli-visualizer.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "07zkm87f2fr8kc6531zrkya7q81sdanm6813y2f54mg13g41y6hi"))))
+         "0mirp8bk398di5xyq95iprmdyvplfghxqmrfj7jdnpy554vx7ppc"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("which" ,which)))
@@ -3440,14 +3432,14 @@ representations.")
     (name "cava")
     (version "0.6.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/karlstav/cava/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/karlstav/cava.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "13d72swnjs894llf0paandmhf1lf90dz6ygkcdw4bv84wzkq1f4q"))))
+                "1kvhqgijs29909w3sq9m0bslx2zxxn4b3i07kdz4hb0dqkppxpjy"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 52afcbc676..c927a14673 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,6 +31,7 @@
 (define-module (gnu packages backup)
   #:use-module (guix packages)
   #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix git-download)
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
@@ -132,22 +134,18 @@ spying and/or modification by the server.")
     (name "par2cmdline")
     (version "0.8.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/Parchive/par2cmdline/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Parchive/par2cmdline.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1jpshmmcr81mxly0md2rr231qz9c8c680bbvcmhh100dg9i4a6s6"))))
+                "0f1jsd5sw2wynjzi7yjqjaf13yhyjfdid91p8yh0jn32y03kjyrz"))))
     (native-inputs
      `(("automake" ,automake)
        ("autoconf" ,autoconf)))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
-           (lambda _ (invoke "autoreconf" "-vfi"))))))
     (synopsis "File verification and repair tools")
     (description "Par2cmdline uses Reed-Solomon error-correcting codes to
 generate and verify PAR2 recovery files.  These files can be distributed
@@ -889,6 +887,7 @@ is like a time machine for your data. ")
                                         ,version)
                ;; Disable 'restic self-update'.  It makes little sense in Guix.
                (substitute* "build.go" (("selfupdate") ""))
+               (setenv "HOME" (getcwd)) ; for $HOME/.cache/go-build
                (invoke "go" "run" "build.go"))))
 
          (replace 'check
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bab6b2b64d..95c722ac40 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -969,3 +969,64 @@ using pre-clustering with the k-means algorithm.  Functions are also provided
 to search for all neighbors within a given distance.  Parallelization is
 achieved for all methods using the BiocParallel framework.")
     (license license:gpl3)))
+
+(define-public r-destiny
+  (package
+    (name "r-destiny")
+    (version "2.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "destiny" version))
+       (sha256
+        (base32
+         "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-fnn" ,r-fnn)
+       ("r-ggthemes" ,r-ggthemes)
+       ("r-hmisc" ,r-hmisc)
+       ("r-igraph" ,r-igraph)
+       ("r-matrix" ,r-matrix)
+       ("r-proxy" ,r-proxy)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)
+       ("r-scales" ,r-scales)
+       ("r-scatterplot3d" ,r-scatterplot3d)
+       ("r-smoother" ,r-smoother)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-vim" ,r-vim)))
+    (home-page "https://bioconductor.org/packages/destiny/")
+    (synopsis "Create and plot diffusion maps")
+    (description "This package provides tools to create and plot diffusion
+maps.")
+    ;; Any version of the GPL
+    (license license:gpl3+)))
+
+(define-public r-savr
+  (package
+    (name "r-savr")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "savR" version))
+       (sha256
+        (base32
+         "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
+    (properties `((upstream-name . "savR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-reshape2" ,r-reshape2)
+       ("r-scales" ,r-scales)
+       ("r-xml" ,r-xml)))
+    (home-page "https://github.com/bcalder/savR")
+    (synopsis "Parse and analyze Illumina SAV files")
+    (description
+     "This package provides tools to parse Illumina Sequence Analysis
+Viewer (SAV) files, access data, and generate QC plots.")
+    (license license:agpl3+)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8820ba0d8e..58cee5cbbe 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7099,13 +7099,13 @@ Bioconductor, CRAN, and Github.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.50.1")
+    (version "1.50.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "0hjm3r58i0r9qhyar9pk250cx7sfijg0lnvi12a9s6brmmbip1a3"))))
+                "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -7268,13 +7268,13 @@ abnormal copy number.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.20.0")
+    (version "0.20.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0qgiykjhnsvvpcp3zwmrnpx3bv3msvj0szchyvb1yb0fxw716xc5"))))
+                "18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -7349,7 +7349,7 @@ possible.")
 (define-public r-genomeinfodbdata
   (package
     (name "r-genomeinfodbdata")
-    (version "1.1.0")
+    (version "1.2.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -7359,7 +7359,7 @@ possible.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0k1hsjx6n2i1sf14hyrgdhxqxm5mxk0bgnivhiax944whcicmzbf"))))
+                "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
     (properties
      `((upstream-name . "GenomeInfoDbData")))
     (build-system r-build-system)
@@ -7657,13 +7657,13 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.50.0")
+    (version "2.50.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "0zw0dj67fnpbz4iqnam5fxs92c1c8w8d7mzl0rkq4ksx0xl8vgg7"))))
+                "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
@@ -7910,7 +7910,7 @@ extracting the desired features in a convenient format.")
 (define-public r-go-db
   (package
     (name "r-go-db")
-    (version "3.6.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.bioconductor.org/packages/"
@@ -7918,7 +7918,7 @@ extracting the desired features in a convenient format.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0fi2qywr9apg5lwfqfq9qq6bgrnv4rdhxx25656qn4bsy62i838j"))))
+                "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
     (properties
      `((upstream-name . "GO.db")))
     (build-system r-build-system)
@@ -8121,7 +8121,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomationdata
   (package
     (name "r-genomationdata")
-    (version "1.10.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8131,7 +8131,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
                                   "genomationData_" version ".tar.gz"))
               (sha256
                (base32
-                "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla"))))
+                "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7"))))
     (build-system r-build-system)
     ;; As this package provides little more than large data files, it doesn't
     ;; make sense to build substitutes.
@@ -8149,7 +8149,7 @@ downloaded from Encode.")
 (define-public r-org-hs-eg-db
   (package
     (name "r-org-hs-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8159,7 +8159,7 @@ downloaded from Encode.")
                                   "org.Hs.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927"))))
+                "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
     (properties
      `((upstream-name . "org.Hs.eg.db")))
     (build-system r-build-system)
@@ -8175,7 +8175,7 @@ on mapping using Entrez Gene identifiers.")
 (define-public r-org-ce-eg-db
   (package
     (name "r-org-ce-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8185,7 +8185,7 @@ on mapping using Entrez Gene identifiers.")
                                   "org.Ce.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9"))))
+                "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
     (properties
      `((upstream-name . "org.Ce.eg.db")))
     (build-system r-build-system)
@@ -8201,7 +8201,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
 (define-public r-org-dm-eg-db
   (package
     (name "r-org-dm-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8211,7 +8211,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
                                   "org.Dm.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d"))))
+                "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
     (properties
      `((upstream-name . "org.Dm.eg.db")))
     (build-system r-build-system)
@@ -8227,7 +8227,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
 (define-public r-org-mm-eg-db
   (package
     (name "r-org-mm-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8237,7 +8237,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
                                   "org.Mm.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g"))))
+                "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
     (properties
      `((upstream-name . "org.Mm.eg.db")))
     (build-system r-build-system)
@@ -8368,7 +8368,7 @@ in Biostrings objects.")
 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
   (package
     (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
-    (version "3.4.0")
+    (version "3.4.4")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8379,7 +8379,7 @@ in Biostrings objects.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
+                "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
     (properties
      `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
     (build-system r-build-system)
@@ -10215,14 +10215,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.6.0")
+    (version "2.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "12jqz9h6w4mxyfr43w5qbwmacn512aw0mnl0zvhsg5i7p4qj45ks"))))
+         "1js05dcv1dj4g2vj7lzlg0rgjcjlk2irdr9rxqpwxmivm8nbvf36"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -14118,6 +14118,85 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering.
 absolute GSEA.")
     (license license:gpl2)))
 
+(define-public jamm
+  (package
+    (name "jamm")
+    (version "1.0.7.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/mahmoudibrahim/JAMM.git")
+             (commit (string-append "JAMMv" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are none
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'build
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (substitute* "JAMM.sh"
+               (("^sPath=.*")
+                (string-append "")))
+             #t))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (libexec (string-append out "/libexec/jamm"))
+                    (bin (string-append out "/bin")))
+               (substitute* '("JAMM.sh"
+                              "SignalGenerator.sh")
+                 (("^sPath=.*")
+                  (string-append "sPath=\"" libexec "\"\n")))
+               (for-each (lambda (file)
+                           (install-file file libexec))
+                         (list "bincalculator.r"
+                               "peakfinder.r"
+                               "peakhelper.r"
+                               "signalmaker.r"
+                               "xcorr.r"
+                               "xcorrhelper.r"
+                               ;; Perl scripts
+                               "peakfilter.pl"
+                               "readshifter.pl"))
+
+               (for-each
+                (lambda (script)
+                  (chmod script #o555)
+                  (install-file script bin)
+                  (wrap-program (string-append bin "/" script)
+                    `("PATH" ":" prefix
+                      (,(string-append (assoc-ref inputs "coreutils") "/bin")
+                       ,(string-append (assoc-ref inputs "gawk") "/bin")
+                       ,(string-append (assoc-ref inputs "perl") "/bin")
+                       ,(string-append (assoc-ref inputs "r-minimal") "/bin")))
+                    `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
+                    `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
+                (list "JAMM.sh" "SignalGenerator.sh")))
+             #t)))))
+    (inputs
+     `(("bash" ,bash)
+       ("coreutils" ,coreutils)
+       ("gawk" ,gawk)
+       ("perl" ,perl)
+       ("r-minimal" ,r-minimal)
+       ;;("r-parallel" ,r-parallel)
+       ("r-signal" ,r-signal)
+       ("r-mclust" ,r-mclust)))
+    (home-page "https://github.com/mahmoudibrahim/JAMM")
+    (synopsis "Peak finder for NGS datasets")
+    (description
+     "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq,
+ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak
+boundaries accurately.  JAMM is applicable to both broad and narrow
+datasets.")
+    (license license:gpl3+)))
+
 (define-public ngless
   (package
     (name "ngless")
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 7f6857d260..6c3d88e7cb 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -133,10 +133,7 @@ in compression.")
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-source
-           (lambda _ (chdir "contrib/minizip") #t))
-         (add-after 'enter-source 'autoreconf
-           (lambda _
-             (invoke "autoreconf" "-vif"))))))
+           (lambda _ (chdir "contrib/minizip") #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
@@ -188,12 +185,7 @@ utility.  Instead of being written in Java, FastJar is written in C.")
               "02cihzl77ia0dcz7z2cga2412vyhhs5pa2355q4wpwbyga2lrwjh"))
             (patches (search-patches "libtar-CVE-2013-4420.patch"))))
    (build-system gnu-build-system)
-   (arguments
-    `(#:tests? #f ;no "check" target
-      #:phases
-      (modify-phases %standard-phases
-        (add-after 'unpack 'autoconf
-          (lambda _ (invoke "sh" "autoreconf" "-vfi"))))))
+   (arguments `(#:tests? #f)) ; no "check" target
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
@@ -1122,13 +1114,14 @@ smaller than those produced by @code{Xdelta}.")
     (version "3.1.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/jmacd/xdelta/archive/v"
-                           version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/jmacd/xdelta.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "17g2pbbqy6h20qgdjq7ykib7kg5ajh8fwbsfgyjqg8pwg19wy5bm"))
-       (file-name (string-append name "-" version ".tar.gz"))
+         "09mmsalc7dwlvgrda56s2k927rpl3a5dzfa88aslkqcjnr790wjy"))
        (snippet
         ;; This file isn't freely distributable and has no effect on building.
         '(begin
@@ -1142,9 +1135,7 @@ smaller than those produced by @code{Xdelta}.")
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-build-directory
-           (lambda _ (chdir "xdelta3") #t))
-         (add-after 'enter-build-directory 'autoconf
-           (lambda _ (invoke "autoreconf" "-vfi"))))))
+           (lambda _ (chdir "xdelta3") #t)))))
     (home-page "http://xdelta.org")
     (synopsis "Delta encoder for binary files")
     (description "xdelta encodes only the differences between two binary files
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ec950ce0ac..6ce9bdd16f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -32,11 +32,15 @@
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system r)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages gl)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages haskell)
+  #:use-module (gnu packages image)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
@@ -45,7 +49,8 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tls)
-  #:use-module (gnu packages web))
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages xorg))
 
 (define-public r-clipr
   (package
@@ -566,14 +571,16 @@ you to rapidly iterate while developing a package.")
 (define-public r-rcpp
   (package
     (name "r-rcpp")
-    (version "0.12.19")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rcpp" version))
        (sha256
-        (base32 "10mmiaawv9iwglc6z4y51mdpsfb1sivqmwr6xnfqkllcnpabdbk3"))))
+        (base32 "1hlbw4k79q9ich4w27b01gsvwrsnrflii8zjlcmgfzm1vpq8ndxp"))))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
     (home-page "http://www.rcpp.org")
     (synopsis "Seamless R and C++ integration")
     (description
@@ -2042,17 +2049,18 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.")
 (define-public r-jomo
   (package
     (name "r-jomo")
-    (version "2.6-4")
+    (version "2.6-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "jomo" version))
        (sha256
         (base32
-         "05g2rj9g7rgyb22b0gybw042nydyqsqsb31v05hifzavri8ij01x"))))
+         "109q5m69clrvvialxdxznd0wdb54ajhx84nj8slx8bf909a427mj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lme4" ,r-lme4)
+       ("r-mass" ,r-mass)
        ("r-ordinal" ,r-ordinal)
        ("r-survival" ,r-survival)))
     (home-page "https://cran.r-project.org/web/packages/jomo/")
@@ -3071,6 +3079,26 @@ Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
 Cambridge University Press, 1993.")
     (license license:gpl2)))
 
+(define-public r-aggregation
+  (package
+    (name "r-aggregation")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "aggregation" version))
+       (sha256
+        (base32
+         "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/aggregation/")
+    (synopsis "Methods for p-value aggregation")
+    (description
+     "This package contains functionality for performing the following methods
+of p-value aggregation: Fisher's method, the Lancaster method (weighted
+Fisher's method), and Sidak correction.")
+    (license license:gpl3)))
+
 (define-public r-quantmod
   (package
     (name "r-quantmod")
@@ -3452,6 +3480,36 @@ dendrograms.")
     ;; Either version of the license.
     (license (list license:gpl2 license:gpl3))))
 
+(define-public r-h5
+  (package
+    (name "r-h5")
+    (version "0.9.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "h5" version))
+       (sha256
+        (base32
+         "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)
+       ("hdf5" ,hdf5)))
+    (native-inputs
+     `(("which" ,which)))
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/mannau/h5")
+    (synopsis "Interface to the HDF5 Library")
+    (description
+     "This package provides an S4 interface to the HDF5 library supporting
+fast storage and retrieval of R-objects like vectors, matrices and arrays to
+binary files in a language independent format.  The HDF5 format can therefore
+be used as an alternative to R's save/load mechanism.  Since h5 is able to
+access only subsets of stored data it can also handle data sets which do not
+fit into memory.")
+    (license license:bsd-2)))
+
 (define-public r-cgdsr
   (package
     (name "r-cgdsr")
@@ -4392,14 +4450,14 @@ and adds the annotation to the plot.")
 (define-public r-ggpubr
   (package
     (name "r-ggpubr")
-    (version "0.1.8")
+    (version "0.1.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggpubr" version))
        (sha256
         (base32
-         "0psl2zndm4wk6nnj1nv305islpxfvfgd87gjh2ph8yqn4mxpnfi1"))))
+         "0rvfgii2gxarra7d33n6c63ky0mivxxyx35acsrn94xkbd8mbcsj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cowplot" ,r-cowplot)
@@ -4670,6 +4728,32 @@ Extract argument descriptions and other parts of the help pages of
 functions.")
     (license license:gpl2+)))
 
+(define-public r-rjags
+  (package
+    (name "r-rjags")
+    (version "4-8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rjags" version))
+       (sha256
+        (base32
+         "17xmjksj69f9wk4x71jxk4cgiqhaf2fj6bjm0mgzp4qln5x84a8m"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-coda" ,r-coda)))
+    (inputs
+     `(("jags" ,jags)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://mcmc-jags.sourceforge.net")
+    (synopsis "Bayesian graphical models using MCMC")
+    (description
+     "This package provides an R interface to the JAGS MCMC library.  JAGS is
+Just Another Gibbs Sampler.  It is a program for analysis of Bayesian
+hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
+    (license license:gpl2)))
+
 (define-public r-rdpack
   (package
     (name "r-rdpack")
@@ -4732,6 +4816,112 @@ be added or removed.  When working with Word documents, a cursor can be used
 to help insert or delete content at a specific location in the document.")
     (license license:gpl3)))
 
