Merge branch 'master' into core-updates

112 files changed, 5311 insertions, 1724 deletions

diff --git a/gnu/bootloader/u-boot.scm b/gnu/bootloader/u-boot.scm
new file mode 100644
index 0000000000..963b0d7597
--- /dev/null
+++ b/gnu/bootloader/u-boot.scm
@@ -0,0 +1,47 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2017 David Craven <david@craven.ch>
+;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu bootloader u-boot)
+  #:use-module (gnu bootloader extlinux)
+  #:use-module (gnu bootloader)
+  #:use-module (gnu system)
+  #:use-module (gnu packages bootloaders)
+  #:use-module (guix gexp)
+  #:use-module (guix monads)
+  #:use-module (guix records)
+  #:use-module (guix utils)
+  #:export (u-boot-bootloader))
+
+(define install-u-boot
+  #~(lambda (bootloader device mount-point)
+      (if bootloader
+        (error "Failed to install U-Boot"))))
+
+
+
+;;;
+;;; Bootloader definitions.
+;;;
+
+(define u-boot-bootloader
+  (bootloader
+   (inherit extlinux-bootloader)
+   (name 'u-boot)
+   (package #f)
+   (installer install-u-boot)))
diff --git a/gnu/build/vm.scm b/gnu/build/vm.scm
index 2d41c5756b..727494ad93 100644
--- a/gnu/build/vm.scm
+++ b/gnu/build/vm.scm
@@ -76,11 +76,14 @@
                            (qemu (qemu-command)) (memory-size 512)
                            linux initrd
                            make-disk-image?
+                           single-file-output?
                            (disk-image-size (* 100 (expt 2 20)))
                            (disk-image-format "qcow2")
                            (references-graphs '()))
   "Run BUILDER, a Scheme file, into a VM running LINUX with INITRD, and copy
-the result to OUTPUT.
+the result to OUTPUT.  If SINGLE-FILE-OUTPUT? is true, copy a single file from
+/xchg to OUTPUT.  Otherwise, copy the contents of /xchg to a new directory
+OUTPUT.
 
 When MAKE-DISK-IMAGE? is true, OUTPUT will contain a VM image of
 DISK-IMAGE-SIZE bytes resulting from the execution of BUILDER, which may
@@ -137,8 +140,17 @@ the #:references-graphs parameter of 'derivation'."
 
   ;; When MAKE-DISK-IMAGE? is true, the image is in OUTPUT already.
   (unless make-disk-image?
-    (mkdir output)
-    (copy-recursively "xchg" output)))
+    (if single-file-output?
+        (let ((graph? (lambda (name stat)
+                        (member (basename name) references-graphs))))
+          (match (find-files "xchg" (negate graph?))
+            ((result)
+             (copy-file result output))
+            (x
+             (error "did not find a single result file" x))))
+        (begin
+          (mkdir output)
+          (copy-recursively "xchg" output)))))
 
 
 ;;;
@@ -157,8 +169,8 @@ the #:references-graphs parameter of 'derivation'."
 (define (estimated-partition-size graphs)
   "Return the estimated size of a partition that can store the store items
 given by GRAPHS, a list of file names produced by #:references-graphs."
-  ;; Simply add a 20% overhead.
-  (round (* 1.2 (closure-size graphs))))
+  ;; Simply add a 25% overhead.
+  (round (* 1.25 (closure-size graphs))))
 
 (define* (initialize-partition-table device partitions
                                      #:key
@@ -354,9 +366,9 @@ SYSTEM-DIRECTORY is the name of the directory of the 'system' derivation."
       (error "failed to create GRUB EFI image"))))
 
 (define* (make-iso9660-image grub config-file os-drv target
-                             #:key (volume-id "GuixSD") (volume-uuid #f))
+                             #:key (volume-id "GuixSD_image") (volume-uuid #f))
   "Given a GRUB package, creates an iso image as TARGET, using CONFIG-FILE as
-Grub configuration and OS-DRV as the stuff in it."
+GRUB configuration and OS-DRV as the stuff in it."
   (let ((grub-mkrescue (string-append grub "/bin/grub-mkrescue")))
     (mkdir-p "/tmp/root/var/run")
     (mkdir-p "/tmp/root/run")
@@ -367,6 +379,19 @@ Grub configuration and OS-DRV as the stuff in it."
                             "var=/tmp/root/var"
                             "run=/tmp/root/run"
                             "--"
+                            ;; Store two copies of the headers.
+                            ;; The resulting ISO-9660 image has a DOS MBR and
+                            ;; one protective partition (with type 0xCD).
+                            ;; Because GuixSD only uses actual partitions
+                            ;; rather than what /proc/partitions returns, work
+                            ;; around it by storing the primary volume
+                            ;; descriptor twice, once where it should be and
+                            ;; once in the partition.
+                            ;; Allegedly, otherwise, many other GNU tools
+                            ;; (automounters etc) would also be confused by
+                            ;; the extra partition so it makes sense to
+                            ;; store two copies in any case.
+                            "-boot_image" "any" "partition_offset=16"
                             "-volid" ,(string-upcase volume-id)
                             ,@(if volume-uuid
                                   `("-volume_date" "uuid"
@@ -427,11 +452,14 @@ passing it a directory name where it is mounted."
 
