Merge remote-tracking branch 'origin/master' into core-updates

36 files changed, 1511 insertions, 177 deletions

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 3d9226299b..34f6c222ce 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -257,7 +257,10 @@ re-executing them as necessary.")
                "05n65k4ixl85dc6rxc51b1b732gnmm8xnqi424dy9f1nz7ppb3xy"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:configure-flags '("--localstatedir=/var")))
+     '(#:configure-flags '("--localstatedir=/var")
+       ;; On some systems, 'libls.sh' may fail with an error such as:
+       ;; "Failed to tell switch -a apart from -A".
+       #:parallel-tests? #f))
     (inputs `(("ncurses" ,ncurses)
               ("readline" ,readline)))        ;for 'ftp'
     (native-inputs `(("netstat" ,net-tools))) ;for tests
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 923b0ba9ed..9e20b9f033 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2015, 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
+;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -622,3 +623,35 @@ NTFS volumes using @code{ntfs-3g}, preserving NTFS-specific attributes.")
     (license (list license:gpl3+
                    license:lgpl3+
                    license:cc0))))
+
+(define-public obnam
+  (package
+    (name "obnam")
+    (version "1.21")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://code.liw.fi/debian/pool/main/o/obnam/obnam_"
+             version ".orig.tar.xz"))
+       (sha256
+        (base32
+         "0qlipsq50hca71zc0dp1mg9zs12qm0sbblw7qfzl0hj6mk2rv1by"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2))
+    (inputs
+     `(("python2-cliapp" ,python2-cliapp)
+       ("python2-larch" ,python2-larch)
+       ("python2-paramiko" ,python2-paramiko)
+       ("python2-pyaml" ,python2-pyaml)
+       ("python2-tracing" ,python2-tracing)
+       ("python2-ttystatus" ,python2-ttystatus)))
+    (home-page "https://obnam.org/")
+    (synopsis "Easy and secure backup program")
+    (description "Obnam is an easy, secure backup program.  Features
+include snapshot backups, data de-duplication and encrypted backups
+using GnuPG.  Backups can be stored on local hard disks, or online via
+the SSH SFTP protocol.  The backup server, if used, does not require
+any special software, on top of SSH.")
+    (license license:gpl3+)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7bf39c6b03..770bea7e32 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -63,6 +63,7 @@
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages java)
+  #:use-module (gnu packages ldc)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages logging)
   #:use-module (gnu packages machine-learning)
@@ -95,6 +96,28 @@
   #:use-module (gnu packages zip)
   #:use-module (srfi srfi-1))
 
+(define-public r-ape
+  (package
+    (name "r-ape")
+    (version "4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ape" version))
+       (sha256
+        (base32
+         "0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk"))))
+    (build-system r-build-system)
+    (home-page "http://ape-package.ird.fr/")
+    (synopsis "Analyses of phylogenetics and evolution")
+    (description
+     "This package provides functions for reading, writing, plotting, and
+manipulating phylogenetic trees, analyses of comparative data in a
+phylogenetic framework, ancestral character analyses, analyses of
+diversification and macroevolution, computing distances from DNA sequences,
+and several other tools.")
+    (license license:gpl2+)))
+
 (define-public aragorn
   (package
     (name "aragorn")
@@ -2838,15 +2861,17 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
   (package
     (name "hmmer")
     (version "3.1b2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "http://eddylab.org/software/hmmer"
-                    (version-prefix version 1) "/"
-                    version "/hmmer-" version ".tar.gz"))
-              (sha256
-               (base32
-                "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://eddylab.org/software/hmmer"
+             (version-prefix version 1) "/"
+             version "/hmmer-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))
+       (patches (search-patches "hmmer-remove-cpu-specificity.patch"))))
     (build-system gnu-build-system)
     (native-inputs `(("perl" ,perl)))
     (home-page "http://hmmer.org/")
@@ -5741,7 +5766,7 @@ track.  The database is exposed as a @code{TxDb} object.")
 (define-public vsearch
   (package
     (name "vsearch")
-    (version "2.4.0")
+    (version "2.4.2")
     (source
      (origin
        (method url-fetch)
@@ -5751,7 +5776,7 @@ track.  The database is exposed as a @code{TxDb} object.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "007q9a50hdw4vs2iajabvbw7qccml4r8cbqzyi5ipkkf42jk3vnr"))
+         "15zy2d9xvgbgdjlxvrhj8s5ga42p13k7a3xv015ingn0bi1p3n6w"))
        (patches (search-patches "vsearch-unbundle-cityhash.patch"))
        (snippet
         '(begin
@@ -8574,3 +8599,99 @@ identifications while not exceeding a specified false discovery rate.  It also
 contains a number of utilities to explore the MS/MS results and assess missed
 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
     (license license:artistic2.0)))
+
+(define htslib-for-sambamba
+  (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
+    (package
+      (inherit htslib)
+      (name "htslib-for-sambamba")
+      (version (string-append "1.3.1-1." (string-take commit 9)))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/lomereiter/htslib.git")
+               (commit commit)))
+         (file-name (string-append "htslib-" version "-checkout"))
+         (sha256
+          (base32
+           "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
+      (arguments
+       (substitute-keyword-arguments (package-arguments htslib)
+         ((#:phases phases)
+          `(modify-phases  ,phases
+             (add-before 'configure 'bootstrap
+               (lambda _
+                 (zero? (system* "autoreconf" "-vif"))))))))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ,@(package-native-inputs htslib))))))
+
+(define-public sambamba
+  (package
+    (name "sambamba")
+    (version "0.6.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/lomereiter/sambamba/"
+                           "archive/v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there is no test target
+       #:make-flags
+       '("D_COMPILER=ldc2"
+         ;; Override "--compiler" flag only.
+         "D_FLAGS=--compiler=ldc2 -IBioD -g -d"
+         "sambamba-ldmd2-64")
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-after 'unpack 'place-biod
+           (lambda* (#:key inputs #:allow-other-keys)
+             (copy-recursively (assoc-ref inputs "biod") "BioD")
+             #t))
+         (add-after 'unpack 'unbundle-prerequisites
+           (lambda _
+             (substitute* "Makefile"
+               ((" htslib-static lz4-static") ""))
+             #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out   (assoc-ref outputs "out"))
+                    (bin   (string-append out "/bin")))
+               (mkdir-p bin)
+               (install-file "build/sambamba" bin)
+               #t))))))
+    (native-inputs
+     `(("ldc" ,ldc)
+       ("rdmd" ,rdmd)
+       ("biod"
+        ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))
+           (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/biod/BioD.git")
+                   (commit commit)))
+             (file-name (string-append "biod-"
+                                       (string-take commit 9)
+                                       "-checkout"))
+             (sha256
+              (base32
+               "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))))
+    (inputs
+     `(("lz4" ,lz4)
+       ("htslib" ,htslib-for-sambamba)))
+    (home-page "http://lomereiter.github.io/sambamba")
+    (synopsis "Tools for working with SAM/BAM data")
+    (description "Sambamba is a high performance modern robust and
+fast tool (and library), written in the D programming language, for
+working with SAM and BAM files.  Current parallelised functionality is
+an important subset of samtools functionality, including view, index,
+sort, markdup, and depth.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/certs.scm b/gnu/packages/certs.scm
index 246e5ca14a..7f5c5b793f 100644
--- a/gnu/packages/certs.scm
+++ b/gnu/packages/certs.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -73,7 +74,7 @@
 (define-public nss-certs
   (package
     (name "nss-certs")
-    (version "3.29.2")
+    (version "3.29.3")
     (source (origin
               (method url-fetch)
               (uri (let ((version-with-underscores
@@ -84,7 +85,7 @@
                       "nss-" version ".tar.gz")))
               (sha256
                (base32
-                "149807rmzb76hnh48rw4m9jw83iw0168njzchz0hmbsgc8mk0i5w"))))
+                "1sz1r2iml9bhd4iqiqz75gii855a25895vpy9scjky0y4lqwrp9m"))))
     (build-system gnu-build-system)
     (outputs '("out"))
     (native-inputs
@@ -139,3 +140,60 @@
 taken from the NSS package and thus ultimately from the Mozilla project.")
     (home-page "https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS")
     (license license:mpl2.0)))
+
+(define-public le-certs
+  (package
+    (name "le-certs")
+    (version "0")
+    (source #f)
+    (build-system trivial-build-system)
+    (arguments
+     '(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((root (assoc-ref %build-inputs "isrgrootx1.pem"))
+               (intermediate (assoc-ref %build-inputs "letsencryptauthorityx3.pem"))
+               (backup (assoc-ref %build-inputs "letsencryptauthorityx4.pem"))
+               (out (string-append (assoc-ref %outputs "out") "/etc/ssl/certs")))
+           (mkdir-p out)
+           (for-each
+             (lambda (cert)
+               (copy-file cert (string-append out "/"
+                                              (strip-store-file-name cert))))
+             (list root intermediate backup))))))
+    (inputs
+     `(; The Let's Encrypt root certificate, "ISRG Root X1".
+       ("isrgrootx1.pem"
+        ,(origin
+           (method url-fetch)
+           (uri "https://letsencrypt.org/certs/isrgrootx1.pem")
+           (sha256
+            (base32
+             "0zhd1ps7sz4w1x52xk3v7ng6d0rcyi7y7rcrplwkmilnq5hzjv1y"))))
+       ;; "Let’s Encrypt Authority X3", the active Let's Encrypt intermediate
+       ;; certificate.
+       ("letsencryptauthorityx3.pem"
+        ,(origin
+           (method url-fetch)
+           (uri "https://letsencrypt.org/certs/letsencryptauthorityx3.pem")
+           (sha256
+            (base32
+             "0zbamj6c7zqw1j9mbqygc8k1ykgj6xiisp9svmlif5lkbnyjhnkk"))))
+       ;; "Let’s Encrypt Authority X4", the backup Let's Encrypt intermediate
+       ;; certificate.  This will be used for disaster recovery and will only be
+       ;; used should Let's Encrypt lose the ability to issue with "Let’s
+       ;; Encrypt Authority X3".
+       ("letsencryptauthorityx4.pem"
+        ,(origin
+           (method url-fetch)
+           (uri "https://letsencrypt.org/certs/letsencryptauthorityx4.pem")
+           (sha256
+            (base32
+             "003dc94c8qwj634h0dq743x7hqv9rdcfaisdksprkmi2jd107xq4"))))))
+    (home-page "https://letsencrypt.org/certificates/")
+    (synopsis "Let's Encrypt root and intermediate certificates")
+    (description "This package provides a certificate store containing only the
+Let's Encrypt root and intermediate certificates.  It is intended to be used
+within Guix.")
+    (license license:public-domain)))
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index c25bc389c0..ae91464a18 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -187,8 +187,8 @@ their dependencies.")
       (license l:gpl3+))))
 