+(define-public r-abn
+  (package
+    (name "r-abn")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abn" version))
+       (sha256
+        (base32
+         "00k0razgdb5y5f62622fm7rxkcxrxg470nyyb02dvpfp60254kvs"))))
+    (build-system r-build-system)
+    (inputs
+     `(("gsl" ,gsl)))
+    (propagated-inputs
+     `(("r-cairo" ,r-cairo)
+       ("r-lme4" ,r-lme4)
+       ("r-mass" ,r-mass)
+       ("r-nnet" ,r-nnet)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rjags" ,r-rjags)))
+    (home-page "http://www.r-bayesian-networks.org")
+    (synopsis "Modelling multivariate data with additive bayesian networks")
+    (description
+     "Bayesian network analysis is a form of probabilistic graphical models
+which derives from empirical data a directed acyclic graph, DAG, describing
+the dependency structure between random variables.  An additive Bayesian
+network model consists of a form of a DAG where each node comprises a
+@dfn{generalized linear model} (GLM).  Additive Bayesian network models are
+equivalent to Bayesian multivariate regression using graphical modelling, they
+generalises the usual multivariable regression, GLM, to multiple dependent
+variables.  This package provides routines to help determine optimal Bayesian
+network models for a given data set, where these models are used to identify
+statistical dependencies in messy, complex data.")
+    (license license:gpl2+)))
+
+(define-public r-acd
+  (package
+    (name "r-acd")
+    (version "1.5.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ACD" version))
+       (sha256
+        (base32
+         "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
+    (properties `((upstream-name . "ACD")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/ACD/")
+    (synopsis "Categorical data analysis with complete or missing responses")
+    (description
+     "This package provides tools for categorical data analysis with complete
+or missing responses.")
+    (license license:gpl2+)))
+
+(define-public r-acdm
+  (package
+    (name "r-acdm")
+    (version "1.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ACDm" version))
+       (sha256
+        (base32
+         "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
+    (properties `((upstream-name . "ACDm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-plyr" ,r-plyr)
+       ("r-rsolnp" ,r-rsolnp)
+       ("r-zoo" ,r-zoo)))
+    (home-page "https://cran.r-project.org/web/packages/ACDm/")
+    (synopsis "Tools for Autoregressive Conditional Duration Models")
+    (description
+     "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
+and Russell, 1998) models.  It creates trade, price or volume durations from
+transactions (tic) data, performs diurnal adjustments, fits various ACD models
+and tests them.")
+    (license license:gpl2+)))
+
+(define-public r-overlap
+  (package
+    (name "r-overlap")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "overlap" version))
+       (sha256
+        (base32
+         "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/overlap/")
+    (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
+    (description
+     "This package provides functions to fit kernel density functions to data
+on temporal activity patterns of animals; estimate coefficients of overlapping
+of densities for two species; and calculate bootstrap estimates of confidence
+intervals.")
+    (license license:gpl3+)))
+
 (define-public r-snakecase
   (package
     (name "r-snakecase")
@@ -6507,14 +6697,14 @@ Bayesian modeling.")
 (define-public r-tmb
   (package
     (name "r-tmb")
-    (version "1.7.14")
+    (version "1.7.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TMB" version))
        (sha256
         (base32
-         "0bpc504nz8xfwr8ack52dj4hpjcykn6zyf8n228z32dw9d5n96dl"))))
+         "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
     (properties `((upstream-name . "TMB")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6885,14 +7075,14 @@ directories or URLs with their associated programs.")
 (define-public r-rcmdcheck
   (package
     (name "r-rcmdcheck")
-    (version "1.3.1")
+    (version "1.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rcmdcheck" version))
        (sha256
         (base32
-         "1ga19jqix0zs7xyz2j155zyagwbv22r6dgv55g6wdjigc67qfsix"))))
+         "0ys1nd7690mhwzslyzg8fq1wxr28nz8g6av5iykkrshb8lkxg7ly"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -7325,3 +7515,242 @@ netCDF files.")
      "This package provides a convenient tool to install and update
 Bioconductor packages.")
     (license license:artistic2.0)))
+
+(define-public r-rgl
+  (package
+    (name "r-rgl")
+    (version "0.99.16")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rgl" version))
+       (sha256
+        (base32
+         "0q8sg8fr0140ilssqhscaxkjc29w1rpp6f4k50amw3zzs9g58ak9"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("freetype" ,freetype)
+       ("libpng" ,libpng)
+       ("glu" ,glu)
+       ("libx11" ,libx11)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-crosstalk" ,r-crosstalk)
+       ("r-htmltools" ,r-htmltools)
+       ("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-knitr" ,r-knitr)
+       ("r-magrittr" ,r-magrittr)
+       ("r-manipulatewidget" ,r-manipulatewidget)
+       ("r-shiny" ,r-shiny)))
+    (home-page "https://r-forge.r-project.org/projects/rgl/")
+    (synopsis "3D visualization using OpenGL")
+    (description
+     "This package provides medium to high level functions for 3D interactive graphics,
+including functions modelled on base graphics (@code{plot3d()}, etc.) as well
+as functions for constructing representations of geometric
+objects (@code{cube3d()}, etc.).  Output may be on screen using OpenGL, or to
+various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
+image formats, including PNG, Postscript, SVG, PGF.")
+    ;; Any version of the GPL.
+    (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-multicool
+  (package
+    (name "r-multicool")
+    (version "0.1-10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "multicool" version))
+       (sha256
+        (base32
+         "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://cran.r-project.org/web/packages/multicool/")
+    (synopsis "Permutations of multisets in cool-lex order")
+    (description
+     "This package provides a set of tools to permute multisets without loops
+or hash tables and to generate integer partitions.  Cool-lex order is similar
+to colexicographical order.")
+    (license license:gpl2)))
+
+(define-public r-misc3d
+  (package
+    (name "r-misc3d")
+    (version "0.8-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "misc3d" version))
+       (sha256
+        (base32
+         "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/misc3d/")
+    (synopsis "Miscellaneous 3D Plots")
+    (description
+     "This package provides a collection of miscellaneous 3d plots, including
+isosurfaces.")
+    ;; Any version of the GPL.
+    (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-ks
+  (package
+    (name "r-ks")
+    (version "1.11.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ks" version))
+       (sha256
+        (base32
+         "0z749c3xzpf6n0g7xcfplrhap1di8k7kcfr7vigh95ywnigyhs8d"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-fnn" ,r-fnn)
+       ("r-kernlab" ,r-kernlab)
+       ("r-kernsmooth" ,r-kernsmooth)
+       ("r-matrix" ,r-matrix)
+       ("r-mclust" ,r-mclust)
+       ("r-mgcv" ,r-mgcv)
+       ("r-misc3d" ,r-misc3d)
+       ("r-multicool" ,r-multicool)
+       ("r-mvtnorm" ,r-mvtnorm)))
+    (home-page "http://www.mvstat.net/tduong/")
+    (synopsis "Kernel smoothing")
+    (description
+     "This package provides kernel smoothers for univariate and multivariate
+data, including density functions, density derivatives, cumulative
+distributions, modal clustering, discriminant analysis, and two-sample
+hypothesis testing.")
+    ;; Either version of the GPL.
+    (license (list license:gpl2 license:gpl3))))
+
+(define-public r-feature
+  (package
+    (name "r-feature")
+    (version "1.2.13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "feature" version))
+       (sha256
+        (base32
+         "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ks" ,r-ks)
+       ("r-misc3d" ,r-misc3d)
+       ("r-rgl" ,r-rgl)))
+    (home-page "http://www.mvstat.net/tduong/")
+    (synopsis "Inferential feature significance for kernel density estimation")
+    (description
+     "The feature package contains functions to display and compute kernel
+density estimates, significant gradient and significant curvature regions.
+Significant gradient and/or curvature regions often correspond to significant
+features (e.g. local modes).")
+    ;; Either version of the GPL.
+    (license (list license:gpl2 license:gpl3))))
+
+(define-public r-arm
+  (package
+    (name "r-arm")
+    (version "1.10-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "arm" version))
+       (sha256
+        (base32
+         "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-abind" ,r-abind)
+       ("r-coda" ,r-coda)
+       ("r-lme4" ,r-lme4)
+       ("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-nlme" ,r-nlme)))
+    (home-page "https://cran.r-project.org/web/packages/arm/")
+    (synopsis "Data analysis using regression and multilevel/hierarchical models")
+    (description
+     "This package provides functions to accompany A. Gelman and J. Hill,
+Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
+University Press, 2007.")
+    (license license:gpl3+)))
+
+(define-public r-circular
+  (package
+    (name "r-circular")
+    (version "0.4-93")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "circular" version))
+       (sha256
+        (base32
+         "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-boot" ,r-boot)
+       ("r-mvtnorm" ,r-mvtnorm)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/circular/")
+    (synopsis "Circular statistics")
+    (description
+     "This package provides tools for circular statistics, from \"Topics in
+circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
+Scientific.")
+    (license license:gpl2+)))
+
+(define-public r-activity
+  (package
+    (name "r-activity")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "activity" version))
+       (sha256
+        (base32
+         "1lqajgxfps2h6amz1791vp3f52rs9ghmanq1nqfxqd2jmk3idkrx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-circular" ,r-circular)
+       ("r-overlap" ,r-overlap)
+       ("r-pbapply" ,r-pbapply)))
+    (home-page "https://cran.r-project.org/web/packages/activity/")
+    (synopsis "Animal activity statistics")
+    (description
+     "This package provides functions to fit kernel density functions to
+animal activity time data; plot activity distributions; quantify overall
+levels of activity; statistically compare activity metrics through
+bootstrapping; and evaluate variation in linear variables with time (or other
+circular variables).")
+    (license license:gpl3)))
+
+(define-public r-ouch
+  (package
+    (name "r-ouch")
+    (version "2.11-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ouch" version))
+       (sha256
+        (base32
+         "0xkwwi62vdahlcg3k32zb1nfwsx87zdssk79mvcxgfsw9bw4gahx"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-subplex" ,r-subplex)))
+    (home-page "http://kingaa.github.io/ouch/")
+    (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
+    (description
+     "This package provides tools to fit and compare Ornstein-Uhlenbeck models
+for evolution along a phylogenetic tree.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index 29d9a3d6ab..e8062f0e1f 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 David Thompson <davet@gnu.org>
-;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -164,34 +164,31 @@ OpenBSD tool of the same name.")
                                           "See base64.c in the distribution for
                                            the license from IBM.")))))
 
-
 (define-public opendht
   (package
     (name "opendht")
     (version "0.6.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append
-         "https://github.com/savoirfairelinux/" name
-         "/archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           (delete-file-recursively "src/argon2")
-           (substitute* "src/Makefile.am"
-             (("./argon2/libargon2.la") "")
-             (("SUBDIRS = argon2") ""))
-           (substitute* "src/crypto.cpp"
-             (("argon2/argon2.h") "argon2.h"))
-           (substitute* "configure.ac"
-             (("src/argon2/Makefile") ""))
-           #t))
-       (sha256
-        (base32
-         "09yvkmbqbym3b5md4n96qc1s9sf2n8ji404hagih45rmsj49599x"))))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/savoirfairelinux/opendht.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (delete-file-recursively "src/argon2")
+                  (substitute* "src/Makefile.am"
+                    (("./argon2/libargon2.la") "")
+                    (("SUBDIRS = argon2") ""))
+                  (substitute* "src/crypto.cpp"
+                    (("argon2/argon2.h") "argon2.h"))
+                  (substitute* "configure.ac"
+                    (("src/argon2/Makefile") ""))
+                  #t))
+              (sha256
+               (base32
+                "1akk613f18rc8kqs0cxdm34iq7wwc9kffhgp5rng09arwlw8gw3w"))))
     (build-system gnu-build-system)
     (inputs
      `(("gnutls" ,gnutls)
@@ -206,11 +203,7 @@ OpenBSD tool of the same name.")
        ("automake" ,automake)
        ("libtool" ,libtool)))
     (arguments
-     `(#:configure-flags '("--disable-tools" "--disable-python")
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'autoconf
-                    (lambda _
-                      (zero? (system* "autoreconf" "-vfi")))))))
+     `(#:configure-flags '("--disable-tools" "--disable-python")))
     (home-page "https://github.com/savoirfairelinux/opendht/")
     (synopsis "Distributed Hash Table (DHT) library")
     (description "OpenDHT is a Distributed Hash Table (DHT) library.  It may
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 1617c28b1e..05bebed6a6 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -803,14 +803,14 @@ as a drop-in replacement of MySQL.")
 (define-public postgresql
   (package
     (name "postgresql")
-    (version "10.5")
+    (version "10.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "04a07jkvc5s6zgh6jr78149kcjmsxclizsqabjw44ld4j5n633kc"))))
+                "0jv26y3f10svrjxzsgqxg956c86b664azyk2wppzpa5x11pjga38"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-uuid=e2fs")
@@ -2087,13 +2087,14 @@ for ODBC.")
     (version "0.7.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/brianb/mdbtools/archive/"
-                           version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/brianb/mdbtools.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "05hbmxcq173kzb899gdi3bz2qcc1vi3n1qbbkwpsvrq7ggf11wyw"))
-       (file-name (string-append name "-" version ".tar.gz"))))
+         "0gwcpp9y09xhs21g7my2fs8ncb8i6ahlyixcx8jd3q97jbzj441l"))))
     (build-system gnu-build-system)
     (inputs
      `(("glib" ,glib)))
@@ -2104,12 +2105,6 @@ for ODBC.")
        ("pkg-config" ,pkg-config)
        ("txt2man" ,txt2man)
        ("which" ,which)))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
-           (lambda _
-             (zero? (system* "autoreconf" "-vfi")))))))
     (home-page "http://mdbtools.sourceforge.net/")
     (synopsis "Read Microsoft Access databases")
     (description "MDB Tools is a set of tools and applications to read the
diff --git a/gnu/packages/datastructures.scm b/gnu/packages/datastructures.scm
index 8517654def..4e5e59a2e3 100644
--- a/gnu/packages/datastructures.scm
+++ b/gnu/packages/datastructures.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -48,6 +49,29 @@ binary trees, binary search trees, red-black trees, 2D arrays, permutations
 and heaps.")
     (license license:gpl2+)))
 
+(define-public marisa
+  (package
+    (name "marisa")
+    (version "0.2.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/s-yata/marisa-trie"
+                           "/releases/download/v" version "/" name "-"
+                           version ".tar.gz"))
+       (sha256
+        (base32 "19ifrcmnbr9whaaf4ly3s9ndyiq9sjqhnfkrxbz9zsb44w2n36hf"))))
+    (build-system gnu-build-system)
+    (home-page "https://github.com/s-yata/marisa-trie")
+    (synopsis "Trie data structure C++ library")
+    (description "Matching Algorithm with Recursively Implemented
+StorAge (MARISA) is a static and space-efficient trie data structure C++
+library.")
+
+    ;; Dual-licensed, according to docs/readme.en.html (source files lack
+    ;; copyright/license headers.)
+    (license (list license:bsd-2 license:lgpl2.1+))))
+
 (define-public sparsehash
   (package
     (name "sparsehash")
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index c6008e6a94..3e32998a9f 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -40,6 +40,7 @@
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
 ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
 ;;; Copyright © 2018 Thorsten Wilms <t_w_@freenet.de>
+;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3848,6 +3849,31 @@ use it, call @code{M-x ivy-yasnippet} (but make sure you have enabled
 @code{yas-minor-mode} first).")
       (license license:gpl3+))))
 