         ;; Create a tiny configuration file telling the embedded grub
         ;; where to load the real thing.
+        ;; XXX This is quite fragile, and can prevent the image from booting
+        ;; when there's more than one volume with this label present.
+        ;; Reproducible almost-UUIDs could reduce the risk (not eliminate it).
         (call-with-output-file grub-config
           (lambda (port)
             (format port
                     "insmod part_msdos~@
-                    search --set=root --label GuixSD~@
+                    search --set=root --label GuixSD_image~@
                     configfile /boot/grub/grub.cfg~%")))
 
         (display "creating EFI firmware image...")
diff --git a/gnu/local.mk b/gnu/local.mk
index 8b3caac629..f01ed62ff9 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -40,6 +40,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/bootloader.scm				\
   %D%/bootloader/grub.scm                       \
   %D%/bootloader/extlinux.scm                   \
+  %D%/bootloader/u-boot.scm                     \
   %D%/packages.scm				\
   %D%/packages/abduco.scm			\
   %D%/packages/abiword.scm			\
@@ -98,6 +99,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/cpio.scm				\
   %D%/packages/cpp.scm 				\
   %D%/packages/cppi.scm				\
+  %D%/packages/cran.scm				\
   %D%/packages/cross-base.scm			\
   %D%/packages/crypto.scm			\
   %D%/packages/cryptsetup.scm			\
@@ -149,6 +151,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/fonts.scm			\
   %D%/packages/fontutils.scm			\
   %D%/packages/fpga.scm				\
+  %D%/packages/forth.scm			\
   %D%/packages/freedesktop.scm			\
   %D%/packages/freeipmi.scm			\
   %D%/packages/ftp.scm				\
@@ -163,7 +166,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/gdb.scm				\
   %D%/packages/geo.scm				\
   %D%/packages/gettext.scm			\
-  %D%/packages/gforth.scm			\
   %D%/packages/ghostscript.scm			\
   %D%/packages/gimp.scm				\
   %D%/packages/gkrellm.scm			\
@@ -264,6 +266,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/maths.scm			\
   %D%/packages/mc.scm				\
   %D%/packages/mcrypt.scm			\
+  %D%/packages/medical.scm			\
   %D%/packages/mes.scm				\
   %D%/packages/messaging.scm			\
   %D%/packages/mingw.scm			\
@@ -327,7 +330,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/pv.scm				\
   %D%/packages/python.scm			\
   %D%/packages/tryton.scm			\
-  %D%/packages/qemu.scm				\
   %D%/packages/qt.scm				\
   %D%/packages/ragel.scm			\
   %D%/packages/rails.scm			\
@@ -363,6 +365,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/skribilo.scm			\
   %D%/packages/slang.scm			\
   %D%/packages/smalltalk.scm			\
+  %D%/packages/sml.scm				\
   %D%/packages/speech.scm			\
   %D%/packages/spice.scm			\
   %D%/packages/ssh.scm				\
@@ -397,6 +400,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/version-control.scm		\
   %D%/packages/video.scm			\
   %D%/packages/vim.scm				\
+  %D%/packages/virtualization.scm		\
   %D%/packages/vpn.scm				\
   %D%/packages/w3m.scm				\
   %D%/packages/wdiff.scm			\
@@ -518,7 +522,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/awesome-reproducible-png.patch		\
   %D%/packages/patches/azr3.patch				\
   %D%/packages/patches/bash-completion-directories.patch	\
-  %D%/packages/patches/bigloo-gc-shebangs.patch			\
   %D%/packages/patches/binutils-ld-new-dtags.patch		\
   %D%/packages/patches/binutils-loongson-workaround.patch	\
   %D%/packages/patches/blast+-fix-makefile.patch		\
@@ -534,6 +537,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ceph-skip-collect-sys-info-test.patch	\
   %D%/packages/patches/ceph-skip-unittest_blockdev.patch	\
   %D%/packages/patches/chicken-CVE-2017-6949.patch		\
+  %D%/packages/patches/chicken-CVE-2017-11343.patch		\
   %D%/packages/patches/chmlib-inttypes.patch			\
   %D%/packages/patches/clang-libc-search-path.patch		\
   %D%/packages/patches/clang-3.8-libc-search-path.patch		\
@@ -574,6 +578,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/emacs-source-date-epoch.patch		\
   %D%/packages/patches/eudev-rules-directory.patch		\
   %D%/packages/patches/evilwm-lost-focus-bug.patch		\
+  %D%/packages/patches/evince-CVE-2017-1000083.patch		\
   %D%/packages/patches/exim-CVE-2017-1000369.patch		\
   %D%/packages/patches/fabric-tests.patch			\
   %D%/packages/patches/fastcap-mulGlobal.patch			\
@@ -684,8 +689,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/hdf-eos5-remove-gctp.patch		\
   %D%/packages/patches/hdf-eos5-fix-szip.patch			\
   %D%/packages/patches/hdf-eos5-fortrantests.patch		\
+  %D%/packages/patches/heimdal-CVE-2017-6594.patch		\
+  %D%/packages/patches/heimdal-CVE-2017-11103.patch		\
+  %D%/packages/patches/hmmer-remove-cpu-specificity.patch	\
   %D%/packages/patches/higan-remove-march-native-flag.patch	\
-  %D%/packages/patches/hop-linker-flags.patch			\
   %D%/packages/patches/hubbub-sort-entities.patch		\
   %D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch        \
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
@@ -696,6 +703,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ilmbase-fix-tests.patch			\