 (define-public cuirass
-  (let ((commit "f695c79eb3b93a0432901844c8ede16de39b8d07")
-        (revision "4"))
+  (let ((commit "8c811abb3174b44601b8996a1fe1718f37d7bd14")
+        (revision "5"))
     (package
       (name "cuirass")
       (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -200,7 +200,7 @@ their dependencies.")
                 (file-name (string-append name "-" version))
                 (sha256
                  (base32
-                  "1zsj3l85d8jq7h9a0zfb2w5pyvlwkirgvis4bv60syhbpblfvmri"))))
+                  "0kz2ys01xlmxagsfr9qf3p212vm31wfl76rvxa7ii5804aidlz5n"))))
       (build-system gnu-build-system)
       (arguments
        '(#:phases
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 4e6a248e8e..dbc4795d02 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -97,6 +97,33 @@ independent of the input data and can be reduced, if necessary, at some cost
 in compression.")
     (license license:zlib)))
 
+(define-public minizip
+  (package
+    (name "minizip")
+    (version (package-version zlib))
+    (source (package-source zlib))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'enter-source
+           (lambda _ (chdir "contrib/minizip") #t))
+         (add-before 'configure 'autoreconf
+           (lambda _
+             (zero? (system* "autoreconf" "-vif")))))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (propagated-inputs `(("zlib" ,zlib)))
+    (home-page (package-home-page zlib))
+    (synopsis "Zip Compression library")
+    (description
+     "Minizip is a minimalistic library that supports compressing,
+extracting and viewing ZIP archives.  This version is extracted from
+the @code{zlib} source.")
+    (license (package-license zlib))))
+
 (define-public fastjar
   (package
    (name "fastjar")
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 1daf8e4e68..3db5527e60 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -16,7 +16,7 @@
 ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2016, 2017 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2016 Alex Vong <alexvong1995@gmail.com>
-;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2016, 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
@@ -366,7 +366,7 @@ when typing parentheses directly or commenting out code line by line.")
 (define-public git-modes
   (package
     (name "git-modes")
-    (version "1.2.2")
+    (version "1.2.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -375,7 +375,7 @@ when typing parentheses directly or commenting out code line by line.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0gb9c18jib8rpm14vig9774104lwmd8353ps0259m861syf6664d"))))
+                "0xxrmf0jnyljxvllc22qa0v8lgi4k1ldnayjm5hf68m25jsr378l"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((guix build gnu-build-system)
@@ -436,7 +436,7 @@ on stdout instead of using a socket as the Emacsclient does.")
 (define-public magit
   (package
     (name "magit")
-    (version "2.10.2")
+    (version "2.10.3")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -444,7 +444,7 @@ on stdout instead of using a socket as the Emacsclient does.")
                    version "/" name "-" version ".tar.gz"))
              (sha256
               (base32
-               "09qcc3a61irxi89x7q82hdy8dk0liiwyz66632wzcd881mhrhx18"))))
+               "03ln65ss420gc3h4pi56dayd1p163xfxrxrd9fkb9xnkl8mjglqk"))))
     (build-system gnu-build-system)
     (native-inputs `(("texinfo" ,texinfo)
                      ("emacs" ,emacs-minimal)))
@@ -3852,3 +3852,32 @@ mode-line.")
      "YASnippet is a template system for Emacs.  It allows you to type an
 abbreviation and automatically expand it into function templates.")
     (license license:gpl3+)))
+
+(define-public emacs-memoize
+  (package
+   (name "emacs-memoize")
+   (version "20130421.b55eab0")
+   (source
+    (origin
+     (method git-fetch)
+     (uri (git-reference
+           (url "https://github.com/skeeto/emacs-memoize")
+           (commit "b55eab0cb6ab05d941e07b8c01f1655c0cf1dd75")))
+     (file-name (string-append name "-" version ".tar.gz"))
+     (sha256
+      (base32
+       "0fjwlrdm270qcrqffvarw5yhijk656q4lam79ybhaznzj0dq3xpw"))))
+   (build-system emacs-build-system)
+   (arguments
+    `(#:phases
+      (modify-phases %standard-phases
+        (add-before 'install 'check
+                    (lambda _
+                      (zero? (system* "emacs" "-batch" "-l" "memoize.el"
+                                      "-l" "memoize-test.el"
+                                      "-f" "ert-run-tests-batch-and-exit")))))))
+   (home-page "https://github.com/skeeto/emacs-memoize")
+   (synopsis "Emacs lisp memoization library")
+   (description "@code{emacs-memoize} is an Emacs library for
+memoizing functions.")
+   (license license:unlicense)))
diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index ce07accbf2..1f01ad6ad0 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -1035,6 +1035,70 @@ designed to work well in user interface environments.")
 vector graphics.")
    (license license:silofl1.1)))
 
+(define-public font-tamzen
+  (package
+    (name "font-tamzen")
+    (version "1.11.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/sunaku/tamzen-font/archive/"
+                           "Tamzen-" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1ryd7gp6qiwaqw73jqbmh4kwlriyd8xykh4j7z90z8xp9fm7lrys"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+
+         (let ((tar      (string-append (assoc-ref %build-inputs "tar")
+                                        "/bin/tar"))
+               (PATH     (string-append (assoc-ref %build-inputs "gzip")
+                                        "/bin"))
+               (font-dir (string-append %output "/share/fonts/misc"))
+               (psf-dir (string-append %output "/share/kbd/consolefonts"))
+               (src-pcf-dir (string-append "tamzen-font-Tamzen-"
+                                            ,version "/pcf")))
+           (setenv "PATH" PATH)
+           (system* tar "xvf" (assoc-ref %build-inputs "source"))
+           (mkdir-p font-dir)
+           (mkdir-p psf-dir)
+           (chdir src-pcf-dir)
+           (for-each (lambda (pcf)
+                       (install-file pcf font-dir))
+                     (find-files "." "\\.pcf$"))
+           (chdir "../psf")
+           (for-each (lambda (psf)
+                       (install-file psf psf-dir))
+                     (find-files "." "\\.psf$"))
+           #t))))
+    (native-inputs
+     `(("tar" ,tar)
+       ("gzip" ,gzip)))
+    (home-page "https://github.com/sunaku/tamzen-font")
+    (synopsis "Monospaced bitmap font for console and X11")
+    (description
+     "Tamzen is a fork of the @code{Tamsyn} font.  It is programatically forked
+from @code{Tamsyn} version 1.11, backporting glyphs from older versions while
+deleting deliberately empty glyphs (which are marked as unimplemented) to
+allow secondary/fallback fonts to provide real glyphs at those codepoints.
+
+The @code{TamzenForPowerline} fonts provide additional @code{Powerline} symbols,
+which are programatically injected with @code{bitmap-font-patcher} and
+later hand-tweaked with the gbdfed(1) editor:
+
+@enumerate
+@item all icons are expanded to occupy the maximum available space
+@item the branch of the fork icon ( U+E0A0) was made larger than the trunk
+@item for the newline icon ( U+E0A1), the @emph{N} was made larger at the bottom
+@item the keyhole in the padlock icon ( U+E0A2) was replaced with @emph{//} lines.
+@end enumerate\n")
+    (license (license:non-copyleft "file://LICENSE"))))
+
 (define-public font-comic-neue
   (package
    (name "font-comic-neue")
diff --git a/gnu/packages/fpga.scm b/gnu/packages/fpga.scm
index f65eae8673..0b98e2db0d 100644
--- a/gnu/packages/fpga.scm
+++ b/gnu/packages/fpga.scm
@@ -231,6 +231,11 @@ For synthesis, the compiler generates netlists in the desired format.")
                 (("-I/usr/local/include") "")
                 (("-L/usr/local/lib") ""))
               #t))
+          (add-after 'remove-usr-local 'fix-usr-local
+            (lambda* (#:key outputs #:allow-other-keys)
+              (substitute* "icebox/icebox_vlog.py"
+                (("/usr/local/share") (string-append (assoc-ref outputs "out") "/share")))
+              #t))
           (delete 'configure))))
     (inputs
      `(("libftdi" ,libftdi)))
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 550652eefd..1ce18658d0 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -1349,7 +1349,7 @@ is programmed in Haskell.")
 (define-public manaplus
   (package
     (name "manaplus")
-    (version "1.7.1.21")
+    (version "1.7.3.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1357,7 +1357,7 @@ is programmed in Haskell.")
                     version "/manaplus-" version ".tar.xz"))
               (sha256
                (base32
-                "0q9hk9jgz5jja1mmba5iafxwavk6991kjpmdxdkgbam0hk15pqmz"))))
+                "0mbxzsgjg16pqa3jnxkd7wwvw1lrx455r7fvwjfhzp0yv7acrn10"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags
@@ -2880,8 +2880,8 @@ the GNU GPL.")
     (version "2.01.2")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://sourceforge.net/projects/tintin"
-                                  "/files/TinTin++ Source Code/" version
+              (uri (string-append "mirror://sourceforge/tintin"
+                                  "/TinTin++ Source Code/" version
                                   "/tintin" "-" version ".tar.gz"))
               (sha256
                (base32
diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index 1b59cf7ecf..532dbf88f7 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -519,7 +519,7 @@ and signature functionality from Python programs.")
 (define-public pius
   (package
    (name "pius")
-   (version "2.2.3")
+   (version "2.2.4")
    (source (origin
             (method url-fetch)
             (uri (string-append
@@ -527,7 +527,7 @@ and signature functionality from Python programs.")
                   version "/pius-" version ".tar.bz2"))
             (sha256
              (base32
-              "0iy0gnms6lv9hpvk29313kc495a2f7pq2mg6ljxhy233vxsmjsk6"))))
+              "0lgc0ipwdfqbq16zax8kn17wbv8xyw4ygc09fawl2yp459z0ql4n"))))
    (build-system python-build-system)
    (inputs `(("perl" ,perl)                ;for 'pius-party-worksheet'
              ("gpg" ,gnupg)))
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index e6e24f6650..55dfda4948 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -186,7 +186,7 @@ in the Mozilla clients.")
 (define-public nss
   (package
     (name "nss")
-    (version "3.29.2")
+    (version "3.29.3")
     (source (origin
               (method url-fetch)
               (uri (let ((version-with-underscores
@@ -197,7 +197,7 @@ in the Mozilla clients.")
                       "nss-" version ".tar.gz")))
               (sha256
                (base32
-                "149807rmzb76hnh48rw4m9jw83iw0168njzchz0hmbsgc8mk0i5w"))
+                "1sz1r2iml9bhd4iqiqz75gii855a25895vpy9scjky0y4lqwrp9m"))
               ;; Create nss.pc and nss-config.
               (patches (search-patches "nss-pkgconfig.patch"))))
     (build-system gnu-build-system)
@@ -221,55 +221,52 @@ in the Mozilla clients.")
                   (ice-9 match)
                   (srfi srfi-26))
        #:phases
-       (alist-replace
-        'configure
-        (lambda* (#:key system inputs #:allow-other-keys)
-          (setenv "CC" "gcc")
-          ;; Tells NSS to build for the 64-bit ABI if we are 64-bit system.
-          (when (string-prefix? "x86_64" system)
-            (setenv "USE_64" "1"))
-          #t)
-        (alist-replace
-         'check
-         (lambda _
-           ;; Use 127.0.0.1 instead of $HOST.$DOMSUF as HOSTADDR for testing.
-           ;; The later requires a working DNS or /etc/hosts.
-           (setenv "DOMSUF" "(none)")
-           (setenv "USE_IP" "TRUE")
-           (setenv "IP_ADDRESS" "127.0.0.1")
-           (zero? (system* "./nss/tests/all.sh")))
-         (alist-replace
-          'install
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let* ((out (assoc-ref outputs "out"))
-                   (bin (string-append (assoc-ref outputs "bin") "/bin"))
-                   (inc (string-append out "/include/nss"))
-                   (lib (string-append out "/lib/nss"))
-                   (obj (match (scandir "dist" (cut string-suffix? "OBJ" <>))
-                          ((obj) (string-append "dist/" obj)))))
-              ;; Install nss-config to $out/bin.
-              (install-file (string-append obj "/bin/nss-config")
-                            (string-append out "/bin"))
-              (delete-file (string-append obj "/bin/nss-config"))
-              ;; Install nss.pc to $out/lib/pkgconfig.
-              (install-file (string-append obj "/lib/pkgconfig/nss.pc")
-                            (string-append out "/lib/pkgconfig"))
-              (delete-file (string-append obj "/lib/pkgconfig/nss.pc"))
-              (rmdir (string-append obj "/lib/pkgconfig"))
-              ;; Install other files.
-              (copy-recursively "dist/public/nss" inc)
-              (copy-recursively (string-append obj "/bin") bin)
-              (copy-recursively (string-append obj "/lib") lib)
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key system inputs #:allow-other-keys)
+             (setenv "CC" "gcc")
+             ;; Tells NSS to build for the 64-bit ABI if we are 64-bit system.
+             (when (string-prefix? "x86_64" system)
+               (setenv "USE_64" "1"))
+             #t))
+         (replace 'check
+           (lambda _
+             ;; Use 127.0.0.1 instead of $HOST.$DOMSUF as HOSTADDR for testing.
+             ;; The later requires a working DNS or /etc/hosts.
+             (setenv "DOMSUF" "(none)")
+             (setenv "USE_IP" "TRUE")
+             (setenv "IP_ADDRESS" "127.0.0.1")
+             (zero? (system* "./nss/tests/all.sh"))))
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (bin (string-append (assoc-ref outputs "bin") "/bin"))
+                      (inc (string-append out "/include/nss"))
+                      (lib (string-append out "/lib/nss"))
+                      (obj (match (scandir "dist" (cut string-suffix? "OBJ" <>))
+                             ((obj) (string-append "dist/" obj)))))
+                 ;; Install nss-config to $out/bin.
+                 (install-file (string-append obj "/bin/nss-config")
+                               (string-append out "/bin"))
+                 (delete-file (string-append obj "/bin/nss-config"))
+                 ;; Install nss.pc to $out/lib/pkgconfig.
+                 (install-file (string-append obj "/lib/pkgconfig/nss.pc")
+                               (string-append out "/lib/pkgconfig"))
+                 (delete-file (string-append obj "/lib/pkgconfig/nss.pc"))
+                 (rmdir (string-append obj "/lib/pkgconfig"))
+                 ;; Install other files.
+                 (copy-recursively "dist/public/nss" inc)
+                 (copy-recursively (string-append obj "/bin") bin)
+                 (copy-recursively (string-append obj "/lib") lib)
 