+(define-public emacs-ivy-rich
+  (package
+    (name "emacs-ivy-rich")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/Yevgnen/ivy-rich/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "14r3mx5rkd4wz0ls5pv5w6c7la3z9iy93d3jfind3xyg4kywy95c"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-ivy" ,emacs-ivy)))
+    (home-page "https://github.com/Yevgnen/ivy-rich")
+    (synopsis "More friendly interface for @code{ivy}")
+    (description
+     "This package extends @code{ivy} by showing more information in the
+minibuffer for each candidate.  It adds columns showing buffer modes, file
+sizes, docstrings, etc.  If @code{emacs-all-the-icons} is installed, it can
+show icons as well.")
+    (license license:gpl3+)))
+
 (define-public emacs-avy
   (package
     (name "emacs-avy")
@@ -7688,17 +7714,17 @@ value of the access token.")
 (define-public emacs-circe
   (package
     (name "emacs-circe")
-    (version "2.6")
+    (version "2.10")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/jorgenschaefer/circe.git")
              (commit (string-append "v" version))))
-       (file-name (string-append name "-" version "-checkout"))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "19h3983zy3f15cgs86irvbdzz55qyjm48qd7gjlzcxplr7vnnh0j"))))
+         "10gi14kwxd81blddpvqh95lgmpbfgp0m955naxix3bs3r6a75n4s"))))
     (build-system emacs-build-system)
     ;; In order to securely connect to an IRC server using TLS, Circe requires
     ;; the GnuTLS binary.
diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm
index 38c76cd737..f20d1e17c7 100644
--- a/gnu/packages/embedded.scm
+++ b/gnu/packages/embedded.scm
@@ -321,12 +321,6 @@ languages are C and C++.")
          ("pkg-config" ,pkg-config)))
       (inputs
        `(("libusb" ,libusb)))
-      (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'autoreconf
-             (lambda _
-               (zero? (system* "autoreconf" "-vfi")))))))
       (home-page "http://repo.or.cz/w/libjaylink.git")
       (synopsis "Library to interface Segger J-Link devices")
       (description "libjaylink is a shared library written in C to access
@@ -404,9 +398,9 @@ language.")
                       "presto" "openjtag")))
        #:phases
        (modify-phases %standard-phases
+         ;; Required because of patched sources.
          (add-before 'configure 'autoreconf
-           (lambda _
-             (zero? (system* "autoreconf" "-vfi"))))
+           (lambda _ (invoke "autoreconf" "-vfi") #t))
          (add-after 'autoreconf 'change-udev-group
            (lambda _
              (substitute* "contrib/60-openocd.rules"
@@ -417,7 +411,8 @@ language.")
              (install-file "contrib/60-openocd.rules"
                            (string-append
                             (assoc-ref outputs "out")
-                            "/lib/udev/rules.d/")))))))
+                            "/lib/udev/rules.d/"))
+             #t)))))
     (home-page "http://openocd.org")
     (synopsis "On-Chip Debugger")
     (description "OpenOCD provides on-chip programming and debugging support
diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index da1675820b..1f73025db7 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -399,13 +399,14 @@ support.")
     (name "tiled")
     (version "1.2.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/bjorn/tiled/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/bjorn/tiled.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "13dlf5kzvhhjkhy19118x3diakmraz4m9kxrsdam8dms6xivb6lp"))))
+                "1rra48hlkcgqxwxi802fb182p1q0723c9hhfvkd5inz9467idd4c"))))
     (build-system gnu-build-system)
     (inputs
      `(("qtbase" ,qtbase)
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 4481e21ddf..fa2b259d7c 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -549,14 +549,14 @@ coordinates.")
 (define-public r-rgooglemaps
   (package
    (name "r-rgooglemaps")
-   (version "1.4.2")
+   (version "1.4.3")
    (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RgoogleMaps" version))
        (sha256
         (base32
-         "112mdm53qx92n2m4ms02sbppckp44l1z19vy99j6gw3jrdprjydl"))))
+         "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4"))))
    (properties `((upstream-name . "RgoogleMaps")))
    (build-system r-build-system)
    (propagated-inputs `(("r-png" ,r-png)))
diff --git a/gnu/packages/gnustep.scm b/gnu/packages/gnustep.scm
index bd28ceaa00..dd7c67d553 100644
--- a/gnu/packages/gnustep.scm
+++ b/gnu/packages/gnustep.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -167,14 +168,7 @@ interface.  It is fast, feature rich, easy to configure, and easy to use.")
                (base32
                 "084a3irxbmgms4bqaga80mlx9wgvlkx6d2w0ns939yrpfzg87laj"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:tests? #f              ; no "check" target
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _
-             (invoke "autoreconf" "-vfi")
-             #t)))))
+    (arguments '(#:tests? #f)) ; no "check" target
     (inputs
      `(("glib" ,glib)
        ("libx11" ,libx11)
@@ -262,18 +256,11 @@ on.")
                (base32
                 "1lx276ba8r2yydhmwj1g586jdqg695ad89ng36fr3mb067gvb2rz"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _
-             (invoke "autoreconf" "-vfi")
-             #t)))))
-    ;; wmclock requires autoreconf to generate its configure script.
     (inputs
      `(("libx11" ,libx11)
        ("libxext" ,libxext)
        ("libxpm" ,libxpm)))
+    ;; wmclock requires autoreconf to generate its configure script.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index 1dd0e930d3..e1abe8c2cd 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -482,83 +482,33 @@ security standards.")
 (define-public icecat
   (package
     (name "icecat")
-    (version "60.2.0-gnu1")
+    (version "60.3.0-gnu1")
     (source
      (origin
       (method url-fetch)
-      ;; Temporary URL pending official release:
-      (uri "https://alpha.gnu.org/gnu/gnuzilla/60.2.0/icecat-60.2.0-gnu1.tar.bz2")
-      #;
       (uri (string-append "mirror://gnu/gnuzilla/"
                           (first (string-split version #\-))
                           "/" name "-" version ".tar.bz2"))
       (sha256
        (base32
-        "0lqx7g79x15941rhjr3qsfwsny6vzc7d7abdmvjy6jjbqkqlc1zl"))
+        "0icnl64nxcyf7dprpdpygxhabsvyhps8c3ixysj9bcdlj9q34ib1"))
       (patches
        (list
         (search-patch  "icecat-avoid-bundled-libraries.patch")
         (search-patch  "icecat-use-system-graphite2+harfbuzz.patch")
         (search-patch  "icecat-use-system-media-libs.patch")
-        (mozilla-patch "icecat-CVE-2018-12385.patch"      "80a4a7ef2813" "1vgcbimpnfjqj934v0cryq1g13xac3wfmd4jyhcb5s60x8xyssf5")
-        (search-patch  "icecat-CVE-2018-12383.patch")
-        (mozilla-patch "icecat-bug-1489744.patch"         "6546ee839d30" "11mhvj77r789b428bfxqq5wdx8yr7lbrdjzr8qjj6fw197pldn51")
-        (mozilla-patch "icecat-CVE-2018-12386.patch"      "4808fcb2e6ca" "05sc881l7sh8bag8whd2ggdn198lskqcxq8f41scfpqscw6xs5d5")
-        (mozilla-patch "icecat-CVE-2018-12387.patch"      "b8f5c37486e1" "0lvmbh126m695kgdbasy1y5xh9n1j08cwdhn071mgvj6yn8cns5z")
-        (mozilla-patch "icecat-bug-1464751.patch"         "d5d00faf0465" "1mj7dbb06brwrk0mvap0z4lfl2hwz1cj6dwjvdrisxm046pdw98i")
-        (mozilla-patch "icecat-bug-1472538.patch"         "11462f2b98f2" "1nxgh0plzilylx8r73r7d74pv66qwjqxmd7nqii33p0snl2jjfzs")
-        (mozilla-patch "icecat-bug-1478685.patch"         "098585dc86fc" "1b0x4qdh6isvffmibvc8ad8z62m3iky9q6jq0z6gyvn8q252cqal")
-        (mozilla-patch "icecat-bug-1486080.patch"         "3f8d57d936ea" "0pz2c18wcgj44v0j8my9xbm90m4bsjcvzmavj569fi8bh6s6zz8p")
-        (mozilla-patch "icecat-bug-1423278.patch"         "878ceaee5634" "0i47s5nvrx9vqbnj6s9y9f4ffww20p8nviqa6frg676y1188xlyl")
-        (mozilla-patch "icecat-CVE-2018-12390-pt01.patch" "87be1b98ec9a" "15f4l18c7hz9aqn89gg3dwmdidfwgn10dywgpzydm8mps45amx7j")
-        (mozilla-patch "icecat-bug-1484559.patch"         "99e58b5307ce" "02fdgbliwzi2r2376wg6k1rky1isfka0smac4ii2cll01jhpfrn6")
-        (mozilla-patch "icecat-CVE-2018-12390-pt02.patch" "f25ce451a492" "18nzg39iyxza1686180qk9cc88l5j2hf1h35d62lrqmdgd9vcj33")
-        (mozilla-patch "icecat-CVE-2018-12390-pt03.patch" "35c26bc231df" "0qh8d4z6y03h5xh7djci26a01l6zq667lg2k11f6zzg7z2j0h67x")
-        (mozilla-patch "icecat-bug-1488061.patch"         "050d0cfa8e3d" "05ql798ynbyz5pvyri4b95j4ixmgnny3zl7sd2ckfrrbm9mxh627")
-        (mozilla-patch "icecat-bug-1434963-pt1.patch"     "1e6dad87efed" "1v00a6cmgswjk54041jyv1ib129fxshpzwk6mn6lr0v5hylk3bx9")
-        (mozilla-patch "icecat-bug-1434963-pt2.patch"     "6558c46df9ea" "0vdy9dm9w5k1flhcfxwvvff0aa415b5mgmmq5r37i83686768xfb")
-        (mozilla-patch "icecat-bug-1434963-pt3.patch"     "686fcfa8abd6" "0ihqr11aq4b0y7mx7bwn8yzn25mv3k2gdphm951mj1g85qg35ann")
-        (mozilla-patch "icecat-bug-1491132.patch"         "14120e0c74d6" "188c5fbhqqhmlk88p70l6d97skh7xy4jhqdby1ri3h9ix967515j")
-        (mozilla-patch "icecat-bug-1492065.patch"         "ec4b5969c6ae" "18gfwn15kh0826vlg6lhrx3q4gv82i7v1k3y5jp72mvrjq154gy0")
-        (mozilla-patch "icecat-bug-1492064.patch"         "528cabdd9665" "0rdwpkfma24hn8namfb9saw4rgi9yyyj4af5h2ijrvadw6r8lyyn")
-        (mozilla-patch "icecat-bug-1489757.patch"         "46f19852aaa6" "0dga7mw847klm8x6il2fyzpjxqxxgx1q5cya658f1w66kxms1f29")
-        (mozilla-patch "icecat-bug-1492897.patch"         "c3a48066f383" "09n6sdck4jzzmznzrq0iixg5nsgrc5ibpdfsh3i7ppwad3fsy2m3")
-        (mozilla-patch "icecat-bug-1492915.patch"         "2d280e557331" "11x2n61pw5way9cg8lbrfl3lqvgfnbmcs1fwm78i06kmfwj0msk3")
-        (mozilla-patch "icecat-CVE-2018-12390-pt04.patch" "b80f94262165" "1hw43h4sgf77x323745rixyp6cci3fb6d3fnp33q82m4ssdb5623")
-        (mozilla-patch "icecat-bug-1492484.patch"         "1b3e6759cf3a" "1yn2cd2227ncg90c88ymdi5fyfs4hk335bd16vkkgljs0924yy0m")
-        (mozilla-patch "icecat-bug-1493590.patch"         "d9fe3b2025fc" "06783hj1aqms2f9a3mp18bk8hgijk3pz70bpccn173v4w0zlbbd4")
-        (mozilla-patch "icecat-CVE-2018-12390-pt05.patch" "20c59797e994" "1vxnhpirjsj040hrq9xmq2xhkpq4l5mnnzqy0nda92dfh47zvidj")
-        (mozilla-patch "icecat-CVE-2018-12390-pt06.patch" "1749661dfd28" "0g0sj2fgp3asj0yvxksnhrc59yxncn35bz5nzlvkpgdf7h06gscd")
-        (mozilla-patch "icecat-CVE-2018-12390-pt07.patch" "a511a9242406" "1hhfrvdmkccnhs4skbi06174x37rmvf4ic86xawyyzr67yga73b2")
-        (mozilla-patch "icecat-bug-1495404.patch"         "3232bb3b622f" "1pnaxf8r9h0wldjc4qgl7z3rk34fpz9h1vd3zmhswa6mvyln5jhg")
-        (mozilla-patch "icecat-bug-1465388.patch"         "a9577451dcc2" "0v29s0v3vv9vblkcachhh46qvwjcrmv2bkcdb7sj2asc503l0lqv")
-        (mozilla-patch "icecat-CVE-2018-12390-pt08.patch" "e965f6f6ed75" "0hh091854xj5j0x1r8pg46xmn00fqi5n212xhzbdpgyf96rsf513")
-        (mozilla-patch "icecat-bug-1445528.patch"         "8a503e022a29" "1y2ll3h0yz8sfdddjmk90qjfxcr1ffhw7a9ww3yw26gyhnbpg404")
-        (mozilla-patch "icecat-bug-1409570.patch"         "8d326641d1c0" "0w29s6dixi7b7q3nicshrp29n9sj5awssdln00yx664m8a8a8ihs")
-        (mozilla-patch "icecat-bug-1496094.patch"         "6cdd6d88eca9" "1ssqa4fy2xpbr63ph3av3hkpl92g4yszx402fq9d2xn9482q43dp")
-        (mozilla-patch "icecat-CVE-2018-12391.patch"      "0fa07c704ca4" "055xdyb3g2l4rj188235i579qnr50v19q36jjpliws9nik129iqy")
-        (mozilla-patch "icecat-bug-1462162.patch"         "739e898cb7c8" "17m9y0pskmqx15dkgkw4k93njph14mpsf37wb1azwkq3xx7s0fhx")
-        (mozilla-patch "icecat-bug-1492764.patch"         "16310ab35452" "1kq5r3w9i4n6q9msmw2qsqa0jd4qw1mjlyyz8aq14fwlbkhvv199")
-        (mozilla-patch "icecat-CVE-2018-12390-pt09.patch" "9b669d047d55" "063ig49gx9468nvc9w8259j819qfdjvq0sbbz8n4kj5r6hcxjc5l")
-        (mozilla-patch "icecat-CVE-2018-12390-pt10.patch" "9d51e65c797a" "0m23cq9zl22w80dvx5rlgpbam1l3d6v56h7g9wzamzl21bwxq9fv")
-        (mozilla-patch "icecat-CVE-2018-12390-pt11.patch" "efc0596dd381" "1alvbb6wvawxxh6isisk9c40vhdiv59fy0af0n10yn1dgy8ffv5i")
-        (mozilla-patch "icecat-CVE-2018-12393.patch"      "c4fb48bb5d28" "09izww9dsg9n8cish8f3y7phxibsnd12bfkcxd7rzcdhg10nr4pl")
-        (mozilla-patch "icecat-CVE-2018-12390-pt12.patch" "b3359becd7b1" "188byxmbgrvrid2fcz34w5xdvaw571frxx1c6nqaa9k03iljdzjr")
-        (mozilla-patch "icecat-CVE-2018-12390-pt13.patch" "791c8ecf252d" "02h37594aba0pklxm3g7w1wv8vz9xmcf30fd0az8pfaccsklmx74")
-        (mozilla-patch "icecat-bug-1494328.patch"         "333276fac37c" "0qyq42jl0al63m6pwj9gva7nj82l76szzbj7sklsygx0a9mqs13z")
-        (mozilla-patch "icecat-CVE-2018-12397.patch"      "cb73374a0e4e" "0x2s1nwgwdag9df5hkwzvjj0qznp5c3d6w6y63rn2y287jn9m3vl")
-        (mozilla-patch "icecat-CVE-2018-12392.patch"      "f6bb138ad0ab" "0f0z9dsyw2a11p4p31mdyic571153jpfgy2q04i4v6dmmcz76pm3")
-        (mozilla-patch "icecat-CVE-2018-12396.patch"      "f27145bd5502" "0vznmlm1fbl3ynax2zpi6xxzr9qp9b83afr3mv90jgrhlgpzdbcz")
-        (mozilla-patch "icecat-CVE-2018-12395-pt1.patch"  "133a99a8f3ca" "0im7m4jmc273mg9kih0i70hxsgzy04j6ydm9zmaz2933hkhdf4iw")
-        (mozilla-patch "icecat-CVE-2018-12395-pt2.patch"  "82176a4a9b14" "0g3yqx4854d4mx5a0ghb7p7saj6y5d5bm2lfhabvkwybcd477zmc")
-        (mozilla-patch "icecat-bug-1474265.patch"         "e8abd9a8ce6e" "1q2sv5h081rvnhsx6g1y8a43hwv6hsg0cr6zdcij58mkgzf6hyvd")
-        (mozilla-patch "icecat-bug-1492737-pt1.patch"     "eeb9060379dc" "1d2mf0x4rni7anvi0sgra4dg87fmc6g7zhizzl9jv2x8va27ycbp")
-        (mozilla-patch "icecat-bug-1492737-pt2.patch"     "99eae0d15092" "0f9j6cvhrbrrxa95p4pkcn285r9wmi9yj13nwj5x0gkglwx6idbk")
-        (mozilla-patch "icecat-CVE-2018-12389-pt1.patch"  "23b23e12c548" "0nsdycggki5rhh59yvmh41nf1ahjmgii89fx38jryprhspy3wg62")
-        (mozilla-patch "icecat-CVE-2018-12390-pt14.patch" "023133ff02ec" "1g22qxnmgiy8bgrn2nv6har6vpz4p2h5pdas8ib1yyz7p2ic8652")
-        (mozilla-patch "icecat-CVE-2018-12390-pt15.patch" "9461988ff462" "0yq2cr5grqskr0kz4nxcwmnywy9g0xyv6k6q44i490jcj8x2y1vw")
-        (mozilla-patch "icecat-CVE-2018-12390-pt16.patch" "09939be135d8" "1546xlk368v4hnjd3hf4w868i6m8r4wfd34qxz4wg1cdpr4m5mik")
-        (mozilla-patch "icecat-CVE-2018-12389-pt2.patch"  "ea9412b18ca8" "0fmdncrylbmjh0bcb6dmw1rq7zww8a0v9v9p1pxqfz0vbc6v9l5d")))
+        (mozilla-patch "icecat-bug-1464061.patch"         "d28761dbff18" "1f58rzwx4s1af66fdwn9lgkcd1ksmq8kn8imvf78p90jqi24h7b4")
+        (mozilla-patch "icecat-bug-1479853.patch"         "4faeb696dd06" "12891xx9c15s6kby6d3zk64v5nqgaq7sw597zv1fkd3a6x69hlva")
+        (mozilla-patch "icecat-bug-1488295.patch"         "12ba39f69876" "1piyq44f0xa0a9z2748aqwpaziaxwp61d86gyhalbyag8lcxfb3p")
+        (mozilla-patch "icecat-bug-1500011.patch"         "a0adabeedf26" "0f5wazha3zxzhy2j8f93hx62l9p02b1p40vi07qah3ar67h4ccj9")
+        (mozilla-patch "icecat-bug-1503082.patch"         "19604eb26230" "1wqxgph4z14ijhk2j2m4av5p6gx72d02lzz83q6yy0k065kw8psb")
+        (mozilla-patch "icecat-bug-1499861.patch"         "98737ab09270" "0fyl6wv0jxcxpkfpsff46y93k49n8lrw0k7c1p45g8da015dx27a")
+        (mozilla-patch "icecat-bug-1504452.patch"         "1cf7d80355d5" "19jp4x32vyxam54d1r9fm7jwf6krhhf3xazfqmxb9aw4iwdil7dl")
+        (mozilla-patch "icecat-bug-1494752.patch"         "c264774b8913" "1hxyi131x8jwawrq90cgkph833iv9ixrdrgzl1r978gbzwq10xz2")
+        (mozilla-patch "icecat-bug-1477773.patch"         "ec13fda7c9b0" "0zj7aylgw55g0y7plaafn5gq8jwcsdr1bpdxacs0hq914nm8zy9z")
+        (mozilla-patch "icecat-bug-1500759.patch"         "5e1a9644aeef" "1qimrpgyrd8zkiri7w57j0aymk20y9b34am5w7rvr6qj1lhrbfla")
+        (mozilla-patch "icecat-bug-1485655.patch"         "9055726e2d89" "1pppxr94zqh6zmi2mn1ih21qap09vk5ivbhnwxqr8iszvygjg44g")
+        (mozilla-patch "icecat-bug-1410214.patch"         "9e641345e2ef" "0542xss2jdb8drh4g50cfy32l300x69dyywgx3dqs03vgr3qplxy")))
       (modules '((guix build utils)))
       (snippet
        '(begin
diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 49fe34f13d..60890bf724 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -537,7 +537,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                  (setenv "GOGC" "400")
                  #t)))))))))
 
-(define-public go go-1.9)
+(define-public go go-1.11)
 
 (define-public go-github-com-alsm-ioprogress
   (let ((commit "063c3725f436e7fba0c8f588547bee21ffec7ac5")
@@ -2161,26 +2161,28 @@ generate ANSI colored strings.")
           (base32
            "1d9hr29i36cza98afj3g6rs3l7xbkprwzz0blcxsr9dd7nak20di"))))
       (build-system go-build-system)
-      (native-inputs
+      ;; From go-1.10 onward, "pkg" compiled libraries are not re-used, so
+      ;; when this package required as input for another one, it will have to
+      ;; be built again.  Thus its CGO requirements must be made available in
+      ;; the environment, that is, they must be propagated.
+      (propagated-inputs
        `(("lua" ,lua)))
       (arguments
        `(#:unpack-path "github.com/aarzilli/golua"
          #:import-path "github.com/aarzilli/golua/lua"
          #:phases
          (modify-phases %standard-phases
-           (replace 'build
-             (lambda* (#:key import-path #:allow-other-keys)
-               (invoke "go" "install"
-                       "-v"  ; print the name of packages as they are compiled
-                       "-x"  ; print each command as it is invoked
-                       "-ldflags=-s -w" ; strip the symbol table and debug
-                       "-tags" "llua" ; Latest Lua on Guix does not have a version number.
-                       import-path)))
-           (replace 'check
-             (lambda* (#:key import-path #:allow-other-keys)
-               (invoke "go" "test"
-                       "-tags" "llua" ; Latest Lua on Guix does not have a version number.
-                       import-path))))))
+           ;; While it's possible to fix the CGO_LDFLAGS with the "-tags"
+           ;; command line argument, go-1.10+ does not re-use the produced pkg
+           ;; for dependencies, which means we would need to propagate the
+           ;; same "-tags" argument to all golua referrers.  A substitution is
+           ;; more convenient here.  We also need to propagate the lua
+           ;; dependency to make it available to referrers.
+           (add-after 'unpack 'fix-lua-ldflags
+             (lambda _
+               (substitute* "src/github.com/aarzilli/golua/lua/lua.go"
+                 (("#cgo linux,!llua,!luaa LDFLAGS: -llua5.3")
+                  "#cgo linux,!llua,!luaa LDFLAGS: -llua")))))))
       (home-page "https://github.com/aarzilli/golua")
       (synopsis "Go Bindings for the Lua C API")
       (description "This package provides @code{lua}, a Go module that can
@@ -2428,11 +2430,24 @@ and lookup requests.  Browse requests are not supported yet.")
           (base32
            "1cpjqnrviwflz150g78iir5ndrp3hh7a93zbp4dwbg6sb2q141p2"))))
       (build-system go-build-system)
-      (native-inputs
+      ;; From go-1.10 onward, "pkg" compiled libraries are not re-used, so
+      ;; when this package required as input for another one, it will have to
+      ;; be built again.  Thus its CGO requirements must be made available in
+      ;; the environment, that is, they must be propagated.
+      (propagated-inputs
        `(("pkg-config" ,pkg-config)
          ("taglib" ,taglib)))
       (arguments
-       `(#:import-path "github.com/wtolson/go-taglib"))
+       `(#:import-path "github.com/wtolson/go-taglib"
+         ;; Tests don't pass "vet" on go-1.11.  See
+         ;; https://github.com/wtolson/go-taglib/issues/12.
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'check
+             (lambda* (#:key import-path #:allow-other-keys)
+               (invoke "go" "test"
+                       "-vet=off"
+                       import-path))))))
       (home-page "https://github.com/wtolson/go-taglib")
       (synopsis "Go wrapper for taglib")
       (description "Go wrapper for taglib")
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 66456ab1e2..08f92df96c 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -19,6 +19,7 @@
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1413,7 +1414,12 @@ information.")
                (string-append (assoc-ref inputs "docbook-xsl")
                               "/xml/xsl/docbook-xsl-"
                               ,(package-version docbook-xsl)
-                              "/html/chunk.xsl")))
+                              "/html/chunk.xsl"))
+              (("http://docbook.sourceforge.net/release/xsl/current/common/en.xml")
+               (string-append (assoc-ref inputs "docbook-xsl")
+                              "/xml/xsl/docbook-xsl-"
+                              ,(package-version docbook-xsl)
+                              "/common/en.xml")))
              #t))
          (add-after 'patch-gtk-doc-scan 'patch-test-out
            (lambda _
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index a77cacffe1..f3eb2dcd36 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2017 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016 Alex Sassmannshausen <alex@pompo.co>
-;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Erik Edrosa <erik.edrosa@gmail.com>
 ;;; Copyright © 2016 Eraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Alex Kost <alezost@gmail.com>
@@ -486,10 +486,7 @@ AM_SCM_LOG_FLAGS =  --no-auto-compile -s")
                  ;; FIXME: one of the database tests fails for unknown
                  ;; reasons.  It does not fail when run outside of Guix.
                  (("tests/database.scm") ""))
-               #t))
-           (add-after 'fix-bug-22 'autogen
-             (lambda _
-               (zero? (system* "sh" "autogen.sh")))))))
+               #t)))))
       (inputs
        `(("guile" ,guile-2.0)))
       (native-inputs
@@ -829,14 +826,6 @@ provides tight coupling to Guix.")
                (base32
                 "0qjjvadr7gibdq9jvwkmlkb4afsw9n2shfj9phpiadinxk3p4m2g"))))
     (build-system gnu-build-system)
-    (arguments
-     '(#:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'autoreconf
-                    (lambda _
-                      ;; Repository comes with a broken symlink
-                      (delete-file "README")
-                      (symlink "README.org" "README")
-                      (zero? (system* "autoreconf" "-fi")))))))
     (native-inputs
      `(("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
@@ -1550,10 +1539,7 @@ $(datadir)/guile/site/$(GUILE_EFFECTIVE_VERSION)\n"))
                         (("^guilesitedir =.*$")
                          "guilesitedir = \
 $(datadir)/guile/site/$(GUILE_EFFECTIVE_VERSION)\n"))
-                      #t))
-                  (add-after 'unpack 'autoreconf
-                    (lambda _
-                      (zero? (system* "autoreconf" "-vfi")))))))
+                      #t)))))
     (home-page "https://github.com/artyom-poptsov/guile-dsv")
     (synopsis "DSV module for Guile")
     (description
@@ -2244,6 +2230,60 @@ using S-expressions.")
 tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
     (license license:gpl3+)))
 