   %D%/packages/patches/intltool-perl-compatibility.patch	\
   %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\
+  %D%/packages/patches/jacal-fix-texinfo.patch			\
   %D%/packages/patches/jbig2dec-ignore-testtest.patch		\
   %D%/packages/patches/jbig2dec-CVE-2016-9601.patch		\
   %D%/packages/patches/jbig2dec-CVE-2017-7885.patch		\
@@ -771,6 +779,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libtool-skip-tests2.patch		\
   %D%/packages/patches/libunwind-CVE-2015-3239.patch		\
   %D%/packages/patches/libunistring-gnulib-multi-core.patch	\
+  %D%/packages/patches/libusb-0.1-disable-tests.patch		\
   %D%/packages/patches/libvpx-CVE-2016-2818.patch		\
   %D%/packages/patches/libxcb-python-3.5-compat.patch		\
   %D%/packages/patches/libxml2-CVE-2016-4658.patch		\
@@ -812,6 +821,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/mesa-skip-disk-cache-test.patch		\
   %D%/packages/patches/mesa-wayland-egl-symbols-check-mips.patch	\
   %D%/packages/patches/metabat-remove-compilation-date.patch	\
+  %D%/packages/patches/metabat-fix-compilation.patch		\
   %D%/packages/patches/mhash-keygen-test-segfault.patch		\
   %D%/packages/patches/mingw-w64-5.0rc2-gcc-4.9.3.patch		\
   %D%/packages/patches/mpc123-initialize-ao.patch		\
@@ -932,17 +942,16 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-statsmodels-fix-tests.patch	\
   %D%/packages/patches/python-configobj-setuptools.patch	\
   %D%/packages/patches/python-cython-fix-tests-32bit.patch	\
-  %D%/packages/patches/python-fake-factory-fix-build-32bit.patch	\
   %D%/packages/patches/python-faker-fix-build-32bit.patch	\
   %D%/packages/patches/python-pandas-skip-failing-tests.patch	\
   %D%/packages/patches/python-paste-remove-website-test.patch	\
   %D%/packages/patches/python-paste-remove-timing-test.patch	\
+  %D%/packages/patches/python-pbr-fix-man-page-support.patch	\
   %D%/packages/patches/python-pillow-freetype-2.7-test-failure.patch	\
   %D%/packages/patches/python-pygit2-disable-network-tests.patch	\
   %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch	\
   %D%/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \
   %D%/packages/patches/python-pygpgme-fix-pinentry-tests.patch	\
-  %D%/packages/patches/python-pyopenssl-17.1.0-test-overflow.patch	\
   %D%/packages/patches/python2-subprocess32-disable-input-test.patch	\
   %D%/packages/patches/qemu-CVE-2017-7493.patch			\
   %D%/packages/patches/qemu-CVE-2017-8112.patch			\
@@ -950,9 +959,11 @@ dist_patch_DATA =						\
   %D%/packages/patches/qemu-CVE-2017-8379.patch			\
   %D%/packages/patches/qemu-CVE-2017-8380.patch			\
   %D%/packages/patches/qemu-CVE-2017-9524.patch			\
+  %D%/packages/patches/qemu-CVE-2017-11334.patch		\
   %D%/packages/patches/qt4-ldflags.patch			\
   %D%/packages/patches/qtscript-disable-tests.patch		\
   %D%/packages/patches/quagga-reproducible-build.patch          \
+  %D%/packages/patches/quassel-fix-tls-check.patch              \
   %D%/packages/patches/quickswitch-fix-dmenu-check.patch	\
   %D%/packages/patches/rapicorn-isnan.patch			\
   %D%/packages/patches/raptor2-heap-overflow.patch		\
@@ -983,11 +994,14 @@ dist_patch_DATA =						\
   %D%/packages/patches/slim-reset.patch				\
   %D%/packages/patches/slim-login.patch				\
   %D%/packages/patches/slurm-configure-remove-nonfree-contribs.patch \
+  %D%/packages/patches/sooperlooper-build-with-wx-30.patch 	\
   %D%/packages/patches/spice-CVE-2016-9577.patch		\
   %D%/packages/patches/spice-CVE-2016-9578-1.patch		\
   %D%/packages/patches/spice-CVE-2016-9578-2.patch		\
+  %D%/packages/patches/spice-CVE-2017-7506.patch		\
   %D%/packages/patches/steghide-fixes.patch			\
   %D%/packages/patches/superlu-dist-scotchmetis.patch		\
+  %D%/packages/patches/supertuxkart-angelscript-ftbfs.patch		\
   %D%/packages/patches/swish-e-search.patch			\
   %D%/packages/patches/swish-e-format-security.patch		\
   %D%/packages/patches/synfigstudio-fix-ui-with-gtk3.patch 	\
@@ -1038,6 +1052,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/vorbis-tools-CVE-2014-9640.patch		\
   %D%/packages/patches/vorbis-tools-CVE-2015-6749.patch		\
   %D%/packages/patches/vpnc-script.patch			\
+  %D%/packages/patches/vsearch-unbundle-cityhash.patch		\
   %D%/packages/patches/vte-CVE-2012-2738-pt1.patch			\
   %D%/packages/patches/vte-CVE-2012-2738-pt2.patch			\
   %D%/packages/patches/weechat-python.patch			\
diff --git a/gnu/packages/acct.scm b/gnu/packages/acct.scm
index c86713cb35..a0aac153b0 100644
--- a/gnu/packages/acct.scm
+++ b/gnu/packages/acct.scm
@@ -25,7 +25,7 @@
 (define-public acct
   (package
     (name "acct")
-    (version "6.6.3")
+    (version "6.6.4")
     (source
      (origin
       (method url-fetch)
@@ -33,7 +33,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "14x0zklwlg7cc7amlyzffqr8az3fqj1h9dyj0hvl1kpi7cr7kbjy"))))
+        "0gv6m8giazshvgpvwbng98chpas09myyfw1zr2y7hqxib0mvy5ac"))))
     (build-system gnu-build-system)
     (home-page "https://gnu.org/software/acct/")
     (synopsis "Standard login and process accounting utilities")