-              ;; FIXME: libgtest1.so is installed in the above step, and it's
-              ;; (unnecessarily) linked with several NSS libraries, but
-              ;; without the needed rpaths, causing the 'validate-runpath'
-              ;; phase to fail.  Here we simply delete libgtest1.so, since it
-              ;; seems to be used only during the tests.
-              (delete-file (string-append lib "/libgtest1.so"))
+                 ;; FIXME: libgtest1.so is installed in the above step, and it's
+                 ;; (unnecessarily) linked with several NSS libraries, but
+                 ;; without the needed rpaths, causing the 'validate-runpath'
+                 ;; phase to fail.  Here we simply delete libgtest1.so, since it
+                 ;; seems to be used only during the tests.
+                 (delete-file (string-append lib "/libgtest1.so"))
 
-              #t))
-          %standard-phases)))))
+                 #t))))))
     (inputs
      `(("sqlite" ,sqlite)
        ("zlib" ,zlib)))
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 8fdd85add9..13ff0e069a 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -220,7 +220,7 @@ without requiring the source code to be rewritten.")
 (define-public guile-next
   (package (inherit guile-2.0)
     (name "guile-next")
-    (version "2.1.7")
+    (version "2.1.8")
     (replacement #f)
     (source (origin
               (method url-fetch)
@@ -228,7 +228,7 @@ without requiring the source code to be rewritten.")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0qf2664bglv5rrj4c99cc7gry7v9x0sqdyzgfg8zi8gm5wbcmqda"))
+                "0rh9vahqqwbyj79p1lc9pljkgxg8rczczf074dr8wl13j5h0y27m"))
               (modules '((guix build utils)))
 
               ;; Remove the pre-built object files.  Instead, build everything
@@ -238,6 +238,7 @@ without requiring the source code to be rewritten.")
                                   (find-files "prebuilt" "\\.go$")))))
     (synopsis "Snapshot of what will become version 2.2 of GNU Guile")
     (properties '((timeout . 72000)               ;20 hours
+                  (max-silent-time . 10800)       ;3 hours (needed on ARM)
                   (upstream-name . "guile")
                   (ftp-server . "alpha.gnu.org")
                   (ftp-directory . "/gnu/guile")))
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d0f659f6e3..2415881e8e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8194,4 +8194,22 @@ or filter messages based on the priority and source.  It also has a syslog
 handler built in.")
     (license license:bsd-3)))
 
+(define-public ghc-unexceptionalio
+  (package
+    (name "ghc-unexceptionalio")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "unexceptionalio-" version "/" "unexceptionalio-"
+                           version ".tar.gz"))
+       (sha256 (base32 "1f7h7zwky4scdcyjspg4ksfh7x6yra0wjybxq70p7vcwpgk2nzlj"))))
+    (build-system haskell-build-system)
+    (home-page "https://github.com/singpolyma/unexceptionalio")
+    (synopsis "IO without any non-error, synchronous exceptions")
+    (description "When you've caught all the exceptions that can be
+handled safely, this is what you're left with.")
+    (license license:isc)))
+
 ;;; haskell.scm ends here
diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index d441485296..6c5537579e 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -42,7 +42,7 @@
 (define-public ibus
   (package
    (name "ibus")
-   (version "1.5.14")
+   (version "1.5.15")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/ibus/ibus/"
@@ -50,7 +50,7 @@
                                  version "/ibus-" version ".tar.gz"))
              (sha256
               (base32
-               "0g4x02d7j5w1lfn4zvmzsq93h17lajgn9d7hlvr6pws28vz40ax4"))))
+               "11g3jf6dgvmszvpgpva0y587kr0sffl79xmymvghrb1sdynvmxs1"))))
    (build-system glib-or-gtk-build-system)
    (arguments
     `(#:tests? #f  ; tests fail because there's no connection to dbus
@@ -237,7 +237,7 @@ Chinese pinyin input methods.")
 (define-public ibus-anthy
   (package
     (name "ibus-anthy")
-    (version "1.5.8")
+    (version "1.5.9")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -245,7 +245,7 @@ Chinese pinyin input methods.")
                     version "/ibus-anthy-" version ".tar.gz"))
               (sha256
                (base32
-                "1aj7vnfky7izl23xyjky78z3qas3q72l3kr8dnql2lnivsrb8q1y"))))
+                "1y8sf837rmp662bv6zakny0xcm7c9c5qda7f9kq9riv9ywpcbw6x"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags
diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm
index 74483965dd..73496ccfc0 100644
--- a/gnu/packages/imagemagick.scm
+++ b/gnu/packages/imagemagick.scm
@@ -46,14 +46,14 @@
     ;; 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 "6.9.7-9")
+    (version "6.9.7-10")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://imagemagick/ImageMagick-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "1fqvi6h96mfbyw292awiwsqs449sjmw6i9ib53c66nnq1zchw7l3"))))
+               "02gvxz1xap5nm1vrgjxhkx13q6ja06vf23n28nc6cfdpb4s2xyqb"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")
@@ -187,6 +187,8 @@ script.")
          (list "--with-frozenpaths"
                "--enable-shared=yes"
                "--with-x=yes"
+               "--with-quantum-depth=16" ; required by Octave
+               "--enable-quantum-library-names"
                (string-append "--with-gs-font-dir="
                               (assoc-ref %build-inputs "gs-fonts")
                               "/share/fonts/type1/ghostscript"))))
diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm
index 6ba950763b..3d06df9ed8 100644
--- a/gnu/packages/irc.scm
+++ b/gnu/packages/irc.scm
@@ -101,7 +101,7 @@ irssi, but graphical.")
 (define-public irssi
   (package
     (name "irssi")
-    (version "1.0.1")
+    (version "1.0.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/irssi/irssi/"
@@ -109,7 +109,7 @@ irssi, but graphical.")
                                  version ".tar.xz"))
              (sha256
               (base32
-               "1krw71n24mj4p3f5nhzj6kdi1kq9ssl53hrqyjpgz61m7wdcaa4l"))))
+               "1sgvfprgrncbxcyg99rkd10kpjzqw00b1ppsfg8al0zirb13q72w"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 8bb05453da..7b90c1436b 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
+;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -42,6 +43,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
@@ -119,12 +121,58 @@ common build settings used in software produced by the KDE community.")
     (arguments
      `(#:configure-flags
        '("-DCMAKE_CXX_FLAGS=-fPIC"
-         "-DPHONON_BUILD_PHONON4QT5=ON")))
+         "-DPHONON_BUILD_PHONON4QT5=ON"
+         "-DPHONON_INSTALL_QT_EXTENSIONS_INTO_SYSTEM_QT=ON")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'patch-installdir
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((regex (string-append "(INSTALL DESTINATION \")"
+                                         (assoc-ref inputs "qtbase"))))
+               (substitute* "cmake_install.cmake"
+                 ((regex all dest)
+                  (string-append dest (assoc-ref outputs "out")))))
+           #t)))))
     (home-page "https://phonon.kde.org")
     (synopsis "KDE's multimedia library")
     (description "KDE's multimedia library.")
     (license license:lgpl2.1+)))
 