+(define-public guile-email
+  (let ((commit "fa52eac55e5946db89621a6c583d2aa357864dee")
+        (revision "1"))
+    (package
+      (name "guile-email")
+      (version (git-version "0.1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://git.systemreboot.net/guile-email")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1037mbz7qd9bzaqp8ysyhnl9ipd97fmj3b9jr8qfzx9179vvsj63"))))
+      (build-system gnu-build-system)
+      (native-inputs
+       `(("pkg-config" ,pkg-config)
+         ("autoconf" ,autoconf)
+         ("automake" ,automake)))
+      (inputs
+       `(("guile" ,guile-2.2)))
+      (home-page "https://git.systemreboot.net/guile-email")
+      (synopsis "Guile email parser")
+      (description "This package provides an email parser written in pure
+Guile.")
+      (license license:agpl3+))))
+
+(define-public guile-debbugs-next
+  (let ((commit "75a331d561c8b6f8efcf16216dab961c17759efe")
+        (revision "1"))
+    (package (inherit guile-debbugs)
+      (name "guile-debbugs")
+      (version (git-version "0.0.3" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.savannah.gnu.org/git/guile-debbugs.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0br3mgbw41bpc9x57jlghl0i8dz9nl63r4wzs5l47aqszf84870y"))))
+      (build-system gnu-build-system)
+      (native-inputs
+       `(("pkg-config" ,pkg-config)
+         ("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("texinfo" ,texinfo)))
+      (inputs
+       `(("guile" ,guile-2.2)
+         ("guile-email" ,guile-email))))))
+
 ;; There has not been any release yet.
 (define-public guile-newt
   (let ((commit "4eaa3cf84b9b426cc0ff7bec48b76cca6ca3ec83")
diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index 08fce5f6fb..a2687ac8c3 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24,185 +25,193 @@
   #:use-module (guix licenses)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (gnu packages)
   #:use-module (gnu packages anthy)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages boost)
+  #:use-module (gnu packages cmake)
   #:use-module (gnu packages databases)
+  #:use-module (gnu packages datastructures)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages iso-codes)
+  #:use-module (gnu packages logging)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages serialization)
+  #:use-module (gnu packages textutils)
   #:use-module (gnu packages xorg))
 
 (define-public ibus
   (package
-   (name "ibus")
-   (version "1.5.19")
-   (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/ibus/ibus/"
-                                 "releases/download/"
-                                 version "/ibus-" version ".tar.gz"))
-             (sha256
-              (base32
-               "0a94bnpm24581317hdnihwr4cniriml10p4ffgxg14xhvaccfrjb"))))
-   (build-system glib-or-gtk-build-system)
-   (arguments
-    `(#:tests? #f  ; tests fail because there's no connection to dbus
-      #:configure-flags `("--disable-emoji-dict" ; cannot find emoji.json path
-                          "--disable-python2"
-                          "--enable-python-library"
-                          ,(string-append "--with-ucd-dir="
-                                          (getcwd) "/ucd")
-                          "--enable-wayland")
-      #:make-flags
-      (list "CC=gcc"
-            (string-append "pyoverridesdir="
-                           (assoc-ref %outputs "out")
-                           "/lib/python3.6/site-packages/gi/overrides/"))
-      #:phases
-      (modify-phases %standard-phases
-        (add-after 'unpack 'prepare-ucd-dir
-          (lambda* (#:key inputs #:allow-other-keys)
-            (mkdir-p "../ucd")
-            (symlink (assoc-ref inputs "unicode-blocks") "../ucd/Blocks.txt")
-            (symlink (assoc-ref inputs "unicode-nameslist") "../ucd/NamesList.txt")
-            #t))
-        (add-before 'configure 'disable-dconf-update
-          (lambda _
-            (substitute* "data/dconf/Makefile.in"
-              (("dconf update") "echo dconf update"))
-            #t))
-        (add-after 'unpack 'delete-generated-files
-          (lambda _
-            (for-each (lambda (file)
-                        (let ((c (string-append (string-drop-right file 4) "c")))
-                          (when (file-exists? c)
-                            (format #t "deleting ~a\n" c)
-                            (delete-file c))))
-                      (find-files "." "\\.vala"))
-            #t))
-        (add-after 'unpack 'fix-paths
-          (lambda* (#:key inputs #:allow-other-keys)
-            (substitute* "src/ibusenginesimple.c"
-              (("/usr/share/X11/locale")
-               (string-append (assoc-ref inputs "libx11")
-                              "/share/X11/locale")))
-            (substitute* "ui/gtk3/xkblayout.vala"
-              (("\"(setxkbmap|xmodmap)\"" _ prog)
-               (string-append "\"" (assoc-ref inputs prog) "\"")))
-            #t))
-        (add-after 'wrap-program 'wrap-with-additional-paths
-          (lambda* (#:key outputs #:allow-other-keys)
-            ;; Make sure 'ibus-setup' runs with the correct PYTHONPATH and
-            ;; GI_TYPELIB_PATH.
-            (let ((out (assoc-ref outputs "out")))
-              (wrap-program (string-append out "/bin/ibus-setup")
-                `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))
-                `("GI_TYPELIB_PATH" ":" prefix
-                  (,(getenv "GI_TYPELIB_PATH")
-                   ,(string-append out "/lib/girepository-1.0")))))
-            #t)))))
-   (inputs
-    `(("dbus" ,dbus)
-      ("dconf" ,dconf)
-      ("gconf" ,gconf)
-      ("gtk2" ,gtk+-2)
-      ("gtk+" ,gtk+)
-      ("intltool" ,intltool)
-      ("json-glib" ,json-glib)
-      ("libnotify" ,libnotify)
-      ("libx11" ,libx11)
-      ("setxkbmap" ,setxkbmap)
-      ("wayland" ,wayland)
-      ("xmodmap" ,xmodmap)
-      ("iso-codes" ,iso-codes)
-      ("pygobject2" ,python-pygobject)
-      ("python" ,python)))
-   (native-inputs
-    `(("glib" ,glib "bin") ; for glib-genmarshal
-      ("gobject-introspection" ,gobject-introspection) ; for g-ir-compiler
-      ("unicode-nameslist"
-       ,(origin
-          (method url-fetch)
-          (uri "https://www.unicode.org/Public/UNIDATA/NamesList.txt")
-          (sha256
-           (base32 "0yr2h0nfqhirfi3bxl33z6cc94qqshlpgi06c25xh9754irqsgv8"))))
-      ("unicode-blocks"
-       ,(origin
-          (method url-fetch)
-          (uri "https://www.unicode.org/Public/UNIDATA/Blocks.txt")
-          (sha256
-           (base32 "0lnh9iazikpr548bd7nkaq9r3vfljfvz0rg2462prac8qxk7ni8b"))))
-      ("vala" ,vala)
-      ("pkg-config" ,pkg-config)))
-   (native-search-paths
-    (list (search-path-specification
-           (variable "IBUS_COMPONENT_PATH")
-           (files '("share/ibus/component")))))
-   (synopsis "Input method framework")
-   (description
-    "IBus is an input framework providing a full-featured and user-friendly
+    (name "ibus")
+    (version "1.5.19")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/ibus/ibus/"
+                                  "releases/download/"
+                                  version "/ibus-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0a94bnpm24581317hdnihwr4cniriml10p4ffgxg14xhvaccfrjb"))))
+    (build-system glib-or-gtk-build-system)
+    (arguments
+     `(#:tests? #f  ; tests fail because there's no connection to dbus
+       #:configure-flags `("--disable-emoji-dict" ; cannot find emoji.json path
+                           "--disable-python2"
+                           "--enable-python-library"
+                           ,(string-append "--with-ucd-dir="
+                                           (getcwd) "/ucd")
+                           "--enable-wayland")
+       #:make-flags
+       (list "CC=gcc"
+             (string-append "pyoverridesdir="
+                            (assoc-ref %outputs "out")
+                            "/lib/python3.6/site-packages/gi/overrides/"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'prepare-ucd-dir
+           (lambda* (#:key inputs #:allow-other-keys)
+             (mkdir-p "../ucd")
+             (symlink (assoc-ref inputs "unicode-blocks") "../ucd/Blocks.txt")
+             (symlink (assoc-ref inputs "unicode-nameslist") "../ucd/NamesList.txt")
+             #t))
+         (add-before 'configure 'disable-dconf-update
+           (lambda _
+             (substitute* "data/dconf/Makefile.in"
+               (("dconf update") "echo dconf update"))
+             #t))
+         (add-after 'unpack 'delete-generated-files
+           (lambda _
+             (for-each (lambda (file)
+                         (let ((c (string-append (string-drop-right file 4) "c")))
+                           (when (file-exists? c)
+                             (format #t "deleting ~a\n" c)
+                             (delete-file c))))
+                       (find-files "." "\\.vala"))
+             #t))
+         (add-after 'unpack 'fix-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "src/ibusenginesimple.c"
+               (("/usr/share/X11/locale")
+                (string-append (assoc-ref inputs "libx11")
+                               "/share/X11/locale")))
+             (substitute* "ui/gtk3/xkblayout.vala"
+               (("\"(setxkbmap|xmodmap)\"" _ prog)
+                (string-append "\"" (assoc-ref inputs prog) "\"")))
+             #t))
+         (add-after 'wrap-program 'wrap-with-additional-paths
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Make sure 'ibus-setup' runs with the correct PYTHONPATH and
+             ;; GI_TYPELIB_PATH.
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/ibus-setup")
+                 `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))
+                 `("GI_TYPELIB_PATH" ":" prefix
+                   (,(getenv "GI_TYPELIB_PATH")
+                    ,(string-append out "/lib/girepository-1.0")))))
+             #t)))))
+    (inputs
+     `(("dbus" ,dbus)
+       ("dconf" ,dconf)
+       ("gconf" ,gconf)
+       ("gtk2" ,gtk+-2)
+       ("gtk+" ,gtk+)
+       ("intltool" ,intltool)
+       ("json-glib" ,json-glib)
+       ("libnotify" ,libnotify)
+       ("libx11" ,libx11)
+       ("setxkbmap" ,setxkbmap)
+       ("wayland" ,wayland)
+       ("xmodmap" ,xmodmap)
+       ("iso-codes" ,iso-codes)
+       ("pygobject2" ,python-pygobject)
+       ("python" ,python)))
+    (native-inputs
+     `(("glib" ,glib "bin") ; for glib-genmarshal
+       ("gobject-introspection" ,gobject-introspection) ; for g-ir-compiler
+       ("unicode-nameslist"
+        ,(origin
+           (method url-fetch)
+           (uri "https://www.unicode.org/Public/UNIDATA/NamesList.txt")
+           (sha256
+            (base32 "0yr2h0nfqhirfi3bxl33z6cc94qqshlpgi06c25xh9754irqsgv8"))))
+       ("unicode-blocks"
+        ,(origin
+           (method url-fetch)
+           (uri "https://www.unicode.org/Public/UNIDATA/Blocks.txt")
+           (sha256
+            (base32 "0lnh9iazikpr548bd7nkaq9r3vfljfvz0rg2462prac8qxk7ni8b"))))
+       ("vala" ,vala)
+       ("pkg-config" ,pkg-config)))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "IBUS_COMPONENT_PATH")
+            (files '("share/ibus/component")))))
+    (synopsis "Input method framework")
+    (description
+     "IBus is an input framework providing a full-featured and user-friendly
 input method user interface.  It comes with multilingual input support.  It
 may also simplify input method development.")
-   (home-page "https://github.com/ibus/ibus/wiki")
-   (license lgpl2.1+)))
+    (home-page "https://github.com/ibus/ibus/wiki")
+    (license lgpl2.1+)))
 
 (define-public ibus-libpinyin
   (package
-   (name "ibus-libpinyin")
-   (version "1.10.0")
-   (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/libpinyin/ibus-libpinyin/"
-                                 "releases/download/" version
-                                 "/ibus-libpinyin-" version ".tar.gz"))
-             (sha256
-              (base32
-               "0yq8aw4lddiviag8cnik6fp52vvk8lxv6bym13a3xya84c6zii3c"))))
-   (build-system glib-or-gtk-build-system)
-   (arguments
-    `(#:phases
-      (modify-phases %standard-phases
-        (add-after 'wrap-program 'wrap-with-additional-paths
-          (lambda* (#:key inputs outputs #:allow-other-keys)
-            ;; Make sure 'ibus-setup-libpinyin' runs with the correct
-            ;; PYTHONPATH and GI_TYPELIB_PATH.
-            (let ((out (assoc-ref outputs "out")))
-              (wrap-program (string-append out "/libexec/ibus-setup-libpinyin")
-                `("PYTHONPATH" ":" prefix
-                  (,(getenv "PYTHONPATH")
-                   ,(string-append (assoc-ref inputs "ibus")
-                                   "/lib/girepository-1.0")))
-                `("GI_TYPELIB_PATH" ":" prefix
-                  (,(string-append (assoc-ref inputs "ibus")
-                                   "/lib/girepository-1.0"))))
-              #t))))))
-   (inputs
-    `(("ibus" ,ibus)
-      ("libpinyin" ,libpinyin)
-      ("bdb" ,bdb)
-      ("sqlite" ,sqlite)
-      ("python" ,python)
-      ("pyxdg" ,python-pyxdg)
-      ("gtk+" ,gtk+)))
-   (native-inputs
-    `(("pkg-config" ,pkg-config)
-      ("intltool" ,intltool)
-      ("glib" ,glib "bin")))
-   (synopsis "Chinese pinyin and ZhuYin input methods for IBus")
-   (description
-    "This package includes a Chinese pinyin input method and a Chinese
+    (name "ibus-libpinyin")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/libpinyin/ibus-libpinyin/"
+                                  "releases/download/" version
+                                  "/ibus-libpinyin-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0yq8aw4lddiviag8cnik6fp52vvk8lxv6bym13a3xya84c6zii3c"))))
+    (build-system glib-or-gtk-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'wrap-program 'wrap-with-additional-paths
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Make sure 'ibus-setup-libpinyin' runs with the correct
+             ;; PYTHONPATH and GI_TYPELIB_PATH.
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/libexec/ibus-setup-libpinyin")
+                 `("PYTHONPATH" ":" prefix
+                   (,(getenv "PYTHONPATH")
+                    ,(string-append (assoc-ref inputs "ibus")
+                                    "/lib/girepository-1.0")))
+                 `("GI_TYPELIB_PATH" ":" prefix
+                   (,(string-append (assoc-ref inputs "ibus")
+                                    "/lib/girepository-1.0"))))
+               #t))))))
+    (inputs
+     `(("ibus" ,ibus)
+       ("libpinyin" ,libpinyin)
+       ("bdb" ,bdb)
+       ("sqlite" ,sqlite)
+       ("python" ,python)
+       ("pyxdg" ,python-pyxdg)
+       ("gtk+" ,gtk+)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("intltool" ,intltool)
+       ("glib" ,glib "bin")))
+    (synopsis "Chinese pinyin and ZhuYin input methods for IBus")
+    (description
+     "This package includes a Chinese pinyin input method and a Chinese
 ZhuYin (Bopomofo) input method based on libpinyin for IBus.")
-   (home-page "https://github.com/libpinyin/ibus-libpinyin")
-   (license gpl2+)))
+    (home-page "https://github.com/libpinyin/ibus-libpinyin")
+    (license gpl2+)))
 