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 5fa9d5b06c..2f58cb3a28 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -271,7 +271,13 @@ re-executing them as necessary.")
                "05n65k4ixl85dc6rxc51b1b732gnmm8xnqi424dy9f1nz7ppb3xy"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:configure-flags '("--localstatedir=/var")
+     `(#:configure-flags '("--localstatedir=/var"
+
+                           ;; Make sure 'PATH_PROCNET_DEV' gets defined when
+                           ;; cross-compiling (by default it does not.)
+                           ,@(if (%current-target-system)
+                                 '("--with-path-procnet-dev=/proc/net/dev")
+                                 '()))
        ;; On some systems, 'libls.sh' may fail with an error such as:
        ;; "Failed to tell switch -a apart from -A".
        #:parallel-tests? #f))
@@ -300,7 +306,7 @@ hostname.")
                 "0hdpai78n63l3v3fgr3kkiqzhd0awrpfnnzz4mf7lmxdh61qb37w"))))
     (build-system gnu-build-system)
     (arguments
-     '(;; Assume System V `setpgrp (void)', which is the default on GNU
+     `(;; Assume System V `setpgrp (void)', which is the default on GNU
        ;; variants (`AC_FUNC_SETPGRP' is not cross-compilation capable.)
        #:configure-flags
        '("--with-libpam" "ac_cv_func_setpgrp_void=yes")
@@ -310,7 +316,10 @@ hostname.")
          (add-before 'build 'set-nscd-file-name
            (lambda* (#:key inputs #:allow-other-keys)
              ;; Use the right file name for nscd.
-             (let ((libc (assoc-ref inputs "libc")))
+             (let ((libc (assoc-ref inputs
+                                    ,(if (%current-target-system)
+                                         "cross-libc"
+                                         "libc"))))
                (substitute* "lib/nscd.c"
                  (("/usr/sbin/nscd")
                   (string-append libc "/sbin/nscd"))))))
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 8a04cfe1b3..40700cae3d 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1136,7 +1136,7 @@ patches that can be used with softsynths such as Timidity and WildMidi.")
 (define-public guitarix
   (package
     (name "guitarix")
-    (version "0.35.4")
+    (version "0.35.5")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -1144,7 +1144,7 @@ patches that can be used with softsynths such as Timidity and WildMidi.")
                    version ".tar.xz"))
              (sha256
               (base32
-               "1vip4d5hc20vjkh8c9bwn92gyqcc6a1ml6hs39djp59mmybr13dp"))))
+               "00pfb6qa3jfa6qaql7isnb8srfdfmk362ygslh7y0qkm36qasmh4"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f ; no "check" target
@@ -2766,7 +2766,8 @@ machine-readable ASCII format.")
     (description "shntool is a multi-purpose WAVE data processing and reporting
 utility.  File formats are abstracted from its core, so it can process any file
 that contains WAVE data, compressed or not---provided there exists a format
-module to handle that particular file type.")
+module to handle that particular file type.  It can also generate CUE files, and
+use them split WAVE data into multiple files.")
     (home-page "http://etree.org/shnutils/shntool/")
     ;; 'install-sh' bears the x11 license
     (license (list license:gpl2+ license:x11))))
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 1ef4e42015..20b375abe1 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -118,7 +118,7 @@ spying and/or modification by the server.")
 (define-public par2cmdline
   (package
     (name "par2cmdline")
-    (version "0.7.2")
+    (version "0.7.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/Parchive/par2cmdline/archive/v"
@@ -126,7 +126,7 @@ spying and/or modification by the server.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0rsrca7903g08zrifv4102gkxrhmzvgwd1sb6vw9pa00qhzsfkzs"))))
+                "0dqwarc2aw5clgpf24d9dxh43b0k0z3l6kksn30arx9bdlmrk5rx"))))
     (native-inputs
      `(("automake" ,automake)
        ("autoconf" ,autoconf)))
@@ -136,10 +136,15 @@ spying and/or modification by the server.")
        (modify-phases %standard-phases
          (add-after 'unpack 'autoreconf
            (lambda _ (zero? (system* "autoreconf" "-vfi")))))))
-    (synopsis "File verification and repair tool")
-    (description "Par2cmdline is a tool for generating RAID-like PAR2 recovery
-files using Reed-Solomon coding.  PAR2 files can be stored along side backups
-or distributed files for recovering from bitrot.")
+    (synopsis "File verification and repair tools")
+    (description "Par2cmdline uses Reed-Solomon error-correcting codes to
+generate and verify PAR2 recovery files.  These files can be distributed
+alongside the source files or stored together with back-ups to protect against
+transmission errors or @dfn{bit rot}, the degradation of storage media over
+time.
+Unlike a simple checksum, PAR2 doesn't merely detect errors: as long as the
+damage isn't too extensive (and smaller than the size of the recovery file), it
+can even repair them.")
     (home-page "https://github.com/Parchive/par2cmdline")
     (license license:gpl3+)))
 