+(define-public phonon-backend-gstreamer
+  (package
+    (name "phonon-backend-gstreamer")
+    (version "4.9.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://kde/stable/phonon/"
+                    name "/" version "/"
+                    name "-" version ".tar.xz"))
+              (sha256
+               (base32
+                "1wc5p1rqglf0n1avp55s50k7fjdzdrhg0gind15k8796w7nfbhyf"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("qtbase" ,qtbase)
+       ("phonon" ,phonon)
+       ("qtbase" ,qtbase)
+       ("qtx11extras" ,qtx11extras)
+       ("gstreamer" ,gstreamer)
+       ("gst-plugins-base" ,gst-plugins-base)
+       ("libxml2" ,libxml2)))
+    (arguments
+     `(#:configure-flags
+       '( "-DPHONON_BUILD_PHONON4QT5=ON")))
+    (home-page "https://phonon.kde.org")
+    (synopsis "Phonon backend which uses GStreamer")
+    (description "Phonon makes use of backend libraries to provide sound.
+Phonon-GStreamer is a backend based on the GStreamer multimedia library.")
+    ;; license: source files mention "either version 2.1 or 3"
+    (license (list license:lgpl2.1 license:lgpl3))))
+
 (define-public gpgmepp
   (package
     (name "gpgmepp")
diff --git a/gnu/packages/ldc.scm b/gnu/packages/ldc.scm
index 614e2d6d0c..fd4d60e8b8 100644
--- a/gnu/packages/ldc.scm
+++ b/gnu/packages/ldc.scm
@@ -276,7 +276,7 @@ latest DMD frontend and uses LLVM as backend.")
 (define-public dub
   (package
     (name "dub")
-    (version "1.2.0")
+    (version "1.2.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/dlang/dub/archive/"
@@ -284,7 +284,7 @@ latest DMD frontend and uses LLVM as backend.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1sd8i1rvxc7y7kk0y6km5zyvaladc5zh56r6afj74ndd63dssv43"))))
+                "02k11x34nck0lbv13ww103niiswnwnslbnswj3b5faszzadbi1v4"))))
    (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; it would have tested itself by installing some packages (vibe etc)
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 53b0f2a678..cd6d32f0fd 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -348,8 +348,8 @@ It has been modified to remove all non-free binary blobs.")
 
 (define %intel-compatible-systems '("x86_64-linux" "i686-linux"))
 
-(define %linux-libre-version "4.10.1")
-(define %linux-libre-hash "0mvwrjny1bjqyjqjxff9m97j48ybfdw8qpdazr5rwk12234v4k3d")
+(define %linux-libre-version "4.10.2")
+(define %linux-libre-hash "01kinnv40lqsk6fyz1k7hkx2diyg4mgp28bwraar5sii1gqmcw7k")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
@@ -358,14 +358,14 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.13"
-                    "16miggwcwfpm7kx0yz256x887rky9wgmp1grg850lf8sdkiz0a1p"
+  (make-linux-libre "4.9.14"
+                    "104715z772if18qi61jbyhvidfh6qnwkiy0m9aa8irxgzs1pk9mn"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.52"
-                    "1fzcq9bbsxiij2fh6kgwrp417sy2j5gnbzs0wwlmznj7mvysl7qg"
+  (make-linux-libre "4.4.53"
+                    "07sfg4i506f3hmd9k4iimnq1w3x0980qxnh649d1sldqxbmhdgjs"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
@@ -2764,7 +2764,7 @@ and copy/paste text in the console and in xterm.")
 (define-public btrfs-progs
   (package
     (name "btrfs-progs")
-    (version "4.9.1")
+    (version "4.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://kernel.org/linux/kernel/"
@@ -2772,7 +2772,7 @@ and copy/paste text in the console and in xterm.")
                                   "btrfs-progs-v" version ".tar.xz"))
               (sha256
                (base32
-                "1ppy2y9vypxw9awchari21yd3s2d7w2a9q3f4jq7dnjy5gyrnjj6"))))
+                "1njw2nrm51380d8arvqfmspa3app9353yd7hiddas3gpkaiwrjs4"))))
     (build-system gnu-build-system)
     (outputs '("out"
                "static"))      ; static versions of binaries in "out" (~16MiB!)
@@ -2839,9 +2839,9 @@ easy administration.")
            (remove-store-references target)
            (chmod target #o555)))))
     (home-page (package-home-page btrfs-progs))
-    (synopsis "Statically-linked btrfs command from btrfsprogs")
-    (description "This package provides statically-linked command of btrfs taken
-from the btrfsprogs package.  It is meant to be used in initrds.")
+    (synopsis "Statically-linked btrfs command from btrfs-progs")
+    (description "This package provides the statically-linked @command{btrfs}
+from the btrfs-progs package.  It is meant to be used in initrds.")
     (license (package-license btrfs-progs))))
 
 (define-public freefall
diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 647c64dcc7..425c273e0d 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -129,7 +129,7 @@ interface to the Tk widget system.")
 (define-public ecl
   (package
     (name "ecl")
-    (version "16.1.2")
+    (version "16.1.3")
     (source
      (origin
        (method url-fetch)
@@ -137,7 +137,7 @@ interface to the Tk widget system.")
              "https://common-lisp.net/project/ecl/static/files/release/"
              name "-" version ".tgz"))
        (sha256
-        (base32 "16ab8qs3awvdxy8xs8jy82v8r04x4wr70l9l2j45vgag18d2nj1d"))
+        (base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn"))
        (modules '((guix build utils)))
        (snippet
         ;; Add ecl-bundle-systems to 'default-system-source-registry'.
@@ -152,9 +152,6 @@ interface to the Tk widget system.")
               ("libffi" ,libffi)))
     (arguments
      '(#:tests? #t
-       #:make-flags `(,(string-append "ECL="
-                                      (assoc-ref %outputs "out")
-                                      "/bin/ecl"))
        #:parallel-tests? #f
        #:phases
        (modify-phases %standard-phases
@@ -182,7 +179,12 @@ interface to the Tk widget system.")
                          `("kernel-headers" ,@libraries)))
                  `("LIBRARY_PATH" suffix ,library-directories)
                  `("LD_LIBRARY_PATH" suffix ,library-directories)))))
-         (add-after 'wrap 'check (assoc-ref %standard-phases 'check)))))
+         (add-after 'wrap 'check (assoc-ref %standard-phases 'check))
+         (add-before 'check 'fix-path-to-ecl
+           (lambda _
+             (substitute* "build/tests/Makefile"
+               (("\\$\\{exec_prefix\\}/") ""))
+             #t)))))
     (native-search-paths
      (list (search-path-specification
             (variable "XDG_DATA_DIRS")
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index b70597b84d..070d9ba093 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -254,7 +254,7 @@ operating systems.")
   (package
     (inherit mutt)
     (name "neomutt")
-    (version "20170225")
+    (version "20170306")
     (source
      (origin
        (method url-fetch)
@@ -263,20 +263,20 @@ operating systems.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "00ll35g9pcanzrxsjp09vrmq6flml249dipcznrq2z4jy2zd386p"))))
+         "0qwcbjm9j1hgzmybw15w53pvfbqcdf47d4sw21s6r2yaj8kx1hag"))))
     (inputs
      `(("cyrus-sasl" ,cyrus-sasl)
        ("gdbm" ,gdbm)
-       ("lmdb" ,lmdb)
-       ("tokyocabinet" ,tokyocabinet)
        ("gpgme" ,gpgme)
        ("ncurses" ,ncurses)
        ("gnutls" ,gnutls)
        ("openssl" ,openssl) ;For smime
        ("perl" ,perl)
+       ("kyotocabinet" ,kyotocabinet)
        ("libxslt" ,libxslt)
        ("libidn" ,libidn)
        ("libxml2" ,libxml2)
+       ("lmdb" ,lmdb)
        ("docbook-xsl" ,docbook-xsl)
        ("notmuch" ,notmuch)))
     (native-inputs
@@ -291,11 +291,12 @@ operating systems.")
              "--enable-gpgme"
 
              ;; database, implies header caching
-             ;; neomutt supports building multiple backends
-             "--with-tokyocabinet"
+             "--without-tokyocabinet"
              "--without-qdbm"
              "--without-bdb"
              "--with-lmdb"
+             (string-append "--with-kyotocabinet="
+                            (assoc-ref %build-inputs "kyotocabinet"))
              "--with-gdbm"
 