 (define-public libpinyin
   (package
@@ -279,3 +288,369 @@ applications allow text input via IBus, installing this package will enable
 Japanese language input in most graphical applications.")
     (home-page "https://github.com/fujiwarat/ibus-anthy")
     (license gpl2+)))
+
+(define-public librime
+  (package
+    (name "librime")
+    (version "1.3.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/rime/librime.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1y0h3nnz97smx9z8h5fzk4c27mvrwv8kajxffqc43bhyvxvb2jd6"))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("boost" ,boost)
+       ("glog" ,glog)
+       ("leveldb" ,leveldb)
+       ("marisa" ,marisa)
+       ("opencc" ,opencc)
+       ("yaml-cpp" ,yaml-cpp)))
+    (home-page "https://rime.im/")
+    (synopsis "The core library of Rime Input Method Engine")
+    (description "@dfn{librime} is the core library of Rime Input Method
+Engine, which is a lightweight, extensible input method engine supporting
+various input schemas including glyph-based input methods, romanization-based
+input methods as well as those for Chinese dialects.  It has the ability to
+compose phrases and sentences intelligently and provide very accurate
+traditional Chinese output.")
+    (license bsd-3)))
+
+(define-public rime-data
+  (package
+    (name "rime-data")
+    (version "0.38.20181029")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/rime/plum.git")
+             (commit "fb4f829da2007f2dbb37d60a79bc67c25ea16568")))
+       (file-name "plum-checkout")
+       (sha256
+        (base32 "1m1wiv9j5bay4saga58c7dj4h8gqivsbyp16y245ifvxvp9czj67"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                  ; no tests
+       #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+                          "no_update=1")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-source
+           (lambda _
+             ;; Set .DEFAULT_GOAL to `all'.
+             ;; Don't build binary schemas. The output is not deterministic.
+             (substitute* "Makefile"
+               (("^\\.DEFAULT_GOAL := preset")
+                ".DEFAULT_GOAL := all"))
+             #t))
+         ;; Add schema packages into "package/rime" directory.
+         (add-after 'unpack 'add-packages
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let* ((dest-dir "package/rime"))
+               (mkdir-p dest-dir)
+               (for-each (lambda (pkg)
+                           (symlink (assoc-ref inputs pkg)
+                                    (string-append dest-dir "/" pkg)))
+                         '("array"
+                           "bopomofo"
+                           "cangjie"
+                           "combo-pinyin"
+                           "double-pinyin"
+                           "emoji"
+                           "essay"
+                           "ipa"
+                           "jyutping"
+                           "luna-pinyin"
+                           "middle-chinese"
+                           "pinyin-simp"
+                           "prelude"
+                           "quick"
+                           "scj"
+                           "soutzoe"
+                           "stenotype"
+                           "stroke"
+                           "terra-pinyin"
+                           "wubi"
+                           "wugniu")))
+             #t))
+         (delete 'configure))))
+    (native-inputs
+     `(("array"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-array.git")
+                 (commit "906e923902147584b0b0247028a782abbfbfd8a0")))
+           (file-name "rime-array-checkout")
+           (sha256
+            (base32
+             "1alk6ghn4ji4kvp7lfm57bwm2gjh99i79r0w9naz6wkdim8idvb1"))))
+       ("bopomofo"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-bopomofo.git")
+                 (commit "8dc44ca1b6ef4e45b452e070b9da737f5da165e3")))
+           (file-name "rime-bopomofo-checkout")
+           (sha256
+            (base32
+             "16k6wfhcrw3a77rmbrp21ca0gmsmb3f68s193c1cfwr8i68k46nf"))))
+       ("cangjie"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-cangjie.git")
+                 (commit "ab085e90856b3399b374dc3c8b4cb40d11f307a8")))
+           (file-name "rime-cangjie-checkout")
+           (sha256
+            (base32
+             "11fgj0rbv9nyzfijwm2l8pm8fznhif4h27ndrrcaaylkp7p5zsx2"))))
+       ("combo-pinyin"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-combo-pinyin.git")
+                 (commit "f1bae63f20504f2b8113c5cbdf2700e858aa91eb")))
+           (file-name "rime-combo-pinyin-checkout")
+           (sha256
+            (base32
+             "1l1079akwm1hw4kkn0q6x9fpylnl2ka6z2fn7lmdpfpsr0xgn0n7"))))
+       ("double-pinyin"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-double-pinyin.git")
+                 (commit "2101a5cd40e511ec38835769aa66d2dddf059c2e")))
+           (file-name "rime-double-pinyin-checkout")
+           (sha256
+            (base32
+             "19hh2qm0njbfk2js678hfm2hw9b796s43vs11yy3m1v9m0gk2vi7"))))
+       ("emoji"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-emoji.git")
+                 (commit "6e6611b315f03ee4c33f958f9dbe960b13a0ed19")))
+           (file-name "rime-emoji-checkout")
+           (sha256
+            (base32
+             "1brfs3214w36j3345di9ygp468hbvbqdqpkjxxs1dbp437rayhyy"))))
+       ("essay"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-essay.git")
+                 (commit "5e5c7a0ef41c9b030abdad81a9df07b56b1661e9")))
+           (file-name "rime-essay-checkout")
+           (sha256
+            (base32
+             "0ana9is0zhh79m4gjshvmaxbrg3jiqysydx5bpm151i7i6vw5y1i"))))
+       ("ipa"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-ipa.git")
+                 (commit "02a9e2c181921a2e95e1a81f88188c41132755c3")))
+           (file-name "rime-ipa-checkout")
+           (sha256
+            (base32
+             "1szrxgvqlgmxapj2aflw2cvbv0p6pl0sw0gyxa13dvdhhf7s9rvr"))))
+       ("jyutping"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-jyutping.git")
+                 (commit "1402ec3d6cc0973f952fe3f9ef531294e4ffe9e0")))
+           (file-name "rime-jyutping-checkout")
+           (sha256
+            (base32
+             "17g03dy4gw6vyc9da1wjn3iy9hx64dfnwiwsfc7bkzan22x2m4dv"))))
+       ("luna-pinyin"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-luna-pinyin.git")
+                 (commit "3b05132576f5c347ff8a70857d2dae080936ac3b")))
+           (file-name "rime-luna-pinyin-checkout")
+           (sha256
+            (base32
+             "0kgnpxjn10dm2d9718r12rdjlwqd2s2h84jvkhxhh5v0dkv1anl2"))))
+       ("middle-chinese"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-middle-chinese.git")
+                 (commit "9ba8d70330654b9a730f882d35cfad7dbeddfd75")))
+           (file-name "rime-middle-chinese-checkout")
+           (sha256
+            (base32
+             "0hwg5zby5kphh0bcfay8mfxwr5bwqhamiw3cmmmf7kp9fbns5s23"))))
+       ("pinyin-simp"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-pinyin-simp.git")
+                 (commit "74357ffd62c05fb60edf6eab5b86bc8c8c1907d0")))
+           (file-name "rime-pinyin-simp-checkout")
+           (sha256
+            (base32
+             "1paw3c7pv5bl54abnp9pidfxrkchdacyxy5m9zb311p5sgm7fhxh"))))
+       ("prelude"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-prelude.git")
+                 (commit "33040568c3ddb2ee6340c9b669494317db21b77c")))
+           (file-name "rime-prelude-checkout")
+           (sha256
+            (base32
+             "1gwcasyyg6f0ib6s4qsrrjcqr1lcs7j3xqxl65rznsw44nhnbwwq"))))
+       ("quick"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-quick.git")
+                 (commit "910a97d403ad8e72f322488da146da79c19d623f")))
+           (file-name "rime-quick-checkout")
+           (sha256
+            (base32
+             "0yrq3gbfmm29xlr52rmxc41mqfrb0295q7sdhbc3ax71677mpr0y"))))
+       ("scj"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-scj.git")
+                 (commit "e0eae889f4376d2a434ac3b38523e0da7400db68")))
+           (file-name "rime-scj-checkout")
+           (sha256
+            (base32
+             "1whnv9zs349kvy0zi7dnmpqwil8i6gqwrzvhy3qdrjzy58y6gwxn"))))
+       ("soutzoe"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-soutzoe.git")
+                 (commit "e47841a8ad6341731c41cdb814b7a25c837603c4")))
+           (file-name "rime-soutzoe-checkout")
+           (sha256
+            (base32
+             "1rgpmkxa72jy6gyy44fn8azpk3amk9s9lrdf7za03nv95d0fvm0p"))))
+       ("stenotype"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-stenotype.git")
+                 (commit "d4ff379314fd95283853d1734854979cf3cbd287")))
+           (file-name "rime-stenotype-checkout")
+           (sha256
+            (base32
+             "1kckpi4l4884hvydr3d6vid3v7rsc1app29kmk7v8jf8vn16afhl"))))
+       ("stroke"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-stroke.git")
+                 (commit "cfd29c675c46cf70b7a7f0a3836a913059316a0a")))
+           (file-name "rime-stroke-checkout")
+           (sha256
+            (base32
+             "135is9c1p4lm98fd9l1gxyflkm69cv5an129ka7sk614bq84m08d"))))
+       ("terra-pinyin"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-terra-pinyin.git")
+                 (commit "15b5c73a796571cd6f9ef6c89f96656cb9df86f9")))
+           (file-name "rime-terra-pinyin-checkout")
+           (sha256
+            (base32
+             "1xsd84h1zw417h5hr4dbgyk5009zi7q2p9774w3ccr5sxgc3i3cm"))))
+       ("wubi"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-wubi.git")
+                 (commit "d44403728a0b1cd8b47cb1f81b83f58e5f790b74")))
+           (file-name "rime-wubi-checkout")
+           (sha256
+            (base32
+             "0ld31bdn94lncxd1ka44w4sbl03skh08mc927dhdmwq5bpvrgn36"))))
+       ("wugniu"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/rime/rime-wugniu.git")
+                 (commit "65bcc354ada3839591d7546a64c71dbdd0592b02")))
+           (file-name "rime-wugniu-checkout")
+           (sha256
+            (base32
+             "0g31awp40s778sp5c290x40s8np86n8aw011s17sslxrqhhb0bkx"))))))
+    (home-page "https://rime.im/")
+    (synopsis "Schema data of Rime Input Method Engine")
+    (description "@dfn{rime-data} provides the schema data of Rime Input
+Method Engine.")
+    (license lgpl3+)))
+
+(define-public ibus-rime
+  (package
+    (name "ibus-rime")
+    (version "1.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/rime/ibus-rime.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1nqi7ymv34a9kx24say3xj98lkrs9nkpv1n2ijb91wdz3cr012ly"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; no tests
+       #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-source
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Define RIME_DATA_DIR. It's required but not used by the code.
+             (substitute* "Makefile"
+               (("cmake")
+                (string-append "cmake -DRIME_DATA_DIR="
+                               (assoc-ref inputs "rime-data")
+                               "/share/rime-data")))
+             ;; rime_config.h defines the actual data directory.
+             (substitute* "rime_config.h"
+               (("^#define IBUS_RIME_INSTALL_PREFIX .*$")
+                (string-append "#define IBUS_RIME_INSTALL_PREFIX \""
+                               (assoc-ref outputs "out")
+                               "\"\n"))
+               (("^#define IBUS_RIME_SHARED_DATA_DIR .*$")
+                (string-append "#define IBUS_RIME_SHARED_DATA_DIR \""
+                               (assoc-ref inputs "rime-data")
+                               "/share/rime-data\"\n")))
+             #t))
+         (delete 'configure))))
+    (inputs
+     `(("gdk-pixbuf" ,gdk-pixbuf)
+       ("glib" ,glib)
+       ("ibus" ,ibus)
+       ("libnotify" ,libnotify)
+       ("librime" ,librime)
+       ("rime-data" ,rime-data)))
+    (native-inputs
+     `(("cmake" ,cmake)
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://rime.im/")
+    (synopsis "Rime Input Method Engine for IBus")
+    (description "@dfn{ibus-rime} provides the Rime input method engine for
+IBus.  Rime is a lightweight, extensible input method engine supporting
+various input schemas including glyph-based input methods, romanization-based
+input methods as well as those for Chinese dialects.  It has the ability to
+compose phrases and sentences intelligently and provide very accurate
+traditional Chinese output.")
+    (license gpl3+)))
diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm
index 518417707f..029d5b5443 100644
--- a/gnu/packages/image-viewers.scm
+++ b/gnu/packages/image-viewers.scm
@@ -60,7 +60,7 @@
 (define-public feh
   (package
     (name "feh")
-    (version "2.28.1")
+    (version "3.0")
     (home-page "https://feh.finalrewind.org/")
     (source (origin
               (method url-fetch)
@@ -68,7 +68,7 @@
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "0wian0gnx0yfxf8x9b8wr57fjd6rnmi3y3xj83ni6x0xqrjnf1lp"))))
+                "00fwf8yz7k8vzd30ly5ndlj6ax9w85dkjzjnlk95vd0zdrf4wyxn"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases (delete 'configure))
diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm
index e29ec6255b..fe0923f479 100644
--- a/gnu/packages/imagemagick.scm
+++ b/gnu/packages/imagemagick.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -47,14 +48,14 @@
     ;; The 7 release series has an incompatible API, while the 6 series is still
     ;; maintained. Don't update to 7 until we've made sure that the ImageMagick
     ;; users are ready for the 7-series API.
-    (version "6.9.10-12")
+    (version "6.9.10-14")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://imagemagick/ImageMagick-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0ri96yqihdk921k5qx23y2sbhraxbp2avdccxiy6m3srjkirym2l"))))
+               "0vcfjvdk9in92x808djvy94l5gylpgds4a7mlr8jrxsv9snx88yi"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 02d30bacf4..955ad436b7 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -423,8 +423,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.19-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.79")
-(define %linux-libre-4.14-hash "000rd4h2yk6k68wjg37v53hqnqw1mgwhdxbcvy8iywy8za9r12c8")
+(define %linux-libre-4.14-version "4.14.80")
+(define %linux-libre-4.14-hash "0h4hi5lqizdx5nk0f3immbcv2n7p5jh26m80v4x6bw4wi5b44fra")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
@@ -433,14 +433,14 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.135"
-                    "07v5s6hl08ls2z9xdkbqq1s210mqayfchqbckhp8hlaw089ap71f"
+  (make-linux-libre "4.9.136"
+                    "1kk6px1jcwbgkpfmf9pdklk6kz90h5l8fvdqwmvnk4bz6b2xrrfp"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.162"
-                    "1anb2k9i03369lvbwlw24vimxvk8zpcql4ryz0ydvf3pxv8lirm2"
+  (make-linux-libre "4.4.163"
+                    "05j0dm0cxilanp5z40n8kgjz9vn1p4rg63kksicd2v48w8ka82z6"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
@@ -1968,20 +1968,15 @@ for systems using the Linux kernel.  This includes commands such as
     (name "inotify-tools")
     (version "3.20.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/rvoicilas/inotify-tools/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/rvoicilas/inotify-tools.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1b22c8x4pjnz3abx4dikpbj43zprjw79pdkd4xw111dsxlfwqcx4"))))
+                "14dci1i4mhsd5sa33k8h3ayphk19kizynh5ql9ryibdpmcanfiyq"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'bootstrap
-                    (lambda _
-                      (invoke "autoreconf" "-vif"))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
@@ -2916,7 +2911,7 @@ MPEG-2 and audio over Linux IEEE 1394.")
 (define-public mdadm
   (package
     (name "mdadm")
-    (version "4.0")
+    (version "4.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2924,7 +2919,7 @@ MPEG-2 and audio over Linux IEEE 1394.")
                     version ".tar.xz"))
               (sha256
                (base32
-                "1ad3mma641946wn5lsllwf0lifw9lps34fv1nnkhyfpd9krffshx"))))
+                "0jjgjgqijpdp7ijh8slzzjjw690kydb1jjadf0x5ilq85628hxmb"))))
     (build-system gnu-build-system)
     (inputs
      `(("udev" ,eudev)))
@@ -3949,7 +3944,7 @@ are exceeded.")
 (define-public mtd-utils
   (package
     (name "mtd-utils")
-    (version "1.5.2")
+    (version "2.0.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3957,18 +3952,18 @@ are exceeded.")
                     "mtd-utils-" version ".tar.bz2"))
               (sha256
                (base32
-                "007lhsd8yb34l899r4m37whhzdw815cz4fnjbpnblfha524p7dax"))))
+                "1f30jszknc5v6ykmil8ajxgksmcg54q3rsp84jsancp9x0dycggv"))))
+    (arguments
+     '(#:configure-flags '("--enable-unit-tests")))
+    (native-inputs
+     `(("cmocka" ,cmocka)
+       ("pkg-config" ,pkg-config)))
     (inputs
-     `(("acl" ,acl)
+     `(("acl" ,acl) ; for XATTR
        ("libuuid" ,util-linux)
        ("lzo" ,lzo)
        ("zlib" ,zlib)))
     (build-system gnu-build-system)
-    (arguments
-     `(#:test-target "tests"
-       #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
-       #:phases (modify-phases %standard-phases
-                  (delete 'configure))))
     (synopsis "MTD Flash Storage Utilities")
     (description "This package provides utilities for testing, partitioning, etc
 of flash storage.")
diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm
index 54a17be8f4..f57e263449 100644
--- a/gnu/packages/llvm.scm
+++ b/gnu/packages/llvm.scm
@@ -91,17 +91,6 @@ languages is in development.  The compiler infrastructure includes mirror sets
 of programming tools as well as libraries with equivalent functionality.")
     (license license:ncsa)))
 
-(define-public llvm-with-rtti
-  (package (inherit llvm)
-    (name "llvm-with-rtti")
-    (arguments
-     (substitute-keyword-arguments (package-arguments llvm)
-       ((#:configure-flags flags)
-        `(append '("-DCMAKE_SKIP_BUILD_RPATH=FALSE"
-                   "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE"
-                   "-DLLVM_REQUIRES_RTTI=1")
-                 ,flags))))))
-
 (define* (clang-runtime-from-llvm llvm hash
                                   #:optional (patches '()))
   (package
@@ -292,6 +281,18 @@ code analysis tools.")
        (base32
         "1ybmnid4pw2hxn12ax5qa5kl1ldfns0njg8533y3mzslvd5cx0kf"))))))
 
+;; This is for Faust 2
+(define-public llvm-3.8-with-rtti
+  (package (inherit llvm-3.8)
+    (name "llvm-with-rtti")
+    (arguments
+     (substitute-keyword-arguments (package-arguments llvm)
+       ((#:configure-flags flags)
+        `(append '("-DCMAKE_SKIP_BUILD_RPATH=FALSE"
+                   "-DCMAKE_BUILD_WITH_INSTALL_RPATH=FALSE"
+                   "-DLLVM_REQUIRES_RTTI=1")
+                 ,flags))))))
+
 (define-public clang-runtime-3.8
   (clang-runtime-from-llvm
    llvm-3.8
diff --git a/gnu/packages/lxde.scm b/gnu/packages/lxde.scm
index c45beb8bbb..1f32ec3bb1 100644
--- a/gnu/packages/lxde.scm
+++ b/gnu/packages/lxde.scm
@@ -7,6 +7,7 @@
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Ison111 <ison111@protonmail.com>
 ;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -419,10 +420,10 @@ in LXDE.")
        (modify-phases %standard-phases
          (add-after 'unpack 'rm-stamp
            (lambda _
-             (for-each delete-file (find-files "." "\\.stamp$"))))
-         (add-after 'rm-stamp 'autoreconf
-           (lambda _
-             (zero? (system* "autoreconf" "-vfi")))))))
+             (for-each delete-file (find-files "." "\\.stamp$"))
+             ;; Force regeneration of configure script.
+             (delete-file "configure")
+             #t)))))
     (inputs
      `(("gtk+-2" ,gtk+-2)
        ("polkit" ,polkit)))
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 35b7d27df3..74b1d489a3 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -110,7 +110,9 @@
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages docbook)
   #:use-module ((guix licenses)
-                #:select (fdl1.1+ gpl2 gpl2+ gpl3 gpl3+ lgpl2.1 lgpl2.1+ lgpl3+
+                #:select (fdl1.1+
+                           agpl3+
+                           gpl2 gpl2+ gpl3 gpl3+ lgpl2.1 lgpl2.1+ lgpl3+
                            non-copyleft (expat . license:expat) bsd-3
                            public-domain bsd-4 isc (openssl . license:openssl)
                            bsd-2 x11-style agpl3 asl2.0 perl-license))
@@ -119,6 +121,7 @@
   #:use-module (guix git-download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system guile)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial))
@@ -2640,3 +2643,50 @@ replacement for the @code{urlview} program.")
      "TNEF is a tar-like program that unpacks MIME attachments of type
 @code{application/ms-tnef}.")
     (license gpl2+)))
+
+(define-public mumi
+  (let ((commit "bfd96ce76b4600ae232e6548b26c9365095fd174")
+        (revision "2"))
+    (package
+      (name "mumi")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.elephly.net/software/mumi.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "05miwfi1bh0v9x2gvn15bwkb3gn4xy53z506ysjzns2y497zkc5h"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'install 'wrap-executable
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (bin (string-append out "/bin"))
+                      (scm (string-append out "/share/guile/site/2.2"))
+                      (go  (string-append out "/lib/guile/2.2/site-ccache")))
+                 (wrap-program (string-append bin "/mumi")
+                   `("GUILE_LOAD_PATH" ":" prefix
+                     (,scm ,(getenv "GUILE_LOAD_PATH")))
+                   `("GUILE_LOAD_COMPILED_PATH" ":" prefix
+                     (,go ,(getenv "GUILE_LOAD_COMPILED_PATH"))))
+                 #t))))))
+      (inputs
+       `(("guile-debbugs" ,guile-debbugs-next)
+         ("guile-email" ,guile-email)
+         ("guile-fibers" ,guile-fibers)
+         ("guile-json" ,guile-json)
+         ("guile-syntax-highlight" ,guile-syntax-highlight)
+         ("guile" ,guile-2.2)))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("pkg-config" ,pkg-config)))
+      (home-page "https://git.elephly.net/software/mumi.git")
+      (synopsis "Debbugs web interface")
+      (description "Mumi is a Debbugs web interface.")
+      (license agpl3+))))
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index de33d737e2..c22cacfd36 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -549,14 +549,14 @@ simultaneously and therefore appear under the same nickname on IRC.")
 (define-public python-nbxmpp
   (package
     (name "python-nbxmpp")
-    (version "0.6.7")
+    (version "0.6.8")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "nbxmpp" version))
        (sha256
         (base32
-         "0fas4iawjfdmkz8vr042wpq6b2qispi6fy35g4a62jw50jb1saav"))))
+         "1iip8ijxp86fx4bl1h67p2lp02p2zm1ga2p3q43nv30smj54nawc"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f))                    ; no tests
@@ -574,7 +574,7 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
 (define-public gajim
   (package
     (name "gajim")
-    (version "1.0.3")
+    (version "1.1.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gajim.org/downloads/"
@@ -582,10 +582,11 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
                                   "/gajim-" version ".tar.bz2"))
               (sha256
                (base32
-                "0ds4rqwfrpj89a489w6yih8gx5zi7qa4ffgld950fk7s0qxvcfnb"))))
+                "1qis8vs7y7g1zn5i5dshwrszidc22qpflycwb4nixvp9lbmkq0va"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
+     `(#:test-target "test_nogui"
+       #:phases
        (modify-phases %standard-phases
          (add-after 'install 'wrap-program
            (lambda* (#:key outputs #:allow-other-keys)
@@ -598,20 +599,6 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
                       `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path)))))
                 '("gajim" "gajim-remote" "gajim-history-manager")))
              #t))
-         (add-before 'check 'remove-test-resolver
-           ;; This test requires network access.
-           (lambda _
-             (substitute* "test/runtests.py"
-               (("'integration.test_resolver',") ""))
-             #t))
-         (add-before 'check 'start-xserver
-           ;; Tests require a running X server.
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((xorg-server (assoc-ref inputs "xorg-server"))
-                   (display ":1"))
-               (setenv "DISPLAY" display)
-               (zero? (system (string-append xorg-server "/bin/Xvfb "
-                                             display " &"))))))
          (add-after 'install 'install-icons
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -636,9 +623,11 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
                ;; For GtkFileChooserDialog.
                `("GSETTINGS_SCHEMA_DIR" =
                  (,(string-append (assoc-ref inputs "gtk+")
-                                  "/share/glib-2.0/schemas")))))))))
+                                  "/share/glib-2.0/schemas"))))
+             #t)))))
     (native-inputs
      `(("intltool" ,intltool)
+       ("python-docutils" ,python-docutils)
        ("xorg-server" ,xorg-server)))
     (inputs
      `(("adwaita-icon-theme" ,adwaita-icon-theme)
@@ -648,12 +637,13 @@ was initially a fork of xmpppy, but uses non-blocking sockets.")
        ("hicolor-icon-theme" ,hicolor-icon-theme)
        ("libsecret" ,libsecret)
        ("python-axolotl" ,python-axolotl)
+       ("python-cssutils" ,python-cssutils)
        ("python-dbus" ,python-dbus)
-       ("python-docutils" ,python-docutils)
        ("python-gnupg" ,python-gnupg)
+       ("python-keyring" ,python-keyring)
        ("python-nbxmpp" ,python-nbxmpp)
        ("python-pillow" ,python-pillow)
-       ("python-pyasn1" ,python-pyasn1)
+       ("python-precis-i18n" ,python-precis-i18n)
        ("python-pycairo" ,python-pycairo)
        ("python-pygobject" ,python-pygobject)
        ("python-pyopenssl" ,python-pyopenssl)
@@ -828,8 +818,8 @@ protocols.")
     (license license:x11)))
 