@@ -456,13 +461,13 @@ detection, and lossless compression.")
 (define-public borg
   (package
     (name "borg")
-    (version "1.0.10")
+    (version "1.0.11")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "borgbackup" version))
               (sha256
                (base32
-                "1sarmpzwr8dhbg0hsvaclcsjfax36ssb32d9klhhah4j8kqji3wp"))
+                "14fjk5dfwmjkn7nmkbhhbrk3g1wfrn8arvqd5r9jaij534nzsvpw"))
               (modules '((guix build utils)))
               (snippet
                '(for-each
diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index d42aa55560..725d91b976 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -835,23 +835,11 @@ GLIBC/HURD for a Hurd host"
          `(modify-phases ,phases
             (add-before 'configure 'fix-pwd
               (lambda _
-                ;; Use `pwd' instead of `/bin/pwd' for glibc-2.21
+                ;; Use `pwd' instead of `/bin/pwd' for glibc-2.22.
                 (substitute* "configure"
                   (("/bin/pwd") "pwd"))
                 #t))))))))
 
-(define-public glibc-2.21
-  (package
-    (inherit glibc-2.22)
-    (version "2.21")
-    (source (origin
-              (inherit (package-source glibc-2.22))
-              (uri (string-append "mirror://gnu/glibc/glibc-"
-                                  version ".tar.xz"))
-              (sha256
-               (base32
-                "1f135546j34s9bfkydmx2nhh9vwxlx60jldi80zmsnln6wj3dsxf"))))))
-
 (define-public glibc-locales
   (package
     (inherit glibc)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 82cd1e420d..3b4cc359ee 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -248,7 +248,7 @@ structure of the predicted RNA.")
        ("python-nose" ,python2-nose)
        ("python-pysam" ,python2-pysam)))
     (inputs
-     `(("htslib" ,htslib)
+     `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+.
        ("samtools" ,samtools)
        ("bwa" ,bwa)
        ("grep" ,grep)
@@ -300,7 +300,7 @@ BAM files.")
 (define-public bcftools
   (package
     (name "bcftools")
-    (version "1.3.1")
+    (version "1.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -308,33 +308,27 @@ BAM files.")
                     version "/bcftools-" version ".tar.bz2"))
               (sha256
                (base32
-                "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj"))
+                "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled htslib.
-               '(delete-file-recursively "htslib-1.3.1"))))
+               '(delete-file-recursively "htslib-1.5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
+       #:configure-flags (list "--with-htslib=system")
        #:make-flags
        (list
         "USE_GPL=1"
+        "LIBS=-lgsl -lgslcblas"
         (string-append "prefix=" (assoc-ref %outputs "out"))
         (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
-        (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.a")
+        (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so")
         (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip")
-        (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix"))
+        (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix")
+        (string-append "PACKAGE_VERSION=" ,version))
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'patch-Makefile
-           (lambda _
-             (substitute* "Makefile"
-               ;; Do not attempt to build htslib.
-               (("^include \\$\\(HTSDIR\\)/htslib\\.mk") "")
-               ;; Link against GSL cblas.
-               (("-lcblas") "-lgslcblas"))
-             #t))
-         (delete 'configure)
          (add-before 'check 'patch-tests
            (lambda _
              (substitute* "test/test.pl"
@@ -1195,7 +1189,7 @@ errors at the end of reads.")
 (define-public bowtie
   (package
     (name "bowtie")
-    (version "2.2.9")
+    (version "2.3.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
@@ -1203,7 +1197,7 @@ errors at the end of reads.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1vp5db8i7is57iwjybcdg18f5ivyzlj5g1ix1nlvxainzivhz55g"))
+                "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90"))
               (modules '((guix build utils)))
               (snippet
                '(substitute* "Makefile"
@@ -1211,28 +1205,28 @@ errors at the end of reads.")
                   (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
                   (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
     (build-system gnu-build-system)
-    (inputs `(("perl" ,perl)
-              ("perl-clone" ,perl-clone)
-              ("perl-test-deep" ,perl-test-deep)
-              ("perl-test-simple" ,perl-test-simple)
-              ("python" ,python-2)
-              ("tbb" ,tbb)))
+    (inputs
+     `(("perl" ,perl)
+       ("perl-clone" ,perl-clone)
+       ("perl-test-deep" ,perl-test-deep)
+       ("perl-test-simple" ,perl-test-simple)
+       ("python" ,python-2)
+       ("tbb" ,tbb)
+       ("zlib" ,zlib)))
     (arguments
      '(#:make-flags
        (list "allall"
              "WITH_TBB=1"
              (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
-       (alist-delete
-        'configure
-        (alist-replace
-         'check
-         (lambda* (#:key outputs #:allow-other-keys)
-           (system* "perl"
-                    "scripts/test/simple_tests.pl"
-                    "--bowtie2=./bowtie2"
-                    "--bowtie2-build=./bowtie2-build"))
-         %standard-phases))))
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'check
+           (lambda* (#:key outputs #:allow-other-keys)
+             (zero? (system* "perl"
+                             "scripts/test/simple_tests.pl"
+                             "--bowtie2=./bowtie2"
+                             "--bowtie2-build=./bowtie2-build")))))))
     (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
     (synopsis "Fast and sensitive nucleotide sequence read aligner")
     (description
@@ -1424,7 +1418,7 @@ multiple sequence alignments.")
 (define-public python-pysam
   (package
     (name "python-pysam")
-    (version "0.10.0")
+    (version "0.11.2.2")
     (source (origin
               (method url-fetch)
               ;; Test data is missing on PyPi.
@@ -1434,7 +1428,7 @@ multiple sequence alignments.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1mmvn91agr238kwz7226xq0i7k84lg2nxywn9712mzj7gvgqhfy8"))
+                "1cfqdxsqs3xhacns9n0271ck6wkc76px66ddjm91wfw2jxxfklvc"))
               (modules '((guix build utils)))
               (snippet
                ;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
@@ -1533,13 +1527,13 @@ UCSC genome browser.")
 (define-public python-plastid
   (package
     (name "python-plastid")
-    (version "0.4.6")
+    (version "0.4.8")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "plastid" version))
               (sha256
                (base32
-                "1sqkz5d3b9kf688mp7k771c87ins42j7j0whmkb49cb3fsg8s8lj"))))
+                "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8"))))
     (build-system python-build-system)
     (arguments
      ;; Some test files are not included.
@@ -3051,7 +3045,7 @@ manipulating HTS data.")
 (define-public htslib
   (package
     (name "htslib")
-    (version "1.3.1")
+    (version "1.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3059,7 +3053,7 @@ manipulating HTS data.")
                     version "/htslib-" version ".tar.bz2"))
               (sha256
                (base32
-                "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))
+                "0bcjmnbwp2bib1z1bkrp95w9v2syzdwdfqww10mkb1hxlmg52ax0"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -3071,7 +3065,9 @@ manipulating HTS data.")
               (("/bin/bash") (which "bash")))
             #t)))))
     (inputs
-     `(("zlib" ,zlib)))
+     `(("openssl" ,openssl)
+       ("curl" ,curl)
+       ("zlib" ,zlib)))
     (native-inputs
      `(("perl" ,perl)))
     (home-page "http://www.htslib.org")
@@ -3083,6 +3079,20 @@ data.  It also provides the bgzip, htsfile, and tabix utilities.")
     ;; the rest is released under the Expat license
     (license (list license:expat license:bsd-3))))
 