              "--with-gnutls"
@@ -410,7 +411,7 @@ and corrections.  It is based on a Bayesian filter.")
 (define-public offlineimap
   (package
     (name "offlineimap")
-    (version "7.0.13")
+    (version "7.0.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/OfflineIMAP/offlineimap/"
@@ -418,7 +419,7 @@ and corrections.  It is based on a Bayesian filter.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1kl72wcxnxb4y5lm2f7ymwjsisnnpwb4w971ajkxlsiwjhzq8i7p"))))
+                "0i5dvygps1ai2qwgamab8kngrp0c5m3bgaw0jk34l8ypsk54wj8r"))))
     (build-system python-build-system)
     (native-inputs
      `(("asciidoc" ,asciidoc)
@@ -662,14 +663,14 @@ invoking @command{notifymuch} from the post-new hook.")
 (define-public notmuch
   (package
     (name "notmuch")
-    (version "0.23.7")
+    (version "0.24")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://notmuchmail.org/releases/notmuch-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "04w90c43zk23pys6prkqb14al408qypifcfj2qznqpwlf46v26zi"))))
+                "1z3m9knsdmchvfjzjhjf2cmdc9yahmvbvzn46wsrsrihfvv4rr7p"))))
     (build-system gnu-build-system)
     (arguments
      '(#:make-flags (list "V=1") ; Verbose test output.
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 9533f5f0a8..d274d50bbc 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -72,6 +72,7 @@
   #:use-module (gnu packages guile)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages gl)
+  #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages m4)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages multiprecision)
@@ -949,7 +950,9 @@ can solve two kinds of problems:
        ("libxft" ,libxft)
        ("mesa" ,mesa)
        ("glu" ,glu)
-       ("zlib" ,zlib)))
+       ("zlib" ,zlib)
+       ("curl" ,curl)
+       ("graphicsmagick" ,graphicsmagick)))
     (native-inputs
      `(("lzip" ,lzip)
        ("gfortran" ,gfortran)
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 0ffc031c85..f2f36ad876 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -265,7 +265,7 @@ supports IPv6, SSL-protected connections as well as PAM for authentication.")
 (define-public pidgin
   (package
     (name "pidgin")
-    (version "2.11.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
@@ -273,7 +273,7 @@ supports IPv6, SSL-protected connections as well as PAM for authentication.")
                            version "/" name "-" version ".tar.bz2"))
        (sha256
         (base32
-         "0crkggjj6y07v1kdwil9vw532b0vrs6p33nmlvdkpnl60m2169pp"))
+         "1y5p2mq3bfw35b66jsafmbva0w5gg1k99y9z8fyp3jfksqv3agcc"))
        (patches (search-patches "pidgin-add-search-path.patch"))))
     (build-system glib-or-gtk-build-system)
     (native-inputs
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index c608f397dc..685636e8ba 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -445,13 +445,13 @@ transactions from C or Python.")
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "77")
+    (version "78")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri name version))
               (sha256
                (base32
-                "0wrb6pl88611frxj19kq3vikhbld40fy1ncrskb1iayxsmbfcbn9"))))
+                "1bx8i6sx2mcvm166nhw0i5442ld6wigkwav8dsnv22y7gnsl9d7n"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/patches/hmmer-remove-cpu-specificity.patch b/gnu/packages/patches/hmmer-remove-cpu-specificity.patch
new file mode 100644
index 0000000000..ba98db4d0e
--- /dev/null
+++ b/gnu/packages/patches/hmmer-remove-cpu-specificity.patch
@@ -0,0 +1,22 @@
+This patch removes compilation flags which make the build for the machine
+where compilation takes place, rendering the build not reproducible.
+
+diff --git a/configure b/configure
+index 8b6aaef..49a6afc 100755
+--- a/configure
++++ b/configure
+@@ -6125,14 +6125,6 @@ fi # guess arch
+ 
+ if test "x$ax_gcc_arch" != x -a "x$ax_gcc_arch" != xno; then
+ for arch in $ax_gcc_arch; do
+-  if test "x$acx_maxopt_portable" = xyes; then # if we require portable code
+-    flags="-mtune=$arch"
+-    # -mcpu=$arch and m$arch generate nonportable code on every arch except
+-    # x86.  And some other arches (e.g. Alpha) don't accept -mtune.  Grrr.
+-    case $host_cpu in i*86|x86_64*) flags="$flags -mcpu=$arch -m$arch";; esac
+-  else
+-    flags="-march=$arch -mcpu=$arch -m$arch"
+-  fi
+   for flag in $flags; do
+     as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$flag" | $as_tr_sh`
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts $flag" >&5
diff --git a/gnu/packages/patches/python-pandas-skip-failing-tests.patch b/gnu/packages/patches/python-pandas-skip-failing-tests.patch
index 31fc912d00..8ac330c18f 100644
--- a/gnu/packages/patches/python-pandas-skip-failing-tests.patch
+++ b/gnu/packages/patches/python-pandas-skip-failing-tests.patch
@@ -2,39 +2,29 @@ These tests fail on 32bit architectures.
 
 Upstream bug URL: https://github.com/pandas-dev/pandas/issues/14866
 
---- a/pandas/tests/test_base.py	2017-03-08 17:49:44.422282717 +0100
-+++ b/pandas/tests/test_base.py	2017-03-08 17:50:59.476701799 +0100
-@@ -363,30 +363,6 @@
-                 self.assertFalse(result.iat[0])
-                 self.assertFalse(result.iat[1])
+--- a/pandas/tests/indexes/common.py	2017-03-09 00:10:26.063996176 +0100
++++ b/pandas/tests/indexes/common.py	2017-03-09 00:10:53.152844191 +0100
+@@ -119,20 +119,6 @@
+         with tm.assertRaisesRegexp(ValueError, 'Invalid fill method'):
+             idx.get_indexer(idx, method='invalid')
  
 -    def test_ndarray_compat_properties(self):
 -
--        for o in self.objs:
+-        idx = self.create_index()
+-        self.assertTrue(idx.T.equals(idx))
+-        self.assertTrue(idx.transpose().equals(idx))
 -
--            # check that we work
--            for p in ['shape', 'dtype', 'flags', 'T', 'strides', 'itemsize',
--                      'nbytes']:
--                self.assertIsNotNone(getattr(o, p, None))
--            self.assertTrue(hasattr(o, 'base'))
+-        values = idx.values
+-        for prop in self._compat_props:
+-            self.assertEqual(getattr(idx, prop), getattr(values, prop))
 -
--            # if we have a datetimelike dtype then needs a view to work
--            # but the user is responsible for that
--            try:
--                self.assertIsNotNone(o.data)
--            except ValueError:
--                pass
+-        # test for validity
+-        idx.nbytes
+-        idx.values.nbytes
 -
--            self.assertRaises(ValueError, o.item)  # len > 1
--            self.assertEqual(o.ndim, 1)
--            self.assertEqual(o.size, len(o))
--
--        self.assertEqual(Index([1]).item(), 1)
--        self.assertEqual(Series([1]).item(), 1)
--
-     def test_ops(self):
-         for op in ['max', 'min']:
-             for o in self.objs:
+     def test_repr_roundtrip(self):
+ 
+         idx = self.create_index()
 --- a/pandas/tools/tests/test_tile.py	2017-03-08 17:47:39.762261841 +0100
 +++ b/pandas/tools/tests/test_tile.py	2017-03-08 17:48:26.831780495 +0100
 @@ -271,19 +271,6 @@
diff --git a/gnu/packages/patches/wget-CVE-2017-6508.patch b/gnu/packages/patches/wget-CVE-2017-6508.patch
new file mode 100644
index 0000000000..0218fceaad
--- /dev/null
+++ b/gnu/packages/patches/wget-CVE-2017-6508.patch
@@ -0,0 +1,45 @@
+Fix CVE-2017-6508:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-6508
+
+Patch copied from upstream source repository:
+
+https://git.savannah.gnu.org/cgit/wget.git/commit/?id=4d729e322fae359a1aefaafec1144764a54e8ad4
+
+From 4d729e322fae359a1aefaafec1144764a54e8ad4 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Tim=20R=C3=BChsen?= <tim.ruehsen@gmx.de>
+Date: Mon, 6 Mar 2017 10:04:22 +0100
+Subject: [PATCH] Fix CRLF injection in Wget host part
+
+* src/url.c (url_parse): Reject control characters in host part of URL
+
+Reported-by: Orange Tsai
+---
+ src/url.c | 11 +++++++++++
+ 1 file changed, 11 insertions(+)
+
+diff --git a/src/url.c b/src/url.c
+index 8f8ff0b8..7d36b27d 100644
+--- a/src/url.c
++++ b/src/url.c
+@@ -925,6 +925,17 @@ url_parse (const char *url, int *error, struct iri *iri, bool percent_encode)
+       url_unescape (u->host);
+       host_modified = true;
+ 
++      /* check for invalid control characters in host name */
++      for (p = u->host; *p; p++)
++        {
++          if (c_iscntrl(*p))
++            {
++              url_free(u);
++              error_code = PE_INVALID_HOST_NAME;
++              goto error;
++            }
++        }
++
+       /* Apply IDNA regardless of iri->utf8_encode status */
+       if (opt.enable_iri && iri)
+         {
+-- 
+2.12.0
+
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 60f0594453..5baf329995 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -30,12 +30,13 @@
 ;;; Copyright © 2016 Stefan Reichoer <stefan@xsteve.at>
 ;;; Copyright © 2016 Dylan Jeffers <sapientech@sapientech@openmailbox.org>
 ;;; Copyright © 2016 Alex Vong <alexvong1995@gmail.com>
-;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2016, 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2016, 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au>
 ;;; Copyright © 2017 Frederick M. Muriithi <fredmanglis@gmail.com>
+;;; Copyright © 2017 humanitiesNerd <catonano@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3433,8 +3434,6 @@ producing implementations of dynamic languages, emphasizing a clean separation
 between language specification and implementation aspects.")
     (license license:expat)))
 