 (define-public libtoxcore
-  (let ((revision "1")
-        (commit "755f084e8720b349026c85afbad58954cb7ff1d4"))
+  (let ((revision "2")
+        (commit "bf69b54f64003d160d759068f4816b2d9b2e1e21"))
     (package
       (name "libtoxcore")
       (version (string-append "0.0.0" "-"
@@ -842,26 +832,19 @@ protocols.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "0ap1gvlyihnfivv235dbrgsxsiiz70bhlmlr5gn1027w3h5kqz8w"))))
+                  "11lqra4yd7v293cp286ynff5lqz1pprzg8vn3wq6vryj08g88zqb"))))
       (build-system gnu-build-system)
+      (arguments `(#:tests? #f)) ; FIXME: tests hang, some fail.
       (native-inputs
        `(("autoconf" ,autoconf)
          ("automake" ,automake)
          ("libtool" ,libtool)
-         ;; TODO: Add when test suite is capable of passing.
-         ;; ("check" ,check)
+         ("check" ,check)
          ("pkg-config" ,pkg-config)))
       (inputs
        `(("libsodium" ,libsodium)
          ("opus" ,opus)
          ("libvpx" ,libvpx)))
-      (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'autoconf
-             (lambda _
-               (zero? (system* "autoreconf" "-vfi")))))
-         #:tests? #f)) ; FIXME: Testsuite fails, reasons unspecific.
       (synopsis "Library for the Tox encrypted messenger protocol")
       (description
        "C library implementation of the Tox encrypted messenger protocol.")
@@ -877,13 +860,14 @@ protocols.")
     (version "0.2.8")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/TokTok/c-toxcore/archive/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/TokTok/c-toxcore.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0qlkimlvbd24nlj7w9b5rpz1r807magqxmfylc1mlxsqhmfi5zj7"))))
+         "0xgnraysz25fbws5zwjk92mwnl8k1yih701qam8kgm3rxh50kyhm"))))
     (arguments
      `(#:tests? #f)) ; FIXME: Testsuite seems to stay stuck on test 3. Disable
                      ; for now.
diff --git a/gnu/packages/mtools.scm b/gnu/packages/mtools.scm
index e4750f579f..5e3c3dd378 100644
--- a/gnu/packages/mtools.scm
+++ b/gnu/packages/mtools.scm
@@ -28,15 +28,15 @@
 (define-public mtools
   (package
     (name "mtools")
-    (version "4.0.19")
+    (version "4.0.20")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://gnu/mtools/mtools-"
-                          version ".tar.gz"))
+                          version ".tar.bz2"))
       (sha256
        (base32
-        "003qnj4rs22v2sih3is55scvav8xq9p1dp5b7gnyl67a60ky516r"))))
+        "1vcahr9s6zv1hnrx2bgjnzcas2y951q90r1jvvv4q9v5kwfd6qb0"))))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/mtools/")
     (synopsis "Access MS-DOS disks without mounting")
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 89ef58e80c..fca26edcbb 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -887,9 +887,10 @@ Sega Master System/Mark III, Sega Genesis/Mega Drive, BBC Micro
             #t))
          (add-after 'install 'install-info
            (lambda _
-             (zero? (system* "make"
-                             "-j" (number->string (parallel-job-count))
-                             "conf=www" "install-info")))))))
+             (invoke "make"
+                     "-j" (number->string (parallel-job-count))
+                     "conf=www" "install-info")
+             #t)))))
     (inputs
      `(("guile" ,guile-1.8)
        ("font-dejavu" ,font-dejavu)
@@ -1255,12 +1256,14 @@ Editor.  It is compatible with Power Tab Editor 1.7 and Guitar Pro.")
     (name "jalv-select")
     (version "0.8")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/brummer10/jalv_select/"
-                                  "archive/V" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/brummer10/jalv_select.git")
+                    (commit (string-append "V" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0zraagwr681b5s3qifxf399c7q93jz23c8sr42gmff9zqnvxc75q"))))
+                "0gqh768sbvn9ffyx1vqg9i57py9x9v4l65bk6wjsvgga4d7m83k1"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
@@ -1275,6 +1278,13 @@ Editor.  It is compatible with Power Tab Editor 1.7 and Guitar Pro.")
                 (string-append "ls -1 " (assoc-ref inputs "jalv") "/bin")))
              (substitute* "jalv.select.h"
                (("gtkmm.h") "gtkmm-2.4/gtkmm.h"))
+             #t))
+         (add-before 'reset-gzip-timestamps 'make-manpages-writable
+           (lambda* (#:key outputs #:allow-other-keys)
+             (for-each make-file-writable
+                       (find-files (string-append (assoc-ref outputs "out")
+                                                  "/share/man")
+                                   ".*\\.gz$"))
              #t)))))
     (inputs
      `(("lilv" ,lilv)
@@ -1857,13 +1867,14 @@ using a system-independent interface.")
     (name "portmidi-for-extempore")
     (version "217")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/extemporelang/portmidi/"
-                                  "archive/" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/extemporelang/portmidi.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0gjikwciyr8kk4y3qiv1pcq58xpgw38ql1m2gs6g0qc1s8sx4235"))))
+                "1inriyrjf7xx2b7r54x0vmf9ngyqgr7g5060c22bwkbsgg53apzv"))))
     (build-system cmake-build-system)
     (arguments `(#:tests? #f)) ; no tests
     (native-inputs '())
@@ -2279,13 +2290,14 @@ follows a traditional multi-track tape recorder control paradigm.")
     (version "1.2.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/blablack/ams-lv2/"
-                           "archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/blablack/ams-lv2.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1xacxyzqcj83g9c1gwfn36gg1c6yi15v7km4vidfidrjzb4x27fq"))))
+         "1n1dnqnj24xhiy9323lj52nswr5120cj56fpckg802miss05sr6x"))))
     (build-system waf-build-system)
     (arguments
      `(#:phases
@@ -2320,13 +2332,14 @@ and hold, etc.")
     (name "gxtuner")
     (version "2.4")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/brummer10/gxtuner/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/brummer10/gxtuner.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1hn5qjac7qd00v0sp7ijhhc3sb26ks9bni06nngivva21h61xrjr"))))
+                "1fxd2akan2njlr7fpkh84830783qhh1gg7yakswqk5dd466dcn96"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
@@ -2432,13 +2445,14 @@ tune-in sender list from @url{http://opml.radiotime.com}.")
     (name "pianobar")
     (version "2016.06.02")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/PromyLOPh/"
-                                  name "/archive/" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/PromyLOPh/pianobar.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1hi5rr6jcr0kwf4xfz007ndwkjkp287lhwlsgfz6iryqa5n6jzcp"))))
+                "058fbdxp7n35hxwy3b8slfy4pb4n63cb173vfmywqa06wh1dv6f6"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no tests
@@ -2719,14 +2733,14 @@ of tools for manipulating and accessing your music.")
     (name "milkytracker")
     (version "1.02.00")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/milkytracker/"
-                                  "MilkyTracker/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/milkytracker/MilkyTracker.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "08v0l4ipvvwkwv4ywkc6c8a6xnpkyb02anj36w8q6gikxrs6xjvb"))
+                "05a6d7l98k9i82dwrgi855dnccm3f2lkb144gi244vhk1156n0ca"))
               (modules '((guix build utils)))
               ;; Remove non-FSDG compliant sample songs.
               (snippet
@@ -2761,14 +2775,14 @@ for improved Amiga ProTracker 2/3 compatibility.")
     (name "schismtracker")
     (version "20180513")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/" name "/" name "/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/schismtracker/schismtracker.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1yjfd02arb51n0vyv11qgpn6imh7hcqnc3953cbvgwb4cnrswk9f"))
+                "0fayix1zbl96zhkfszgj71qr25dnddgy9hr6149nslww4gl7jk36"))
               (modules '((guix build utils)))
               (snippet
                ;; Remove use of __DATE__ and __TIME__ for reproducibility.
@@ -2781,8 +2795,6 @@ for improved Amiga ProTracker 2/3 compatibility.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _ (invoke "autoreconf" "-vfi")))
          (add-before 'configure 'link-libm
            (lambda _ (setenv "LIBS" "-lm") #t)))))
     (native-inputs
@@ -3520,13 +3532,14 @@ are a C compiler and glib.  Full API documentation and examples are included.")
     (version "1.1.3")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/LMMS/lmms/archive/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/LMMS/lmms.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1g76z7ha3hd53vbqaq9n1qg6s3lw8zzaw51iny6y2bz0j1xqwcsr"))))
+         "03hhymc6d73fa3wbcqb7rm1l03zkw605k5i9kvkvjmv488bqh3pd"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ; no tests
@@ -4143,17 +4156,15 @@ at @code{musicbrainz.org}.")
     (version "0.10")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/trizen/clyrics/archive/"
-             version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/trizen/clyrics.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1l0cg26afnjv8cgk0jbiavbyvq55q1djyigzmi526rpcjjwq9jwn"))
-       (file-name (string-append name "-" version ".tar.gz"))))
+         "1qvj4dyipkkdccx5hci4z0q23i54ldk6hh7x5m35a7f70rrj6fbk"))))
     (build-system trivial-build-system)
-    (native-inputs `(("tar" ,tar)
-                     ("gzip" ,gzip)))
     (inputs
      `(("bash" ,bash)                             ;for the wrapped program
        ("perl" ,perl)
@@ -4170,17 +4181,12 @@ at @code{musicbrainz.org}.")
                                 (ice-9 match)
                                 (srfi srfi-26))
                    (let* ((source (assoc-ref %build-inputs "source"))
-                          (tar (assoc-ref %build-inputs "tar"))
-                          (gzip (assoc-ref %build-inputs "gzip"))
                           (output (assoc-ref %outputs "out")))
                      (setenv "PATH"
                              (string-append
-                              (assoc-ref %build-inputs "gzip") "/bin" ":"
                               (assoc-ref %build-inputs "bash") "/bin" ":"
                               (assoc-ref %build-inputs "perl") "/bin" ":"))
-                     (invoke (string-append tar "/bin/tar") "xvf"
-                             source)
-                     (chdir ,(string-append "clyrics-" version))
+                     (copy-recursively source (getcwd))
                      (patch-shebang "clyrics")
                      (substitute* "clyrics"
                        (("/usr/share") output))
diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm
index 8f96b605a6..057e8c3bd9 100644
--- a/gnu/packages/nano.scm
+++ b/gnu/packages/nano.scm
@@ -30,7 +30,7 @@
 (define-public nano
   (package
     (name "nano")
-    (version "3.1")
+    (version "3.2")
     (source
      (origin
       (method url-fetch)
@@ -38,7 +38,7 @@
                           version ".tar.xz"))
       (sha256
        (base32
-        "17kinzyv6vwgyx2d0ym1kp65qbf7kxzwpyg21ic1rijv1aj2rh0l"))))
+        "0jb3zq0v84xb0chyynkcp2jhs9660wmpkic294p4p6c96npp69yi"))))
     (build-system gnu-build-system)
     (inputs
      `(("gettext" ,gettext-minimal)
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 717e7021cf..fe784ffaa1 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -102,8 +102,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "0.15.0")
-        (commit "f9a8fce10f2d99efec7cb1dd0f6c5f0df9d1b2df")
-        (revision 6))
+        (commit "f5a2724ae453f4a4b55ff848f4ad7e30efb6eef8")
+        (revision 7))
     (package
       (name "guix")
 
@@ -119,7 +119,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "1733d5id0h44rrkyj9xw4fcqr1wawcfi8igpgk5wsn1iq4qqwv5f"))
+                  "12glmvifbwvl6lmxh1mc8nbcp0f5qgw40rmf8n1icxvj0mnjrwp4"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
diff --git a/gnu/packages/patches/icecat-CVE-2018-12383.patch b/gnu/packages/patches/icecat-CVE-2018-12383.patch
deleted file mode 100644
index 17ca0f3773..0000000000
--- a/gnu/packages/patches/icecat-CVE-2018-12383.patch
+++ /dev/null
@@ -1,103 +0,0 @@
-Based on upstream changeset:
-  https://hg.mozilla.org/releases/mozilla-esr60/rev/300efdbc9fe1
-but with the git binary patch and related test changes omitted,
-and adapted to apply cleanly to GNU IceCat.
-
-# HG changeset patch
-# User David Keeler <dkeeler@mozilla.com>
-# Date 1531860660 25200
-# Node ID 300efdbc9fe1f9165428c7934861033935b5abfa
-# Parent  80a4a7ef281374dbb2afda8edac54665b14b9ef8
-Bug 1475775 - Clean up old NSS DB file after upgrade if necessary. r=franziskus, r=mattn, a=RyanVM
-
-Reviewers: franziskus, mattn
-
-Bug #: 1475775
-
-Differential Revision: https://phabricator.services.mozilla.com/D2202
-
-diff --git a/security/manager/ssl/nsNSSComponent.cpp b/security/manager/ssl/nsNSSComponent.cpp
---- a/security/manager/ssl/nsNSSComponent.cpp
-+++ b/security/manager/ssl/nsNSSComponent.cpp
-@@ -1935,16 +1935,61 @@ AttemptToRenameBothPKCS11ModuleDBVersion
-   NS_NAMED_LITERAL_CSTRING(sqlModuleDBFilename, "pkcs11.txt");
-   nsresult rv = AttemptToRenamePKCS11ModuleDB(profilePath,
-                                               legacyModuleDBFilename);
-   if (NS_FAILED(rv)) {
-     return rv;
-   }
-   return AttemptToRenamePKCS11ModuleDB(profilePath, sqlModuleDBFilename);
- }
-+
-+// When we changed from the old dbm database format to the newer sqlite
-+// implementation, the upgrade process left behind the existing files. Suppose a
-+// user had not set a password for the old key3.db (which is about 99% of
-+// users). After upgrading, both the old database and the new database are
-+// unprotected. If the user then sets a password for the new database, the old
-+// one will not be protected. In this scenario, we should probably just remove
-+// the old database (it would only be relevant if the user downgraded to a
-+// version of IceCat before 58, but we have to trade this off against the
-+// user's old private keys being unexpectedly unprotected after setting a
-+// password).
-+// This was never an issue on Android because we always used the new
-+// implementation.
-+static void
-+MaybeCleanUpOldNSSFiles(const nsACString& profilePath)
-+{
-+  UniquePK11SlotInfo slot(PK11_GetInternalKeySlot());
-+  if (!slot) {
-+    return;
-+  }
-+  // Unfortunately we can't now tell the difference between "there already was a
-+  // password when the upgrade happened" and "there was not a password but then
-+  // the user added one after upgrading".
-+  bool hasPassword = PK11_NeedLogin(slot.get()) &&
-+                     !PK11_NeedUserInit(slot.get());
-+  if (!hasPassword) {
-+    return;
-+  }
-+  nsCOMPtr<nsIFile> dbFile = do_CreateInstance("@mozilla.org/file/local;1");
-+  if (!dbFile) {
-+    return;
-+  }
-+  nsresult rv = dbFile->InitWithNativePath(profilePath);
-+  if (NS_FAILED(rv)) {
-+    return;
-+  }
-+  NS_NAMED_LITERAL_CSTRING(keyDBFilename, "key3.db");
-+  rv = dbFile->AppendNative(keyDBFilename);
-+  if (NS_FAILED(rv)) {
-+    return;
-+  }
-+  // Since this isn't a directory, the `recursive` argument to `Remove` is
-+  // irrelevant.
-+  Unused << dbFile->Remove(false);
-+}
- #endif // ifndef ANDROID
- 
- // Given a profile directory, attempt to initialize NSS. If nocertdb is true,
- // (or if we don't have a profile directory) simply initialize NSS in no DB mode
- // and return. Otherwise, first attempt to initialize in read/write mode, and
- // then read-only mode if that fails. If both attempts fail, we may be failing
- // to initialize an NSS DB collection that has FIPS mode enabled. Attempt to
- // ascertain if this is the case, and if so, rename the offending PKCS#11 module
-@@ -1966,16 +2011,19 @@ InitializeNSSWithFallbacks(const nsACStr
- 
-   // Try read/write mode. If we're in safeMode, we won't load PKCS#11 modules.
- #ifndef ANDROID
-   PRErrorCode savedPRErrorCode1;
- #endif // ifndef ANDROID
-   SECStatus srv = ::mozilla::psm::InitializeNSS(profilePath, false, !safeMode);
-   if (srv == SECSuccess) {
-     MOZ_LOG(gPIPNSSLog, LogLevel::Debug, ("initialized NSS in r/w mode"));
-+#ifndef ANDROID
-+    MaybeCleanUpOldNSSFiles(profilePath);
-+#endif // ifndef ANDROID
-     return NS_OK;
-   }
- #ifndef ANDROID
-   savedPRErrorCode1 = PR_GetError();
-   PRErrorCode savedPRErrorCode2;
- #endif // ifndef ANDROID
-   // That failed. Try read-only mode.
-   srv = ::mozilla::psm::InitializeNSS(profilePath, true, !safeMode);
diff --git a/gnu/packages/patches/poppler-CVE-2018-19149.patch b/gnu/packages/patches/poppler-CVE-2018-19149.patch
new file mode 100644
index 0000000000..3641f5f078
--- /dev/null
+++ b/gnu/packages/patches/poppler-CVE-2018-19149.patch
@@ -0,0 +1,80 @@
+Fix CVE-2018-19149:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-19149
+https://gitlab.freedesktop.org/poppler/poppler/issues/664
+
+Patch copied from upstream source repository:
+
+https://gitlab.freedesktop.org/poppler/poppler/commit/f162ecdea0dda5dbbdb45503c1d55d9afaa41d44
+
+From f162ecdea0dda5dbbdb45503c1d55d9afaa41d44 Mon Sep 17 00:00:00 2001
+From: Marek Kasik <mkasik@redhat.com>
+Date: Fri, 20 Apr 2018 11:38:13 +0200
+Subject: [PATCH] Fix crash on missing embedded file
+
+Check whether an embedded file is actually present in the PDF
+and show warning in that case.
+
+https://bugs.freedesktop.org/show_bug.cgi?id=106137
+https://gitlab.freedesktop.org/poppler/poppler/issues/236
+---
+ glib/poppler-attachment.cc | 26 +++++++++++++++++---------
+ glib/poppler-document.cc   |  3 ++-
+ 2 files changed, 19 insertions(+), 10 deletions(-)
+
+diff --git a/glib/poppler-attachment.cc b/glib/poppler-attachment.cc
+index c6502e9d..11ba5bb5 100644
+--- a/glib/poppler-attachment.cc
++++ b/glib/poppler-attachment.cc
+@@ -111,17 +111,25 @@ _poppler_attachment_new (FileSpec *emb_file)
+     attachment->description = _poppler_goo_string_to_utf8 (emb_file->getDescription ());
+ 
+   embFile = emb_file->getEmbeddedFile();
+-  attachment->size = embFile->size ();
++  if (embFile != NULL && embFile->streamObject()->isStream())
++    {
++      attachment->size = embFile->size ();
+ 
+-  if (embFile->createDate ())
+-    _poppler_convert_pdf_date_to_gtime (embFile->createDate (), (time_t *)&attachment->ctime);
+-  if (embFile->modDate ())
+-    _poppler_convert_pdf_date_to_gtime (embFile->modDate (), (time_t *)&attachment->mtime);
++      if (embFile->createDate ())
++        _poppler_convert_pdf_date_to_gtime (embFile->createDate (), (time_t *)&attachment->ctime);
++      if (embFile->modDate ())
++        _poppler_convert_pdf_date_to_gtime (embFile->modDate (), (time_t *)&attachment->mtime);
+ 
+-  if (embFile->checksum () && embFile->checksum ()->getLength () > 0)
+-    attachment->checksum = g_string_new_len (embFile->checksum ()->getCString (),
+-                                             embFile->checksum ()->getLength ());
+-  priv->obj_stream = embFile->streamObject()->copy();
++      if (embFile->checksum () && embFile->checksum ()->getLength () > 0)
++        attachment->checksum = g_string_new_len (embFile->checksum ()->getCString (),
++                                                 embFile->checksum ()->getLength ());
++      priv->obj_stream = embFile->streamObject()->copy();
++    }
++  else
++    {
++      g_warning ("Missing stream object for embedded file");
++      g_clear_object (&attachment);
++    }
+ 
+   return attachment;
+ }
+diff --git a/glib/poppler-document.cc b/glib/poppler-document.cc
+index 83f6aea6..ea319344 100644
+--- a/glib/poppler-document.cc
++++ b/glib/poppler-document.cc
+@@ -670,7 +670,8 @@ poppler_document_get_attachments (PopplerDocument *document)
+       attachment = _poppler_attachment_new (emb_file);
+       delete emb_file;
+ 
+-      retval = g_list_prepend (retval, attachment);
++      if (attachment != NULL)
++        retval = g_list_prepend (retval, attachment);
+     }
+   return g_list_reverse (retval);
+ }
+-- 
+2.19.1
+
diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 062ef02efe..28737c36e4 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -82,6 +82,7 @@
 (define-public poppler
   (package
    (name "poppler")
+   (replacement poppler/fixed)
    (version "0.68.0")
    (source (origin
             (method url-fetch)
@@ -131,6 +132,14 @@
    (license license:gpl2+)
    (home-page "https://poppler.freedesktop.org/")))
 