+;; This package should be removed once no packages rely upon it.
+(define htslib-1.3
+  (package
+    (inherit htslib)
+    (version "1.3.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/samtools/htslib/releases/download/"
+                    version "/htslib-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))))
+
 (define-public idr
   (package
     (name "idr")
@@ -3457,23 +3467,20 @@ form of assemblies or reads.")
                    license:cpl1.0))))     ; Open Bloom Filter
 
 (define-public metabat
-  ;; We package from a git commit because compilation of the released version
-  ;; fails.
-  (let ((commit "cbdca756993e66ae57e50a27970595dda9cbde1b"))
-    (package
-      (name "metabat")
-      (version (string-append "0.32.4-1." (string-take commit 8)))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://bitbucket.org/berkeleylab/metabat.git")
-               (commit commit)))
-         (file-name (string-append name "-" version))
-         (sha256
-          (base32
-           "0byia8nsip6zvc4ha0qkxkxxyjf4x7jcvy48q2dvb0pzr989syzr"))
-         (patches (search-patches "metabat-remove-compilation-date.patch"))))
+  (package
+    (name "metabat")
+    (version "2.11.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0ll00l81aflscgggs5nfhj12cbvdiz3gg7f7n5f537a3xhx60vn9"))
+       (patches (search-patches "metabat-remove-compilation-date.patch"
+                                "metabat-fix-compilation.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -3490,35 +3497,35 @@ form of assemblies or reads.")
                 "#include \"htslib/kseq.h\""))
              #t))
          (add-after 'unpack 'fix-scons
-            (lambda* (#:key inputs #:allow-other-keys)
-              (substitute* "SConstruct"
-                (("^htslib_dir = 'samtools'")
-                 (string-append "hitslib_dir = '"
-                                (assoc-ref inputs "htslib")
-                                "'"))
-                (("^samtools_dir = 'samtools'")
-                 (string-append "samtools_dir = '"
-                                (assoc-ref inputs "htslib")
-                                "'"))
-                (("^findStaticOrShared\\('bam', hts_lib")
-                 (string-append "findStaticOrShared('bam', '"
-                                (assoc-ref inputs "samtools")
-                                "/lib'"))
-                ;; Do not distribute README.
-                (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
-              #t))
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "SConstruct"
+               (("^htslib_dir += 'samtools'")
+                (string-append "htslib_dir = '"
+                               (assoc-ref inputs "htslib")
+                               "'"))
+               (("^samtools_dir = 'samtools'")
+                (string-append "samtools_dir = '"
+                               (assoc-ref inputs "samtools")
+                               "'"))
+               (("^findStaticOrShared\\('bam', hts_lib")
+                (string-append "findStaticOrShared('bam', '"
+                               (assoc-ref inputs "samtools")
+                               "/lib'"))
+               ;; Do not distribute README.
+               (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
+             #t))
          (delete 'configure)
          (replace 'build
-                  (lambda* (#:key inputs outputs #:allow-other-keys)
-                    (mkdir (assoc-ref outputs "out"))
-                    (zero? (system* "scons"
-                                    (string-append
-                                     "PREFIX="
-                                     (assoc-ref outputs "out"))
-                                    (string-append
-                                     "BOOST_ROOT="
-                                     (assoc-ref inputs "boost"))
-                                    "install"))))
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (mkdir (assoc-ref outputs "out"))
+             (zero? (system* "scons"
+                             (string-append
+                              "PREFIX="
+                              (assoc-ref outputs "out"))
+                             (string-append
+                              "BOOST_ROOT="
+                              (assoc-ref inputs "boost"))
+                             "install"))))
          ;; Check and install are carried out during build phase.
          (delete 'check)
          (delete 'install))))
@@ -3539,8 +3546,8 @@ sequences to deconvolute complex microbial communities, or metagenome binning,
 enables the study of individual organisms and their interactions.  MetaBAT is
 an automated metagenome binning software, which integrates empirical
 probabilistic distances of genome abundance and tetranucleotide frequency.")
-   (license (license:non-copyleft "file://license.txt"
-                                  "See license.txt in the distribution.")))))
+    (license (license:non-copyleft "file://license.txt"
+                                   "See license.txt in the distribution."))))
 