-;; This version of numpy is missing the documentation and is only used to
-;; build matplotlib which is required to build numpy's documentation.
 (define-public python-numpy
   (package
     (name "python-numpy")
@@ -3581,10 +3580,10 @@ association studies (GWAS) on extremely large data sets.")
            (method git-fetch)
            (uri (git-reference
                  (url "https://github.com/scipy/scipy-sphinx-theme.git")
-                 (commit "c466764e22")))
+                 (commit "c466764e2231ba132c09826b5b138fffa1cfcec3")))
            (sha256
             (base32
-                "0q2y87clwlsgc7wvlsn9pzyssybcq10plwhq2w1ydykfsyyqbmkl"))))
+             "0q2y87clwlsgc7wvlsn9pzyssybcq10plwhq2w1ydykfsyyqbmkl"))))
        ,@(package-native-inputs python-numpy)))
     (arguments
      `(#:tests? #f ; we're only generating the documentation
@@ -13479,3 +13478,188 @@ specified to apply on the key before comparison (e.g. @code{string.lower})).")
 Python.  It is based on Parsing Expression Grammars, PEG.  With pyPEG you can
 parse many formal languages.")
     (license license:gpl2)))
+
+(define-public python2-cliapp
+  (package
+    (name "python2-cliapp")
+    (version "1.20160724")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://git.liw.fi/cgi-bin/cgit/cgit.cgi/cliapp/snapshot/cliapp-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "025cyi75vxyghbm4hav8dz4fzwksshddavy9g9fwr440awcvw74f"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2))
+    (propagated-inputs
+     `(("python2-pyaml" ,python2-pyaml)))
+    (home-page "https://liw.fi/cliapp/")
+    (synopsis "Python framework for command line programs")
+    (description "@code{python2-cliapp} is a python framework for
+command line programs.  It contains the typical stuff such programs
+need to do, such as parsing the command line for options, and
+iterating over input files.")
+    (license license:gpl2+)))
+
+(define-public python2-ttystatus
+  (package
+    (name "python2-ttystatus")
+    (version "0.32")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://git.liw.fi/cgi-bin/cgit/cgit.cgi/ttystatus/snapshot/ttystatus-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "0b5g889jj23r2w1hi300cdldx6jvspanp0ybf5n1qvdvl150aamf"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2))
+    (home-page "https://liw.fi/ttystatus/")
+    (synopsis "Python library for showing progress reporting and
+status updates on terminals")
+    (description "@code{python2-ttystatus} is a python library for
+showing progress reporting and status updates on terminals, for
+command line programs.  Output is automatically adapted to the width
+of the terminal: truncated if it does not fit, and resized if the
+terminal size changes.")
+    (license license:gpl3+)))
+
+(define-public python2-tracing
+  (package
+    (name "python2-tracing")
+    (version "0.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://git.liw.fi/cgi-bin/cgit/cgit.cgi/python-tracing/snapshot/tracing-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "06cw4zg42fsvqy372vi2whj26w56vzg5axhzwdjc2bgwf03garbw"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2))
+    (home-page "https://liw.fi/tracing/")
+    (synopsis "Python debug logging helper")
+    (description "@code{python2-tracing} is a python library for
+logging debug messages.  It provides a way to turn debugging messages
+on and off, based on the filename they occur in.  It is much faster
+than using @code{logging.Filter} to accomplish the same thing, which
+matters when code is run in production mode.  The actual logging still
+happens using the @code{logging} library.")
+    (license license:gpl3+)))
+
+(define-public python2-larch
+  (package
+    (name "python2-larch")
+    (version "1.20151025")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://git.liw.fi/cgi-bin/cgit/cgit.cgi/larch/snapshot/larch-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "1p4knkkavlqymgciz2wbcnfrdgdbafhg14maplnk4vbw0q8xs663"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2))
+    (propagated-inputs
+     `(("python2-tracing" ,python2-tracing)))
+    (home-page "https://liw.fi/larch/")
+    (synopsis "Python copy-on-write B-tree library")
+    (description "@code{python2-larch} is an implementation of
+particular kind of B-tree, based on research by Ohad Rodeh.  See
+@url{http://liw.fi/larch/ohad-btrees-shadowing-clones.pdf} for details
+on the data structure.
+
+The distinctive feature of this B-tree is that a node is never
+(conceptually) modified.  Instead, all updates are done by
+copy-on-write.  This makes it easy to clone a tree, and modify only the
+clone, while other processes access the original tree.")
+    (license license:gpl3+)))
+
+(define-public python-htmlmin
+  (package
+    (name "python-htmlmin")
+    (version "0.1.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "htmlmin" version))
+       (sha256
+        (base32
+         "0qxa93j3p1ak32qh8d9kshqv8v3z0hkc13dwbhp5cn7sn3xmsp6a"))))
+    (arguments
+     `(#:tests? #f)) ;htmlmin has no tests
+    (build-system python-build-system)
+    (home-page "https://htmlmin.readthedocs.org/en/latest/")
+    (synopsis "HTML minifier")
+    (description "@code{htmlmin} is an HTML minifier that just works.
+It comes with safe defaults and easily configurable options.")
+    (license license:bsd-3)))
+
+(define-public python2-htmlmin
+  (package-with-python2 python-htmlmin))
+
+(define-public python-flask-htmlmin
+  (package
+    (name "python-flask-htmlmin")
+    (version "1.2")
+    (source
+    (origin
+      (method url-fetch)
+      (uri (pypi-uri "Flask-HTMLmin" version))
+      (sha256
+       (base32
+        "1n6zlq72kakkw0z2jpq6nh74lfsmxybm4g053pwhc14fbr809348"))))
+    (propagated-inputs
+     `(("python-flask" ,python-flask)
+       ("python-htmlmin" ,python-htmlmin)))
+    (build-system python-build-system)
+    (home-page "https://github.com/hamidfzm/Flask-HTMLmin")
+    (synopsis "HTML response minifier for Flask")
+    (description
+     "Minify @code{text/html} MIME type responses when using @code{Flask}.")
+    (license license:bsd-3)))
+
+(define-public python2-flask-htmlmin
+  (package-with-python2 python-flask-htmlmin))
+
+(define-public python-flask-login
+  (package
+    (name "python-flask-login")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/maxcountryman/flask-login/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1pdqp7a2gyb7k06xda004x0fi2w66s6kn2i0ndkqndmg12d83f9w"))))
+    (arguments
+     ;; Tests fail PEP8 compliance. See:
+     ;; https://github.com/maxcountryman/flask-login/issues/340
+     `(#:tests? #f))
+    (build-system python-build-system)
+    (home-page "https://github.com/maxcountryman/flask-login")
+    (synopsis "User session management for Flask")
+    (description
+     "@code{Flask-Login} provides user session management for Flask.  It
+handles the common tasks of logging in, logging out, and remembering your
+users' sessions over extended periods of time.")
+    (license license:expat)))
+
+(define-public python2-flask-login
+  (package-with-python2 python-flask-login))
diff --git a/gnu/packages/regex.scm b/gnu/packages/regex.scm
index 11f4716033..f55faaf042 100644
--- a/gnu/packages/regex.scm
+++ b/gnu/packages/regex.scm
@@ -22,7 +22,8 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
-  #:use-module (guix build-system gnu))
+  #:use-module (guix build-system gnu)
+  #:use-module (guix utils))
 