+(define poppler/fixed
+  (package
+    (inherit poppler)
+    (source (origin
+              (inherit (package-source poppler))
+              (patches (append (origin-patches (package-source poppler))
+                               (search-patches "poppler-CVE-2018-19149.patch")))))))
+
 (define-public poppler-data
   (package
     (name "poppler-data")
@@ -162,14 +171,14 @@ When present, Poppler is able to correctly render CJK and Cyrillic text.")
                    license:gpl2))))
 
 (define-public poppler-qt4
-  (package (inherit poppler)
+  (package/inherit poppler
    (name "poppler-qt4")
    (inputs `(("qt-4" ,qt-4)
              ,@(package-inputs poppler)))
    (synopsis "Qt4 frontend for the Poppler PDF rendering library")))
 
 (define-public poppler-qt5
-  (package (inherit poppler)
+  (package/inherit poppler
    (name "poppler-qt5")
    (inputs `(("qtbase" ,qtbase)
              ,@(package-inputs poppler)))
@@ -227,26 +236,23 @@ Poppler PDF rendering library.")
    (name "libharu")
    (version "2.3.0")
    (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/libharu/libharu/archive/"
-                                 "RELEASE_"
-                                 (string-join (string-split version #\.) "_")
-                                 ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/libharu/libharu.git")
+                   (commit (string-append
+                            "RELEASE_"
+                            (string-join (string-split version #\.) "_")))))
+             (file-name (git-file-name name version))
              (sha256
               (base32
-               "1lm4v539y9cb1lvbq387j57sy7yxda3yv8b1pk8m6zazbp66i7lg"))))
+               "15s9hswnl3qqi7yh29jyrg0hma2n99haxznvcywmsp8kjqlyg75q"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags
       (list (string-append "--with-zlib="
                            (assoc-ref %build-inputs "zlib"))
             (string-append "--with-png="
-                           (assoc-ref %build-inputs "libpng")))
-      #:phases
-      (modify-phases %standard-phases
-        (add-after 'unpack 'autogen
-          (lambda _ (invoke "autoreconf" "-vif"))))))
+                           (assoc-ref %build-inputs "libpng")))))
    (inputs
     `(("zlib" ,zlib)
       ("libpng" ,libpng)))
diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm
index 466b26c238..a28cb31e5c 100644
--- a/gnu/packages/php.scm
+++ b/gnu/packages/php.scm
@@ -53,7 +53,7 @@
 (define-public php
   (package
     (name "php")
-    (version "7.2.10")
+    (version "7.2.12")
     (home-page "https://secure.php.net/")
     (source (origin
               (method url-fetch)
@@ -61,7 +61,7 @@
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1w0432i5wjga9z8x3rhc72h2ij1jd2aimg5xmhc0hg4f7951bhh1"))
+                "1qbz2j9kzqxxp0mmx02zavvz20ji7izqdnri25g1mrwyhz60974q"))
               (modules '((guix build utils)))
               (snippet
                '(with-directory-excursion "ext"
@@ -176,6 +176,11 @@
              (substitute* "ext/standard/tests/streams/bug60602.phpt"
                (("'ls'") (string-append "'" (which "ls") "'")))
 
+             ;; The expected output is slightly different from what is given,
+             ;; in a section that's not related to the actual test
+             (substitute* "sapi/cli/tests/upload_2G.phpt"
+               (("Test\\\\n") "Test\n\n"))
+
              ;; Drop tests that are known to fail.
              (for-each delete-file
                        '("ext/posix/tests/posix_getgrgid.phpt"    ; Requires /etc/group.
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 41c2a1f7ee..c2f73e3f5c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14626,3 +14626,22 @@ on regular expressions.")
              (propagated-inputs
               `(("python2-enum34" ,python2-enum34)
                 ,@(package-propagated-inputs reparser))))))
+
+(define-public python-precis-i18n
+  (package
+    (name "python-precis-i18n")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "precis_i18n" version))
+       (sha256
+        (base32
+         "0gjhvwd8aifx94rl1ag08vlmndyx2q3fkyqb0c4i46x3p2bc2yi2"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/byllyfish/precis_i18n")
+    (synopsis "Implementation of the PRECIS framework")
+    (description
+     "This module implements the PRECIS Framework as described in RFC 8264,
+RFC 8265 and RFC 8266.")
+    (license license:expat)))
diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm
index 48dc3cddb9..22ea21dd94 100644
--- a/gnu/packages/rdf.scm
+++ b/gnu/packages/rdf.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -22,6 +22,7 @@
   #:use-module ((guix licenses)
                 #:select (non-copyleft isc gpl2 lgpl2.1 lgpl2.1+))
   #:use-module (guix packages)
+  #:use-module (guix git-download)
   #:use-module (guix download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
@@ -122,13 +123,14 @@ Java Lucene text search engine API to C++.")
     (name "lrdf")
     (version "0.6.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/swh/LRDF/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/swh/LRDF.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1vxii4mlcpyi16dizcmnqfl2j9gffgr986yd8ic67hvs8xy42yfm"))))
+                "00wzkfb8y0aqd519ypz067cq099dpc89w69zw8ln39vl6f9x2pd4"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -140,9 +142,9 @@ Java Lucene text search engine API to C++.")
                (("instances_test remove_test") "instances_test")
                (("\\$\\(TESTS\\) remove_test") "$(TESTS)"))
              #t))
-         (add-after 'remove-out-of-tree-references 'autoreconf
-           (lambda _
-             (zero? (system* "autoreconf" "-vfi")))))))
+         ;; The default bootstrap phase executes autogen.sh, which fails.
+         (replace 'bootstrap
+           (lambda _ (invoke "autoreconf" "-vif") #t)))))
     (inputs
      `(("raptor" ,raptor2)
        ("cyrus-sasl" ,cyrus-sasl)
diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm
index 470643ec4f..b927bbbf9b 100644
--- a/gnu/packages/samba.scm
+++ b/gnu/packages/samba.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -73,10 +74,6 @@
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         ;; The 6.7 tarball is missing ‘install.sh’. Create it.
-         (add-after 'unpack 'autoreconf
-           (lambda _
-             (invoke "autoreconf" "-i")))
          (add-before 'configure 'set-root-sbin
            (lambda _ ; Don't try to install in "/sbin".
              (setenv "ROOTSBINDIR"
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 40b3d1bae0..2df0ce1364 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -99,7 +99,6 @@ arbitrary data types and reversibly turns them into different representations,
 such as compact binary encodings, XML, or JSON.")
     (license license:bsd-3)))
 
-
 (define-public msgpack
   (package
     (name "msgpack")
@@ -132,13 +131,6 @@ such as compact binary encodings, XML, or JSON.")
     ;; zbuffer.hpp) which #include <zlib.h>.  However, 'guix gc --references'
     ;; does not detect a store reference to zlib since these headers are not
     ;; compiled.
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _
-             (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
diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm
index 3e9d797e2c..38eeaa7831 100644
--- a/gnu/packages/shells.scm
+++ b/gnu/packages/shells.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016 Stefan Reichör <stefan@xsteve.at>
-;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2018 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
@@ -414,10 +414,7 @@ use of experts and novices alike.")
                                              "/rx")))
                  (delete-file-recursively "rx")
                  (symlink rxpath "rx"))
-               #t))
-           (add-after 'unpack 'autoreconf
-             (lambda _
-               (invoke "autoreconf"))))))
+               #t)))))
       (inputs
        `(("scheme48" ,scheme48)
          ("scheme48-rx" ,scheme48-rx)))
diff --git a/gnu/packages/shellutils.scm b/gnu/packages/shellutils.scm
index 3020fdd210..0978300c9b 100644
--- a/gnu/packages/shellutils.scm
+++ b/gnu/packages/shellutils.scm
@@ -116,9 +116,10 @@ are already there.")
      '(#:test-target "test"
        #:make-flags (list (string-append "DESTDIR=" (assoc-ref %outputs "out")))
        #:phases (modify-phases %standard-phases (delete 'configure))))
+    (inputs
+     `(("go" ,go-1.9)))
     (native-inputs
-      `(("go" ,go)
-        ("which" ,which)))
+      `(("which" ,which)))
     (home-page "https://direnv.net/")
     (synopsis "Environment switcher for the shell")
     (description
diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm
index e708d726bb..fb121a0581 100644
--- a/gnu/packages/spice.scm
+++ b/gnu/packages/spice.scm
@@ -250,7 +250,7 @@ Internet and from a wide variety of machine architectures.")
          (add-after 'unpack 'patch-spice-vdagent.desktop
            (lambda* (#:key outputs #:allow-other-keys)
             (substitute* "data/spice-vdagent.desktop"
-              (("Exec=/usr/bin/spice-vdagent\n")
+              (("Exec=/usr/bin/spice-vdagent")
                (string-append "Exec=" (assoc-ref outputs "out")
                               "/bin/spice-vdagent")))
              #t)))))
diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm
index f12c6ed1b0..5c954eae35 100644
--- a/gnu/packages/ssh.scm
+++ b/gnu/packages/ssh.scm
@@ -71,13 +71,7 @@
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                     ;; git.libssh.org does not support the fast "smart" HTTP
-                     ;; Git protocol. The "dumb" HTTP Git protocol is extremely
-                     ;; slow, and does not support shallow clones, so we use the
-                     ;; plain Git protocol despite its flaws. This offers an
-                     ;; incredible speedup and reduces the size of the the
-                     ;; source by more than half.
-                     (url "git://git.libssh.org/projects/libssh.git")
+                     (url "https://git.libssh.org/projects/libssh.git")
                      (commit (string-append "libssh-" version))))
               (patches (search-patches "libssh-hostname-parser-bug.patch"))
               (sha256
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 9bfa4c5683..57fb99ef28 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -115,6 +115,36 @@ can be imported from spreadsheets, text files and database sources and it can
 be output in text, PostScript, PDF or HTML.")
     (license license:gpl3+)))
 