 (define-public minced
   (package
@@ -4320,6 +4327,8 @@ extremely diverse sets of genomes.")
     (description
      "RAxML is a tool for phylogenetic analysis and post-analysis of large
 phylogenies.")
+    ;; The source includes x86 specific code
+    (supported-systems '("x86_64-linux" "i686-linux"))
     (license license:gpl2+)))
 
 (define-public rsem
@@ -4512,7 +4521,7 @@ to the user's query of interest.")
 (define-public samtools
   (package
     (name "samtools")
-    (version "1.3.1")
+    (version "1.5")
     (source
      (origin
        (method url-fetch)
@@ -4521,7 +4530,7 @@ to the user's query of interest.")
                        version "/samtools-" version ".tar.bz2"))
        (sha256
         (base32
-         "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc"))))
+         "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
@@ -4529,36 +4538,35 @@ to the user's query of interest.")
                   (guix build gnu-build-system)
                   (guix build utils))
        #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
-       #:configure-flags (list "--with-ncurses")
+       #:configure-flags (list "--with-ncurses" "--with-htslib=system")
        #:phases
-       (alist-cons-after
-        'unpack 'patch-tests
-        (lambda _
-          (substitute* "test/test.pl"
-            ;; The test script calls out to /bin/bash
-            (("/bin/bash") (which "bash")))
-          #t)
-        (alist-cons-after
-         'install 'install-library
-         (lambda* (#:key outputs #:allow-other-keys)
-           (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
-             (install-file "libbam.a" lib)
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-tests
+           (lambda _
+             (substitute* "test/test.pl"
+               ;; The test script calls out to /bin/bash
+               (("/bin/bash") (which "bash")))
              #t))
-         (alist-cons-after
-          'install 'install-headers
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let ((include (string-append (assoc-ref outputs "out")
-                                          "/include/samtools/")))
-              (for-each (lambda (file)
-                          (install-file file include))
-                        (scandir "." (lambda (name) (string-match "\\.h$" name))))
-              #t))
-          %standard-phases)))))
+         (add-after 'install 'install-library
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
+               (install-file "libbam.a" lib)
+               #t)))
+         (add-after 'install 'install-headers
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((include (string-append (assoc-ref outputs "out")
+                                           "/include/samtools/")))
+               (for-each (lambda (file)
+                           (install-file file include))
+                         (scandir "." (lambda (name) (string-match "\\.h$" name))))
+               #t))))))
     (native-inputs `(("pkg-config" ,pkg-config)))
-    (inputs `(("ncurses" ,ncurses)
-              ("perl" ,perl)
-              ("python" ,python)
-              ("zlib" ,zlib)))
+    (inputs
+     `(("htslib" ,htslib)
+       ("ncurses" ,ncurses)
+       ("perl" ,perl)
+       ("python" ,python)
+       ("zlib" ,zlib)))
     (home-page "http://samtools.sourceforge.net")
     (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
     (description
@@ -5316,6 +5324,8 @@ and operational taxonomic unit (OTU) picking of next generation
 sequencing (NGS) reads.  The core algorithm is based on approximate seeds and
 allows for fast and sensitive analyses of nucleotide sequences.  The main
 application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
+    ;; The source includes x86 specific code
+    (supported-systems '("x86_64-linux" "i686-linux"))
     (license license:lgpl3)))
 