 (define-public re2
    (package
@@ -42,7 +43,16 @@
      (arguments
       `(#:test-target "test"
         ;; There is no configure step, but the Makefile respects a prefix.
-        #:make-flags (list (string-append "prefix=" %output))
+        ;; As ./configure does not know anything about the target CXX
+        ;; we need to specify TARGET-g++ explicitly.
+        #:make-flags (list (string-append "prefix=" %output)
+                           (string-append
+                             "CXX=" ,(string-append
+                                       (if (%current-target-system)
+                                           (string-append
+                                             (%current-target-system) "-")
+                                           "")
+                                       "g++")))
         #:phases
         (modify-phases %standard-phases
           (delete 'configure)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 64b0b0e940..49bb24e594 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3227,14 +3227,17 @@ and tidyr provides no margins or aggregation.")
 (define-public r-hexbin
   (package
     (name "r-hexbin")
-    (version "1.27.1")
+    ;; The package tarball was updated in place, resulting in a change in the
+    ;; hash value.  We decided to bump the version to 1.27.1-1 instead of
+    ;; keeping the version at upstream's 1.27.1.
+    (version "1.27.1-1")
     (source
      (origin
        (method url-fetch)
-       (uri (cran-uri "hexbin" version))
+       (uri (cran-uri "hexbin" "1.27.1"))
        (sha256
         (base32
-         "0xi6fbf1fvyn2gffr052n3viibqzpr3603sgi4xaminbzja4syjh"))))
+         "025d609z1nyy684hwvp34b9mjzkgvild7fvfr95f941dmsikan87"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -4170,3 +4173,671 @@ perform @dfn{independent component analysis} (ICA) and projection pursuit.")
 "This package provides the Breiman and Cutler's random forests algorithm, based on a
 forest of trees using random inputs, for classification and regression.")
     (license license:gpl2+)))
+
+(define-public r-diptest
+  (package
+    (name "r-diptest")
+    (version "0.75-7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "diptest" version))
+       (sha256
+        (base32
+         "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/diptest")
+    (synopsis "Hartigan's dip test statistic for unimodality")
+    (description
+     "This package computes Hartigan's dip test statistic for unimodality,
+multimodality and provides a test with simulation based p-values, where the
+original public code has been corrected.")
+    (license license:gpl2+)))
+
+(define-public r-modeltools
+  (package
+    (name "r-modeltools")
+    (version "0.2-21")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "modeltools" version))
+       (sha256
+        (base32
+         "0ynds453xprxv0jqqzi3blnv5w6vrdww9pvd1sq4lrr5ar3k3cq7"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/modeltools")
+    (synopsis "Tools and classes for statistical models")
+    (description
+     "This package provides a collection of tools to deal with statistical
+models.  The functionality is experimental and the user interface is likely
+to change in the future.")
+    (license license:gpl2)))
+
+(define-public r-flexmix
+  (package
+    (name "r-flexmix")
+    (version "2.3-13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "flexmix" version))
+       (sha256
+        (base32
+         "1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-modeltools" ,r-modeltools)))
+    (home-page "http://cran.r-project.org/web/packages/flexmix")
+    (synopsis "Flexible mixture modeling")
+    (description
+     "This package implements a general framework for finite mixtures of
+regression models using the EM algorithm.  FlexMix provides the E-step and
+all data handling, while the M-step can be supplied by the user to easily
+define new models.  Existing drivers implement mixtures of standard linear
+models, generalized linear models and model-based clustering.")
+    (license license:gpl2+)))
+
+(define-public r-mclust
+  (package
+    (name "r-mclust")
+    (version "5.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mclust" version))
+       (sha256
+        (base32
+         "19cbg7p5h2b6h9mvcx9rjppyd3awma18ymaljakbnclpvhwbqpwd"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://www.stat.washington.edu/mclust/")
+    (synopsis "Gaussian mixture modelling for model-based clustering etc.")
+    (description
+     "This package provides Gaussian finite mixture models fitted via EM
+algorithm for model-based clustering, classification, and density estimation,
+including Bayesian regularization, dimension reduction for visualisation,
+and resampling-based inference.")
+    (license license:gpl2+)))
+
+(define-public r-prabclus
+  (package
+    (name "r-prabclus")
+    (version "2.2-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "prabclus" version))
+       (sha256
+        (base32
+         "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mclust" ,r-mclust)))
+    (home-page "https://cran.r-project.org/web/packages/prabclus")
+    (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
+    (description
+     "This package provides a distance-based parametric bootstrap tests
+for clustering with spatial neighborhood information.  Some distance measures,
+clustering of presence-absence, abundance and multilocus genetical data for
+species delimitation, nearest neighbor based noise detection.")
+    (license license:gpl2+)))
+
+(define-public r-deoptimr
+  (package
+    (name "r-deoptimr")
+    (version "1.0-8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "DEoptimR" version))
+       (sha256
+        (base32
+         "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
+    (properties `((upstream-name . "DEoptimR")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/DEoptimR")
+    (synopsis "Differential evolution optimization in pure R")
+    (description
+     "This package provides a differential evolution (DE) stochastic
+algorithms for global optimization of problems with and without constraints.
+The aim is to curate a collection of its state-of-the-art variants that (1) do
+not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
+can be efficiently implemented directly in the R language.")
+    (license license:gpl2+)))
+
+(define-public r-robustbase
+  (package
+    (name "r-robustbase")
+    (version "0.92-7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "robustbase" version))
+       (sha256
+        (base32
+         "13xz4am7y0s0kl5bmbcw3dlhl7ji8h9sjx56wsgmj6r9n35nrggw"))))
+    (build-system r-build-system)
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (propagated-inputs
+     `(("r-deoptimr" ,r-deoptimr)))
+    (home-page "http://robustbase.r-forge.r-project.org/")
+    (synopsis "Basic robust statistics")
+    (description
+     "This packages allows to analyze data with robust methods such as
+regression methodology including model selections and multivariate statistics.")
+    (license license:gpl2+)))
+
+(define-public r-trimcluster
+  (package
+    (name "r-trimcluster")
+    (version "0.1-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "trimcluster" version))
+       (sha256
+        (base32
+         "0lsgbg93hm0w1rdb813ry0ks2l0jfpyqzqkf3h3bj6fch0avcbv2"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/trimcluster")
+    (synopsis "Cluster analysis with trimming")
+    (description
+     "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
+Matran (1997).  This optimizes the k-means criterion under trimming a portion
+of the points.")
+    (license license:gpl2+)))
+
+(define-public r-fpc
+  (package
+    (name "r-fpc")
+    (version "2.1-10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fpc" version))
+       (sha256
+        (base32
+         "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-diptest" ,r-diptest)
+       ("r-flexmix" ,r-flexmix)
+       ("r-kernlab" ,r-kernlab)
+       ("r-mclust" ,r-mclust)
+       ("r-mvtnorm" ,r-mvtnorm)
+       ("r-prabclus" ,r-prabclus)
+       ("r-robustbase" ,r-robustbase)
+       ("r-trimcluster" ,r-trimcluster)))
+    (home-page "http://cran.r-project.org/web/packages/fpc")
+    (synopsis "Flexible procedures for clustering")
+    (description
+     "This package provides various methods for clustering and cluster validation.
+For example, it provides fixed point clustering, linear regression clustering,
+clustering by merging Gaussian mixture components, as well as symmetric and
+asymmetric discriminant projections for visualisation of the separation of
+groupings.")
+  (license license:gpl2+)))
+
+(define-public r-vgam
+  (package
+    (name "r-vgam")
+    (version "1.0-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "VGAM" version))
+       (sha256
+        (base32
+         "0wr6szcpj8r4a1rlzgd6iym7khin69fmvxcf37iyvs8mms86dfr3"))))
+    (properties `((upstream-name . "VGAM")))
+    (build-system r-build-system)
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
+    (synopsis "Vector generalized linear and additive models")
+    (description
+    "This package is an implementation of about 6 major classes of statistical
+regression models.  Currently only fixed-effects models are implemented, i.e.,
+no random-effects models.  Many (150+) models and distributions are estimated
+by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
+VGLMs can be loosely thought of as multivariate generalised linear models.")
+    (license license:gpl2+)))
+
+(define-public r-pbapply
+  (package
+    (name "r-pbapply")
+    (version "1.3-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pbapply" version))
+       (sha256
+        (base32
+         "1sdmjlnwxb99f95g5v8k8mirrkzw99yig377v0qi9lzwjgd6fqqr"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/psolymos/pbapply")
+    (synopsis "Adding progress bar to apply functions")
+    (description
+     "This lightweight package that adds progress bar to vectorized R
+functions apply.  The implementation can easily be added to functions where
+showing the progress is useful e.g. bootstrap.")
+    (license license:gpl2)))
+
+(define-public r-fnn
+  (package
+    (name "r-fnn")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "FNN" version))
+       (sha256
+        (base32
+         "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
+    (properties `((upstream-name . "FNN")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/FNN")
+    (synopsis "Fast nearest neighbor search algorithms and applications")
+    (description
+     "This package provides cover-tree and kd-tree fast k-nearest neighbor
+search algorithms and related applications including KNN classification,
+regression and information measures.")
+    (license license:gpl2+)))
+
+(define-public r-minqa
+  (package
+    (name "r-minqa")
+    (version "1.2.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "minqa" version))
+       (sha256
+        (base32
+         "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://optimizer.r-forge.r-project.org")
+    (synopsis "Derivative-free optimization algorithms by quadratic approximation")
+    (description
+      "This package provides a derivative-free optimization by quadratic approximation
+based on an interface to Fortran implementations by M. J. D. Powell.")
+    (license license:gpl2)))
+
+(define-public r-rcppeigen
+  (package
+    (name "r-rcppeigen")
+    (version "0.3.2.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppEigen" version))
+       (sha256
+        (base32
+         "0fy9kr03160f1ywzff3p380s8a59jz7d2d0rggb14g2y0slzpbr5"))))
+    (properties `((upstream-name . "RcppEigen")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "http://eigen.tuxfamily.org")
+    (synopsis "Rcpp integration for the Eigen templated linear algebra library")
+    (description
+      "This package provides an integration of Eigen in R using a C++ template
+library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
+It supports dense and sparse matrices on integer, floating point and complex numbers,
+decompositions of such matrices, and solutions of linear systems.")
+    (license license:gpl2+)))
+
+(define-public r-modelmetrics
+  (package
+    (name "r-modelmetrics")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+        (uri (cran-uri "ModelMetrics" version))
+        (sha256
+         (base32
+          "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8"))))
+    (properties `((upstream-name . "ModelMetrics")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "http://cran.r-project.org/web/packages/ModelMetrics")
+    (synopsis "Rapid calculation of model metrics")
+    (description
+     "Written in C++ using @code{Rcpp}, this package provides a collection of
+metrics for evaluating models.")
+    (license license:gpl2+)))
+
+(define-public r-matrixmodels
+  (package
+    (name "r-matrixmodels")
+    (version "0.4-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "MatrixModels" version))
+       (sha256
+        (base32
+         "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
+    (properties `((upstream-name . "MatrixModels")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/MatrixModels")
+    (synopsis "Modelling with sparse and dense matrices")
+    (description
+     "This package models with sparse and dense matrix matrices,
+using modular prediction and response module classes.")
+    (license license:gpl2+)))
+
+(define-public r-quantreg
+  (package
+    (name "r-quantreg")
+    (version "5.29")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "quantreg" version))
+       (sha256
+        (base32
+         "098gy8xv9kcl5y0cm93b8chr5sm6crrdxi20bkx9lmwmybl3himv"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (propagated-inputs
+     `(("r-matrixmodels" ,r-matrixmodels)
+       ("r-sparsem" ,r-sparsem)))
+    (home-page "http://www.r-project.org")
+    (synopsis "Quantile regression")
+    (description
+     "This package provides an estimation and inference methods for models
+of conditional quantiles: linear and nonlinear parametric and non-parametric
+models for conditional quantiles of a univariate response and several methods
+for handling censored survival data.  Portfolio selection methods based on
+expected shortfall risk are also included.")
+    (license license:gpl2+)))
+
+(define-public r-nloptr
+  (package
+    (name "r-nloptr")
+    (version "1.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nloptr" version))
+       (sha256
+        (base32
+         "1cypz91z28vhvwq2rzqjrbdc6a2lvfr2g16vid2sax618q6ai089"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("nlopt" ,nlopt)))
+    (home-page "http://cran.r-project.org/web/packages/nloptr")
+    (synopsis "R interface to NLopt")
+    (description
+     "This package is interface to NLopt, a library for nonlinear
+optimization.  NLopt is a library for nonlinear optimization, providing a
+common interface for a number of different free optimization routines
+available online as well as original implementations of various other
+algorithms.")
+    (license license:lgpl3)))
+
+(define-public r-lme4
+  (package
+    (name "r-lme4")
+    (version "1.1-12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lme4" version))
+       (sha256
+        (base32
+         "0j60l5kgx1wvw2wm3jwfqwi63hammaq8gfcxzwa4h552likvaxi9"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)))
+    (propagated-inputs
+     `(("r-minqa" ,r-minqa)
+       ("r-nloptr" ,r-nloptr)))
+    (home-page "http://cran.r-project.org/web/packages/lme4")
+    (synopsis "Linear mixed-effects models using eigen and S4")
+    (description
+      "This package provides fit linear and generalized linear mixed-effects
+models.  The models and their components are represented using S4 classes and
+methods.  The core computational algorithms are implemented using the Eigen
+C++ library for numerical linear algebra and RcppEigen glue.")
+    (license license:gpl2+)))
+
+(define-public r-pbkrtest
+  (package
+    (name "r-pbkrtest")
+    (version "0.4-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pbkrtest" version))
+       (sha256
+        (base32
+         "00cw18q7wvddzjrbxz917wkix6r7672vi2wmsp4gwgzady8vha4x"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lme4" ,r-lme4)))
+    (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
+    (synopsis "Methods for linear mixed model comparison")
+    (description
+     "This package implements a parametric bootstrap test and a Kenward Roger
+modification of F-tests for linear mixed effects models and a parametric
+bootstrap test for generalized linear mixed models.")
+    (license license:gpl2+)))
+
+(define-public r-car
+  (package
+    (name "r-car")
+    (version "2.1-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "car" version))
+       (sha256
+        (base32
+         "0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-pbkrtest" ,r-pbkrtest)
+       ("r-quantreg" ,r-quantreg)))
+    (home-page "https://r-forge.r-project.org/projects/car/")
+    (synopsis "Companion to applied regression")
+    (description
+      "This package provides functions and datasets from book Companion
+to Applied regression, Second Edition, Sage, 2011.")
+    (license license:gpl2+)))
+
+(define-public r-caret
+  (package
+    (name "r-caret")
+    (version "6.0-73")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "caret" version))
+       (sha256
+        (base32
+         "1jzaqwv4glyqqnfbpalgajd0ag866247vvdh5i83ffqs1yhs984h"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-car" ,r-car)
+       ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-modelmetrics" ,r-modelmetrics)
+       ("r-plyr" ,r-plyr)
+       ("r-reshape2" ,r-reshape2)))
+    (home-page "https://github.com/topepo/caret")
+    (synopsis "Classification and regression training")
+    (description
+     "This package provides misc functions for training and plotting
+classification and regression models.")
+    (license license:gpl2+)))
+
+(define-public r-rcppprogress
+  (package
+    (name "r-rcppprogress")
+    (version "0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppProgress" version))
+       (sha256
+        (base32
+         "0796g11w7iv3ix1wfm3fh09qq7jki4r4cp1mjagq77igri3xrr9x"))))
+    (properties `((upstream-name . "RcppProgress")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/kforner/rcpp_progress")
+    (synopsis "Interruptible progress bar for C++ in R packages")
+    (description
+     "This package allows to display a progress bar in the R console for long running
+computations taking place in C++ code, and support for interrupting those computations
+even in multithreaded code, typically using OpenMP.")
+    (license license:gpl3+)))
+
+(define-public r-mnormt
+  (package
+    (name "r-mnormt")
+    (version "1.5-5")
+    (source
+     (origin
+       (method url-fetch)
+        (uri (cran-uri "mnormt" version))
+        (sha256
+          (base32
+           "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
+    (synopsis "Multivariate normal and \"t\" distributions")
+    (description
+     "This package provides functions for computing the density and the
+distribution function of multivariate normal and \"t\" random variables, and
+for generating random vectors sampled from these distributions.  Probabilities
+are computed via non-Monte Carlo methods.")
+    (license license:gpl2+)))
+
+(define-public r-numderiv
+  (package
+    (name "r-numderiv")
+    (version "2016.8-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "numDeriv" version))
+       (sha256
+        (base32
+         "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
+    (properties `((upstream-name . "numDeriv")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/numDeriv")
+    (synopsis "Accurate numerical derivatives")
+    (description
+     "This package provides methods for calculating accurate numerical
+first and second order derivatives.")
+    (license license:gpl2)))
+
+(define-public r-sn
+  (package
+    (name "r-sn")
+    (version "1.5-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sn" version))
+       (sha256
+        (base32
+         "0fh7xjsfd2x8d9lbnss7raldh24b72b3pvcv7zqa1qprzg7zfr01"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mnormt" ,r-mnormt)
+       ("r-numderiv" ,r-numderiv)))
+    (home-page "http://azzalini.stat.unipd.it/SN")
+    (synopsis "The skew-normal and skew-t distributions")
+    (description
+     "This packages provides functionalities to build and manipulate
+probability distributions of the skew-normal family and some related
+ones, notably the skew-t family, and provides related statistical
+methods for data fitting and diagnostics, in the univariate and the
+multivariate case.")
+    (license license:gpl2+)))
+
+(define-public r-tclust
+  (package
+    (name "r-tclust")
+    (version "1.2-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tclust" version))
+       (sha256
+        (base32
+         "0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mclust" ,r-mclust)
+       ("r-mvtnorm" ,r-mvtnorm)
+       ("r-sn" ,r-sn)))
+    (home-page "http://cran.r-project.org/web/packages/tclust")
+    (synopsis "Robust trimmed clustering")
+    (description
+     "This package implements different robust clustering
+algorithms (@code{tclust}) based on trimming and including some graphical
+diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
+    (license license:gpl3)))
+
+(define-public r-ranger
+  (package
+    (name "r-ranger")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ranger" version))
+       (sha256
+        (base32
+         "1fwqwbi0dnla16x6zj14rf95qr5gmilfmlrwnv7s960h4yiw4n97"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/imbs-hl/ranger")
+    (synopsis "Fast implementation of random forests")
+    (description
+     "This package provides a fast implementation of Random Forests,
+particularly suited for high dimensional data.  Ensembles of classification,
+regression, survival and probability prediction trees are supported.  Data from
+genome-wide association studies can be analyzed efficiently.")
+    (license license:gpl3)))
+
+(define-public r-tsne
+  (package
+    (name "r-tsne")
+    (version "0.1-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tsne" version))
+       (sha256
+        (base32
+         "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/jdonaldson/rtsne/")
+    (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
+    (description
+     "This package provides a pure R implementation of the t-SNE algorithm.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 9f73a7ad59..34ffabb483 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -980,7 +980,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2017.03.02")
+    (version "2017.03.07")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -988,7 +988,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0f86qnppxnbh2c8bmpf0c1xhwk5vqjdzz7pqh9sydhscv8r0209g"))))
+                "19acz9m3gazd1ims4l9a9ni1p7jw8z4y0ncqn99xlx9kna8ryjnv"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index dab30df13d..a0e76d52c4 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4459,10 +4459,9 @@ functions of Tidy.")
     (home-page "https://www.hiawatha-webserver.org")
     (synopsis "Webserver with focus on security")
     (description
-     "Hiawatha has been written with security in mind.  This resulted in a
-highly secure webserver in both code and features.  Hiawatha can stop SQL
-injections, XSS and CSRF attacks and exploit attempts.  Via a specially
-crafted monitoring tool, you can keep track of all your webservers.")
+     "Hiawatha has been written with security in mind.
+Features include the ability to stop SQL injections, XSS and CSRF attacks and
+exploit attempts.")
     (license l:gpl2)))
 