+(define-public jags
+  (package
+    (name "jags")
+    (version "4.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
+                                  (version-major version) ".x/Source/"
+                                  "JAGS-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
+    (build-system gnu-build-system)
+    (home-page "http://mcmc-jags.sourceforge.net/")
+    (native-inputs
+     `(("gfortran" ,gfortran)
+       ("lapack" ,lapack)))
+    (synopsis "Gibbs sampler")
+    (description "JAGS is Just Another Gibbs Sampler.  It is a program for
+analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
+simulation not wholly unlike BUGS.  JAGS was written with three aims in mind:
+
+@enumerate
+@item To have a cross-platform engine for the BUGS language;
+@item To be extensible, allowing users to write their own functions,
+  distributions and samplers;
+@item To be a platform for experimentation with ideas in Bayesian modelling.
+@end enumerate\n")
+    (license license:gpl2)))
+
 ;; Update this package together with the set of recommended packages: r-boot,
 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
@@ -1620,13 +1650,13 @@ and printing capabilities than traditional data frames.")
 (define-public r-dplyr
   (package
     (name "r-dplyr")
-    (version "0.7.7")
+    (version "0.7.8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "dplyr" version))
               (sha256
                (base32
-                "196lwck3i3m25jnn1f1nrda9svnjqqi89s0is79gbrphamddnlq5"))))
+                "06p59nhli8c1sarghzxq0y4pk6lyyz3xwkarp55b252dfg2rly9p"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -2528,13 +2558,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.100.5.0")
+    (version "0.9.200.4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1iyjqhfjip1nxrkllzh7r1m01jjnx7cahqkf3s557w34p987f2l1"))))
+                "1ayvpyi4hgaqrhx1kqi640iillc2byj4kam7vydlgqmdrzpgrfvz"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (native-inputs
@@ -3268,14 +3298,14 @@ the way current RNG settings can be changed.")
 (define-public r-rtsne
   (package
     (name "r-rtsne")
-    (version "0.13")
+    (version "0.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rtsne" version))
        (sha256
         (base32
-         "17crbdi80q4g2pwp9v7j3bdaznk96qlrqx01zvj3wwqippizyfqw"))))
+         "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
     (properties `((upstream-name . "Rtsne")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5123,14 +5153,14 @@ algorithms.")
 (define-public r-lme4
   (package
     (name "r-lme4")
-    (version "1.1-18-1")
+    (version "1.1-19")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lme4" version))
        (sha256
         (base32
-         "01ar4fak8zj7c1vmh9m576wchxj5qzpfqn637s7fh3fl6cpz0alq"))))
+         "0j8xhkkcdv45ilab960s9jrcjk6jbzvd7w7myswv5fmalrpq52pf"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -5325,14 +5355,14 @@ first and second order derivatives.")
 (define-public r-sn
   (package
     (name "r-sn")
-    (version "1.5-2")
+    (version "1.5-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sn" version))
        (sha256
         (base32
-         "16gwr68zzj5v83bqfmzxnzwig3dnjrkxdhs6clri1caqkvrq6aig"))))
+         "10via4lg0vx9pzq350vwhz5wv1dhzxr2l3r6jq99nk37vmyvj8fc"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mnormt" ,r-mnormt)
diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 5d681b816e..c29c88a588 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -900,7 +900,16 @@ the current goroutine's ID.")
                   "0bg26pfg25vr16jmczig2m493mja2nxjxyswz3hha7avxw20rpi5"))))
       (build-system go-build-system)
       (arguments
-       '(#:import-path "github.com/AudriusButkevicius/cli"))
+       '(#:import-path "github.com/AudriusButkevicius/cli"
+         ;; Tests don't pass "vet" on go-1.11.  See
+         ;; https://github.com/AudriusButkevicius/cli/pull/1.
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'check
+             (lambda* (#:key import-path #:allow-other-keys)
+               (invoke "go" "test"
+                       "-vet=off"
+                       import-path))))))
       (synopsis "Library for building command-line interfaces in Go")
       (description "This package provides a library for building command-line
 interfaces in Go.")
@@ -1097,7 +1106,14 @@ message streaming.")
                       (string-append (assoc-ref outputs "out")
                                      "/src/github.com/prometheus/common/expfmt/testdata/")
                       ".*\\.gz$"))
-               #t)))))
+               #t))
+           (replace 'check
+             ;; Tests don't pass "vet" on go-1.11.  See
+             ;; https://github.com/syncthing/syncthing/issues/5311.
+             (lambda* (#:key import-path #:allow-other-keys)
+               (invoke "go" "test"
+                       "-vet=off"
+                       import-path))))))
       (propagated-inputs
        `(("go-github-com-golang-protobuf-proto"
           ,go-github-com-golang-protobuf-proto)
@@ -1251,7 +1267,16 @@ Prometheus HTTP API.")
                 "1y8bvzbxpw0lfnn7pbcdwzqj4l90qj6xf88dvv9pxd9yl5g6cskx"))))
     (build-system go-build-system)
     (arguments
-     '(#:import-path "gopkg.in/asn1-ber.v1"))
+     '(#:import-path "gopkg.in/asn1-ber.v1"
+       ;; Tests don't pass "vet" on go-1.11.  See
+       ;; https://github.com/go-asn1-ber/asn1-ber/issues/20.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key import-path #:allow-other-keys)
+             (invoke "go" "test"
+                     "-vet=off"
+                     import-path))))))
     (synopsis "ASN.1 BER encoding and decoding in Go")
     (description "This package provides ASN.1 BER encoding and decoding in the
 Go language.")
diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm
index 05916cde5c..63709935c3 100644
--- a/gnu/packages/telephony.scm
+++ b/gnu/packages/telephony.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
 ;;; Copyright © 2016 Francesco Frassinelli <fraph24@gmail.com>
 ;;; Copyright © 2016, 2017 Nils Gillmann <ng0@n0.is>
-;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Jovany Leandro G.C <bit4bit@riseup.net>
 ;;;
@@ -295,26 +295,19 @@ protocol (RFC 3550).")
       (version (string-append "0.0.0-1." (string-take commit 7)))
       (source
        (origin
-         (method url-fetch)
-         (uri
-          (string-append
-           "https://gitlab.savoirfairelinux.com/sflphone/libiax2/"
-           "repository/archive.tar.gz?ref="
-           commit))
-         (file-name (string-append name "-" version ".tar.gz"))
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.savoirfairelinux.com/sflphone/libiax2.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
          (sha256
           (base32
-           "0cj5293bixp3k5x3hjwyd0iq7z8w5p7yavxvvkqk5817hjq386y2"))))
+           "0d269474kk1933c55hx4azw3sak5ycfrxkw6ida0sb2cm00kfich"))))
       (build-system gnu-build-system)
       (native-inputs
        `(("autoconf" ,autoconf)
          ("automake" ,automake)
          ("libtool" ,libtool)))
-      (arguments
-       `(#:phases (modify-phases %standard-phases
-                    (add-after 'unpack 'autoconf
-                      (lambda _
-                        (invoke "autoreconf" "-vfi"))))))
       (home-page "https://gitlab.savoirfairelinux.com/sflphone/libiax2")
       (synopsis "Inter-Asterisk-Protocol library")
       (description "LibIAX2 implements the Inter-Asterisk-Protocol for relaying
diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 084017dbde..e9a4ab3d68 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2015 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Jelle Licht <jlicht@fsfe.org>
@@ -15,6 +15,7 @@
 ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -197,11 +198,6 @@ encoding, supporting Unicode version 9.0.0.")
        (sha256
         (base32 "0jiybkb2z58wa2msvllnphr4js2hvjvh988pavb3mzkgr6ihwbkr"))))
     (build-system gnu-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
-           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
@@ -572,22 +568,16 @@ categories.")
     (name "dotconf")
     (version "1.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/williamh/dotconf/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/williamh/dotconf.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0lsnh0yaw44psmx59hq94cj1932gscp5h8d3cnh05l0svr0cy7kz"))))
+                "1sc95hw5k2xagpafny0v35filmcn05k1ds5ghkldfpf6xw4hakp7"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:tests? #f ; FIXME maketest.sh does not work.
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
-           (lambda _
-             (zero? (system* "autoreconf" "-vif")))))))
+    (arguments `(#:tests? #f))  ; FIXME maketest.sh does not work.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
@@ -756,3 +746,26 @@ indentation.
 @end itemize\n")
     (home-page "http://docx2txt.sourceforge.net")
     (license license:gpl3+)))
+
+(define-public opencc
+  (package
+    (name "opencc")
+    (version "1.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/BYVoid/OpenCC"
+                           "/archive/ver." version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "01870gbkf711msirf3206k0ajaabypjhnx3fny5wikw0ladn9q8w"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("python" ,python-wrapper)))
+    (home-page "https://github.com/BYVoid/OpenCC")
+    (synopsis "Convert between Traditional Chinese and Simplified Chinese")
+    (description "Open Chinese Convert (OpenCC) converts between Traditional
+Chinese and Simplified Chinese, supporting character-level conversion,
+phrase-level conversion, variant conversion, and regional idioms among
+Mainland China, Taiwan, and Hong-Kong.")
+    (license license:asl2.0)))
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index d9fc601066..48dceaec33 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -522,13 +522,13 @@ netcat implementation that supports TLS.")
   (package
     (name "python-acme")
     ;; Remember to update the hash of certbot when updating python-acme.
-    (version "0.27.1")
+    (version "0.28.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "acme" version))
               (sha256
                (base32
-                "142gynlfx7yv0sdba3gpdxlnhg9chhz7hpdxdrp630z17h1bk9ri"))))
+                "11dvcbdifn5d02p4k5li8r6r39bl3p5ap9p3zjwvasm24hf2yz5z"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -579,7 +579,7 @@ netcat implementation that supports TLS.")
               (uri (pypi-uri name version))
               (sha256
                (base32
-                "0anh3vjy9sif1bkp25nj76ii37xx8hh0igcx60ppag12xlabsw1m"))))
+                "02h959qkq7z0s13ivgf7jyl3gnc55wcck6n546k0kh155bpf5qri"))))
     (build-system python-build-system)
     (arguments
      `(,@(substitute-keyword-arguments (package-arguments python-acme)
diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm
index 61b0c82e30..e28a6d4f48 100644
--- a/gnu/packages/tor.scm
+++ b/gnu/packages/tor.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -140,14 +141,6 @@ rejects UDP traffic from the application you're using.")
        #:configure-flags (list (string-append "--sysconfdir="
                                               (assoc-ref %outputs "out")
                                               "/etc/privoxy"))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _
-             ;; Unfortunately, this is not a tarball produced by
-             ;; "make dist".
-             (invoke "autoreconf" "-vfi")
-             #t)))
        #:tests? #f))
     (inputs
      `(("w3m" ,w3m)
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index a482ef2515..94c5cf3a67 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1269,7 +1269,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2018.11.03")
+    (version "2018.11.07")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1277,7 +1277,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "11phhwhr1g050h4625d5jsgcsjnnv7jc6xcrbn7zdzd32f6gy2lj"))))
+                "1rvc2m2kbm2kycqsa7fkcg5gql9f0w3hn1a7jg48zzl06ayggxk9"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm
index c6906b12cf..c974ebc439 100644
--- a/gnu/packages/vim.scm
+++ b/gnu/packages/vim.scm
@@ -718,7 +718,7 @@ refactor Vim in order to:
 (define-public vifm
   (package
     (name "vifm")
-    (version "0.9.1")
+    (version "0.10")
     (source
       (origin
         (method url-fetch)
@@ -729,7 +729,7 @@ refactor Vim in order to:
                               "vifm-" version ".tar.bz2")))
         (sha256
          (base32
-          "1cz7vjjmghgdxd1lvsdwv85gvx4kz8idq14qijpwkpfrf2va9f98"))))
+          "1f380xcyjnm4xmcdazs6dj064bwddhywvn3mgm36k7r7b2gnjnp0"))))
     (build-system gnu-build-system)
     (arguments
     '(#:configure-flags '("--disable-build-timestamp")
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 3732f26eba..d56b82ce48 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -6761,14 +6761,14 @@ compressed JSON header blocks.
                     (srfi srfi-26)
                     (ice-9 popen)
                     (ice-9 rdelim))
-
          #:phases
          (modify-phases %standard-phases
-           (add-before 'configure 'autoconf
+           (add-before 'configure 'set-variables
              (lambda _
+               ;; This prevents a few warnings
                (setenv "GUILE_AUTO_COMPILE" "0")
                (setenv "XDG_CACHE_HOME" (getcwd))
-               (invoke "autoreconf" "-vif")))
+               #t))
            (add-after 'install 'wrap-program
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((out      (assoc-ref outputs "out"))
diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm
index d1890c8b32..82f03c7f94 100644
--- a/gnu/packages/webkit.scm
+++ b/gnu/packages/webkit.scm
@@ -4,6 +4,7 @@
 ;;; 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>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -31,6 +32,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages databases)
+  #:use-module (gnu packages docbook)
   #:use-module (gnu packages enchant)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gcc)
@@ -66,11 +68,13 @@
                (base32
                 "147r7an41920zl4x9srdva7fxvw2znjin5ldjkhay1cndv9gih0m"))))
     (build-system cmake-build-system)
+    (outputs '("out" "doc"))
     (arguments
      '(#:tests? #f ; no tests
        #:build-type "Release" ; turn off debugging symbols to save space
        #:configure-flags (list
                           "-DPORT=GTK"
+                          "-DENABLE_GTKDOC=ON" ; No doc by default
                           (string-append ; uses lib64 by default
                            "-DLIB_INSTALL_DIR="
                            (assoc-ref %outputs "out") "/lib")
@@ -87,7 +91,26 @@
                           ;; XXX Disable WOFF2 ‘web fonts’.  These were never
                           ;; supported in our previous builds.  Enabling them
                           ;; requires building libwoff2 and possibly woff2dec.
-                          "-DUSE_WOFF2=OFF")))
+                          "-DUSE_WOFF2=OFF")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-gtk-doc-scan
+           (lambda* (#:key inputs #:allow-other-keys)
+             (for-each (lambda (file)
+                         (substitute* file
+                           (("http://www.oasis-open.org/docbook/xml/4.1.2/docbookx.dtd")
+                            (string-append (assoc-ref inputs "docbook-xml")
+                                           "/xml/dtd/docbook/docbookx.dtd"))))
+                       (find-files "Source" "\\.sgml$"))
+             #t))
+         (add-after 'install 'move-doc-files
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (doc (assoc-ref outputs "doc")))
+               (mkdir-p (string-append doc "/share"))
+               (rename-file (string-append out "/share/gtk-doc")
+                            (string-append doc "/share/gtk-doc"))
+               #t))))))
     (native-inputs
      `(("bison" ,bison)
        ("gettext" ,gettext-minimal)
@@ -97,6 +120,8 @@
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("python" ,python-2) ; incompatible with Python 3 (print syntax)
+       ("gtk-doc" ,gtk-doc) ; For documentation generation
+       ("docbook-xml" ,docbook-xml) ; For documentation generation
        ("ruby" ,ruby)))
     (propagated-inputs
      `(("gtk+" ,gtk+)
@@ -155,12 +180,13 @@ HTML/CSS applications to full-fledged web browsers.")
      `(("gcc" ,gcc-7)  ; webkitgtk-2.22 requires gcc-6 or newer
        ,@(package-native-inputs webkitgtk)))
     (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (add-before 'configure 'work-around-gcc-7-include-path-issue
-                    ;; FIXME: Work around a problem with gcc-7 includes (see
-                    ;; <https://bugs.gnu.org/30756>).
-                    (lambda _
-                      (unsetenv "C_INCLUDE_PATH")
-                      (unsetenv "CPLUS_INCLUDE_PATH")
-                      #t)))
-       ,@(package-arguments webkitgtk)))))
+     (substitute-keyword-arguments (package-arguments webkitgtk)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-before 'configure 'work-around-gcc-7-include-path-issue
+             ;; FIXME: Work around a problem with gcc-7 includes (see
+             ;; <https://bugs.gnu.org/30756>).
+             (lambda _
+               (unsetenv "C_INCLUDE_PATH")
+               (unsetenv "CPLUS_INCLUDE_PATH")
+               #t))))))))
diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index 60b2a81de8..85c71b5abb 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -225,7 +225,7 @@ integrate Windows applications into your desktop.")
 (define-public wine-staging-patchset-data
   (package
    (name "wine-staging-patchset-data")
-   (version "3.19")
+   (version "3.20")
    (source
     (origin
       (method git-fetch)
@@ -235,7 +235,7 @@ integrate Windows applications into your desktop.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-        "0nmlhc6jamz0zb4b1w165l8j1a1b0j5ad1sv06aasc9jy8s12b22"))))
+        "049cwllf4aybrhj4l2i3vd5jvagjz4d448404zkyy0lfxr08id3p"))))
    (build-system trivial-build-system)
    (native-inputs
     `(("bash" ,bash)
@@ -281,7 +281,7 @@ integrate Windows applications into your desktop.")
               (file-name (string-append name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0slwgbxclx2dx0glj8az3mv0bqxmx119v9s0jvg1b5zhmqkcc8gg"))))
+                "063garmflbna3mhph8k0dv0bkzq8x75x5xrd0j8y0mjh10i13mik"))))
     (inputs `(("autoconf" ,autoconf) ; for autoreconf
               ("gtk+" ,gtk+)
               ("libva" ,libva)
diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index 79e3b47684..f2338783d2 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -10,7 +10,7 @@
 ;;; Copyright © 2015 xd1le <elisp.vim@gmail.com>
 ;;; Copyright © 2015 Florian Paul Schmidt <mista.tapas@gmx.net>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
-;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Alex Kost <alezost@gmail.com>
@@ -1338,15 +1338,11 @@ invert colors on a specific display/screen.")
     (build-system gnu-build-system)
     (arguments '(#:configure-flags `("--enable-sound"
                                      "--enable-wave"
-                                     "--enable-alsa")
-                 #:phases (modify-phases %standard-phases
-                           (add-before 'configure 'autoreconf
-                             (lambda _
-                               (invoke "autoreconf" "-vfi"))))))
-   (native-inputs `(("autoconf" ,autoconf)
-                    ("automake" ,automake)
-                    ("pkg-config" ,pkg-config)
-                    ("perl" ,perl)))
+                                     "--enable-alsa")))
+    (native-inputs `(("autoconf" ,autoconf)
+                     ("automake" ,automake)
+                     ("pkg-config" ,pkg-config)
+                     ("perl" ,perl)))
     (inputs `(("libx11" ,libx11)
               ("alsa-lib" ,alsa-lib)))
     (synopsis "Daemon that performs an action every time the X11 bell is rung")
diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index d3e68c4c07..5adb04a86a 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -3174,14 +3174,14 @@ This driver is intended for the spice qxl virtio device.")
 (define-public xf86-video-r128
   (package
     (name "xf86-video-r128")
-    (version "6.11.0")
+    (version "6.12.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://xorg/individual/driver/"
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "0snvwmrh8dqyyaq7ggicym6yrsg4brygkx9156r0m095m7fp3rav"))))
+                "0mz0v5mqmmbncr2drd5zvia1fb7frz2xqwflhhqbnaxx5j48c740"))))
     (build-system gnu-build-system)
     (inputs `(("mesa" ,mesa)
               ("xorgproto" ,xorgproto)
diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index 3409bd352c..228d3c5926 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -1252,18 +1252,57 @@ the tty to run, among other things."
                                 (string-concatenate
                                  (map cache->config caches)))))))
 
+(define (nscd-action-procedure nscd config option)
+  ;; XXX: This is duplicated from mcron; factorize.
+  #~(lambda (_ . args)
+      ;; Run 'nscd' in a pipe so we can explicitly redirect its output to
+      ;; 'current-output-port', which at this stage is bound to the client
+      ;; connection.
+      (let ((pipe (apply open-pipe* OPEN_READ #$nscd
+                         "-f" #$config #$option args)))
+        (let loop ()
+          (match (read-line pipe 'concat)
+            ((? eof-object?)
+             (catch 'system-error
+               (lambda ()
+                 (zero? (close-pipe pipe)))
+               (lambda args
+                 ;; There's a race with the SIGCHLD handler, which could
+                 ;; call 'waitpid' before 'close-pipe' above does.  If we
+                 ;; get ECHILD, that means we lost the race, but that's
+                 ;; fine.
+                 (or (= ECHILD (system-error-errno args))
+                     (apply throw args)))))
+            (line
+             (display line)
+             (loop)))))))
+
+(define (nscd-actions nscd config)
+  "Return Shepherd actions for NSCD."
+  ;; Make this functionality available as actions because that's a simple way
+  ;; to run the right 'nscd' binary with the right config file.
+  (list (shepherd-action
+         (name 'statistics)
+         (documentation "Display statistics about nscd usage.")
+         (procedure (nscd-action-procedure nscd config "--statistics")))
+        (shepherd-action
+         (name 'invalidate)
+         (documentation
+          "Invalidate the given cache--e.g., 'hosts' for host name lookups.")
+         (procedure (nscd-action-procedure nscd config "--invalidate")))))
+
 (define (nscd-shepherd-service config)
   "Return a shepherd service for CONFIG, an <nscd-configuration> object."
-  (let ((nscd.conf     (nscd.conf-file config))
+  (let ((nscd          (file-append (nscd-configuration-glibc config)
+                                    "/sbin/nscd"))
+        (nscd.conf     (nscd.conf-file config))
         (name-services (nscd-configuration-name-services config)))
     (list (shepherd-service
            (documentation "Run libc's name service cache daemon (nscd).")
            (provision '(nscd))
            (requirement '(user-processes))
            (start #~(make-forkexec-constructor
-                     (list #$(file-append (nscd-configuration-glibc config)
-                                          "/sbin/nscd")
-                           "-f" #$nscd.conf "--foreground")
+                     (list #$nscd "-f" #$nscd.conf "--foreground")
 
                      ;; Wait for the PID file.  However, the PID file is
                      ;; written before nscd is actually listening on its
@@ -1277,7 +1316,12 @@ the tty to run, among other things."
                                                   (string-append dir "/lib"))
                                                 (list #$@name-services))
                                            ":")))))
-           (stop #~(make-kill-destructor))))))
+           (stop #~(make-kill-destructor))
+           (modules `((ice-9 popen)               ;for the actions
+                      (ice-9 rdelim)
+                      (ice-9 match)
+                      ,@%default-modules))
+           (actions (nscd-actions nscd nscd.conf))))))
 
 (define nscd-activation
   ;; Actions to take before starting nscd.
diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm
index 573efa0433..fcaedd038b 100644
--- a/gnu/services/mail.scm
+++ b/gnu/services/mail.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Andy Wingo <wingo@igalia.com>
-;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
@@ -290,11 +290,21 @@ the section name.")
    "Listeners for the service.  A listener is either an
 @code{unix-listener-configuration}, a @code{fifo-listener-configuration}, or
 an @code{inet-listener-configuration}.")
+  (client-limit
+   (non-negative-integer 0)
+   "Maximum number of simultaneous client connections per process.  Once this
+number of connections is received, the next incoming connection will prompt
+Dovecot to spawn another process.  If set to 0, @code{default-client-limit} is
+used instead.")
   (service-count
    (non-negative-integer 1)
    "Number of connections to handle before starting a new process.
 Typically the only useful values are 0 (unlimited) or 1.  1 is more
 secure, but 0 is faster.  <doc/wiki/LoginProcess.txt>.")
+  (process-limit
+   (non-negative-integer 0)
+   "Maximum number of processes that can exist for this service.  If set to 0,
+@code{default-process-limit} is used instead.")
   (process-min-avail
    (non-negative-integer 0)
    "Number of processes to always keep waiting for more connections.")
@@ -475,6 +485,8 @@ complex, customize the address and port fields of the
     (list
      (service-configuration
       (kind "imap-login")
+      (client-limit 0)
+      (process-limit 0)
       (listeners
        (list
         (inet-listener-configuration (protocol "imap") (port 143) (ssl? #f))
@@ -487,24 +499,33 @@ complex, customize the address and port fields of the
         (inet-listener-configuration (protocol "pop3s") (port 995) (ssl? #t)))))
      (service-configuration
       (kind "lmtp")
+      (client-limit 1)
+      (process-limit 0)
       (listeners
        (list (unix-listener-configuration (path "lmtp") (mode "0666")))))
-     (service-configuration (kind "imap"))
-     (service-configuration (kind "pop3"))
-     (service-configuration (kind "auth")
-      ;; In what could be taken to be a bug, the default value of 1 for
-      ;; service-count makes it so that a PAM auth worker can't fork off
-      ;; subprocesses for making blocking queries.  The result is that nobody
-      ;; can log in -- very secure, but not very useful!  If we simply omit
-      ;; the service-count, it will default to the value of
-      ;; auth-worker-max-count, which is 30, instead of defaulting to 1, which
-      ;; is the default for all other services.  As a hack, bump this value to
-      ;; 30.
-      (service-count 30)
+     (service-configuration
+      (kind "imap")
+      (client-limit 1)
+      (process-limit 1024))
+     (service-configuration
+      (kind "pop3")
+      (client-limit 1)
+      (process-limit 1024))
+     (service-configuration
+      (kind "auth")
+      (service-count 0)
+      (client-limit 0)
+      (process-limit 1)
       (listeners
        (list (unix-listener-configuration (path "auth-userdb")))))
-     (service-configuration (kind "auth-worker"))
-     (service-configuration (kind "dict")
+     (service-configuration
+      (kind "auth-worker")
+      (client-limit 1)
+      (process-limit 0))
+     (service-configuration
+      (kind "dict")
+      (client-limit 1)
+      (process-limit 0)
       (listeners (list (unix-listener-configuration (path "dict")))))))
    "List of services to enable.  Available services include @samp{imap},
 @samp{imap-login}, @samp{pop3}, @samp{pop3-login}, @samp{auth}, and
diff --git a/gnu/services/mcron.scm b/gnu/services/mcron.scm
index 5757bf8cf6..120b663e3e 100644
--- a/gnu/services/mcron.scm
+++ b/gnu/services/mcron.scm
@@ -86,7 +86,7 @@ files."
                  (lambda ()
                    (zero? (close-pipe pipe)))
                  (lambda args
-                   ;; There's with race between the SIGCHLD handler, which
+                   ;; There's a race with the SIGCHLD handler, which
                    ;; could call 'waitpid' before 'close-pipe' above does.  If
                    ;; we get ECHILD, that means we lost the race, but that's
                    ;; fine.
diff --git a/gnu/tests/base.scm b/gnu/tests/base.scm
index 896d4a8f88..02882f4b46 100644
--- a/gnu/tests/base.scm
+++ b/gnu/tests/base.scm
@@ -335,6 +335,20 @@ info --version")
               (x
                (pk 'failure x #f))))
 
+          (test-equal "nscd invalidate action"
+            '(#t)                                 ;one value, #t
+            (marionette-eval '(with-shepherd-action 'nscd ('invalidate "hosts")
+                                                    result
+                                                    result)
+                             marionette))
+
+          (test-equal "nscd invalidate action, wrong table"
+            '(#f)                                 ;one value, #f
+            (marionette-eval '(with-shepherd-action 'nscd ('invalidate "xyz")
+                                                    result
+                                                    result)
+                             marionette))
+
           (test-equal "host not found"
             #f
             (marionette-eval
author	Marius Bakke <mbakke@fastmail.com>	2018-11-14 21:20:46 +0100
committer	Marius Bakke <mbakke@fastmail.com>	2018-11-14 21:20:46 +0100
commit	79ee97a144aaaa890be0724aaf796e2a771179d7 (patch)
tree	fddd2f20003d60e42eed7a614acea91a13d854d7 /gnu
parent	7d9d521fbcf1423f66d6f33208c03d5dacb7ba50 (diff)
parent	e921993c25626541385f191f0463cad8e5e5c5c7 (diff)
download	guix-79ee97a144aaaa890be0724aaf796e2a771179d7.tar.gz