 (define-public qutebrowser
diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm
index 9ac21b4db1..1c56e14a66 100644
--- a/gnu/packages/wget.scm
+++ b/gnu/packages/wget.scm
@@ -20,6 +20,7 @@
 
 (define-module (gnu packages wget)
   #:use-module (guix licenses)
+  #:use-module (gnu packages)
   #:use-module (gnu packages libidn)
   #:use-module (gnu packages python)
   #:use-module (gnu packages perl)
@@ -39,6 +40,7 @@
       (method url-fetch)
       (uri (string-append "mirror://gnu/wget/wget-"
                           version ".tar.xz"))
+      (patches (search-patches "wget-CVE-2017-6508.patch"))
       (sha256
        (base32
         "1ljcfhbkdsd0zjfm520rbl1ai62fc34i7c45sfj244l8f6b0p58c"))))
diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index d28e2dd4e4..40e1dd5cfc 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -54,15 +54,14 @@
 (define-public wine
   (package
     (name "wine")
-    (version "2.0")
+    (version "2.3")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://dl.winehq.org/wine/source/"
-                                  (version-major+minor version)
-                                  "/wine-" version ".tar.bz2"))
+              (uri (string-append "https://dl.winehq.org/wine/source/2.x"
+                                  "/wine-" version ".tar.xz"))
               (sha256
                (base32
-                "1ik6q0h3ph3jizmp7bxhf6kcm1pzrdrn2m0yf2x86slv2aigamlp"))))
+                "0zh6kvs4d6d99x5qgxbb5jq2wilwzifhmib2nhq0g3ychxx5rjdg"))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)
                      ("gettext" ,gettext-minimal)
diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 18354271ee..191dc7dd19 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -2392,7 +2392,7 @@ including most mice, keyboards, tablets and touchscreens.")
 (define-public xf86-input-libinput
   (package
     (name "xf86-input-libinput")
-    (version "0.24.0")
+    (version "0.25.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2400,7 +2400,7 @@ including most mice, keyboards, tablets and touchscreens.")
                     name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "0a1nn65qq71bbfhxq39zdb4b1h6ickzv98cjdacv4ngd18shgjyx"))))
+                "0vsmijamfzf6vcljrr0am2qcz33zl2l0lj2mzmbwgrm7ixjx2zxv"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags
@@ -2811,10 +2811,10 @@ X server.")
 
 
 (define-public xf86-video-intel
-  (let ((commit "e4fe79cf0d9a05ee3f3a027148ef0aeb2b1b34e1"))
+  (let ((commit "7e9e92c86b0fc4c848d164fe571798add5e1e36e"))
     (package
       (name "xf86-video-intel")
-      (version (string-append "2.99.917-3-" (string-take commit 7)))
+      (version (string-append "2.99.917-4-" (string-take commit 7)))
       (source
        (origin
          ;; there's no current tarball
@@ -2824,7 +2824,7 @@ X server.")
                (commit commit)))
          (sha256
           (base32
-           "0hf3fxv5jchyh820h449c1ld9x19gc8081w1yk98mab6zr89zswp"))
+           "0igfw8vpz1q0a2526j81fl65z6avfh6lzzrijcs72gwihqqhb1sv"))
          (file-name (string-append name "-" version))))
       (build-system gnu-build-system)
       (inputs `(("mesa" ,mesa)
@@ -2994,7 +2994,7 @@ supported, and the RENDER extension is not accelerated by this driver.")
 (define-public xf86-video-nouveau
   (package
     (name "xf86-video-nouveau")
-    (version "1.0.13")
+    (version "1.0.14")
     (source
      (origin
        (method url-fetch)
@@ -3004,7 +3004,7 @@ supported, and the RENDER extension is not accelerated by this driver.")
              ".tar.bz2"))
        (sha256
         (base32
-         "1js7vak68g2800f1cy5r41wl5x2j7dbmbd7zxypzfgcw2fx454kd"))))
+         "1h9izq510m2pvg77d0y9krc0cvvbhp2y3xlrrz6id7y47jdzkpsd"))))
     (build-system gnu-build-system)
     (inputs `(("xorg-server" ,xorg-server)))
     (native-inputs `(("pkg-config" ,pkg-config)))