 (define-public star
@@ -6528,13 +6538,13 @@ abnormal copy number.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.14.0")
+    (version "0.14.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0ywwrs4d752xfk0p0w122kvi0xvp6nmxnyynchbsa8zciqymhgv8"))))
+                "1r7s4pfw026qazzic090mhk8d9m39j2nwl87dyqcpdylyq7gq5qs"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -6780,13 +6790,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.28.0")
+    (version "1.28.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "10x9zx0b7j05d1j6p0xs4q4f4wzbhf3rq64wzi9cgv7f44q43a5n"))))
+                "1y15kg1q81h8rmga83ljiwr8whkajcargfjiljr212d6if17ys1z"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -7559,7 +7569,7 @@ Stephens (1990).")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
+                "0479qx4bapgcp5chj10a63chk0s28x9cx1gamz3f5m3yd7jzwcf2"))))
     (properties
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
     (build-system r-build-system)
diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 76dad2923e..53cf7741a9 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -40,8 +40,8 @@
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
-  #:use-module (gnu packages qemu)
   #:use-module (gnu packages texinfo)
+  #:use-module (gnu packages virtualization)
   #:use-module (guix build-system gnu)
   #:use-module (guix download)
   #:use-module (guix git-download)
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 66f46433f9..353c9c8efb 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -23,6 +23,7 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (gnu packages)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages python)
   #:use-module (gnu packages ninja)
   #:use-module (guix build-system gnu)
@@ -69,7 +70,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
 (define-public meson
   (package
     (name "meson")
-    (version "0.40.1")
+    (version "0.41.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/mesonbuild/meson/"
@@ -77,7 +78,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0yl6iryh89nn6hzhwv7kg16ki1chh9h0x1yk1y130h87iq42a35r"))))
+                "12ygjh1dxi8z06nl704rfb6zj0m2zjqp279nymfgzfgy5zq032d4"))))
     (build-system python-build-system)
     (inputs `(("ninja", ninja)))
     (home-page "https://mesonbuild.com/")
@@ -90,3 +91,37 @@ Autoconf/Automake/make combo.  Build specifications, also known as @dfn{Meson
 files}, are written in a custom domain-specific language (DSL) that resembles
 Python.")
     (license license:asl2.0)))
+
+(define-public premake4
+  (package
+    (name "premake")
+    (version "4.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/premake/Premake/"
+                                  version "/premake-" version "-src.zip"))
+              (sha256
+               (base32
+                "1017rd0wsjfyq2jvpjjhpszaa7kmig6q1nimw76qx3cjz2868lrn"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("unzip" ,unzip))) ; for unpacking the source
+    (arguments
+     `(#:make-flags '("CC=gcc")
+       #:tests? #f ; No test suite
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-after 'unpack 'enter-source
+           (lambda _ (chdir "build/gmake.unix") #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (install-file "../../bin/release/premake4"
+                           (string-append (assoc-ref outputs "out") "/bin"))
+             #t)))))
+    (synopsis "Portable software build tool")
+    (description "@code{premake4} is a command line utility that reads a
+scripted definition of a software project and outputs @file{Makefile}s or
+other lower-level build files.")
+    (home-page "https://premake.github.io")
+    (license license:bsd-3)))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
new file mode 100644
index 0000000000..9ebfbbed2d
--- /dev/null
+++ b/gnu/packages/cran.scm
@@ -0,0 +1,44 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages cran)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix utils)
+  #:use-module (guix build-system r))
+
+(define-public r-colorspace
+  (package
+    (name "r-colorspace")
+    (version "1.3-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "colorspace" version))
+       (sha256
+        (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/colorspace")
+    (synopsis "Color space manipulation")
+    (description
+     "This package carries out a mapping between assorted color spaces
+including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
+CIELAB.  Qualitative, sequential, and diverging color palettes based on HCL
+colors are provided.")
+    (license license:bsd-3)))
diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index 6f02d8691d..d02bc20f20 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -57,7 +57,7 @@
 (define-public libsodium
   (package
     (name "libsodium")
-    (version "1.0.12")
+    (version "1.0.13")
     (source (origin
             (method url-fetch)
             (uri (list (string-append
@@ -68,7 +68,7 @@
                         "releases/old/libsodium-" version ".tar.gz")))
             (sha256
              (base32
-              "159givfh5jgli3cifxgssivkklfyfq6lzyjgrx8h4jx5ncdqyr5q"))))
+              "1z93wfg4k5svg8yck6cgdr6ysj91kbpn03nyzwxanncy3b5sq4ww"))))
     (build-system gnu-build-system)
     (synopsis "Portable NaCl-based crypto library")
     (description
diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index cb852e7268..af06ec43f0 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -339,14 +339,14 @@ device-specific programs to convert and print many types of files.")
 (define-public hplip
   (package
     (name "hplip")
-    (version "3.16.11")
+    (version "3.17.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/hplip/hplip/" version
                                   "/hplip-" version ".tar.gz"))
               (sha256
                (base32
-                "094vkyr0rjng72m13dgr824cdl7q20x23qjxzih4w7l9njn0rqpn"))))
+                "0zhhnp3ksd9i2maaqrsjn4p3y7im3llgylp2y8qgmqypm8s7ha40"))))
     (build-system gnu-build-system)
     (home-page "http://hplipopensource.com/")
     (synopsis "HP Printer Drivers")
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 4aafba02f1..3caada25bd 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -293,7 +293,7 @@ mapping from string keys to string values.")
 (define-public mysql
   (package
     (name "mysql")
-    (version "5.7.18")
+    (version "5.7.19")
     (source (origin
              (method url-fetch)
              (uri (list (string-append
@@ -305,7 +305,7 @@ mapping from string keys to string values.")
                           name "-" version ".tar.gz")))
              (sha256
               (base32
-               "18m1mr55k9zmvnyqs0wr50csqsz3scs09fykh60wsml6c3np2p8b"))))
+               "1c8y54yk756179nx4dgg79dijmjdq5n8l057cnqsg70pjdpyfl9y"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index 27193c8bba..34c1061418 100644
--- a/gnu/packages/debug.scm
+++ b/gnu/packages/debug.scm
@@ -32,7 +32,7 @@
   #:use-module (gnu packages llvm)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pretty-print)
-  #:use-module (gnu packages qemu)
+  #:use-module (gnu packages virtualization)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1))
 
diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index e9fb7cc496..ccb13d4fec 100644
--- a/gnu/packages/dns.scm
+++ b/gnu/packages/dns.scm
@@ -443,17 +443,17 @@ served by AS112.  Stub and forward zones are supported.")
 (define-public yadifa
   (package
     (name "yadifa")
-    (version "2.2.4")
+    (version "2.2.5")
     (source
-     (let ((revision "6924"))
+     (let ((build "6937"))
        (origin
          (method url-fetch)
          (uri
           (string-append "http://cdn.yadifa.eu/sites/default/files/releases/"
-                         name "-" version "-" revision ".tar.gz"))
+                         name "-" version "-" build ".tar.gz"))
          (sha256
           (base32
-           "060ydcfn9876bs6p5xi3p1k20ca547f4jck25r5x1hnxjlv7ss03")))))
+           "146fs52izf6dfwsxal3srpwin2yyl41g31cy4pyvbi5mqy2craj7")))))
     (build-system gnu-build-system)
     (native-inputs
      `(("which" ,which)))
@@ -470,10 +470,7 @@ served by AS112.  Stub and forward zones are supported.")
                                "--enable-shared"        "--disable-static"
                                "--enable-messages"      "--enable-ctrl"
                                "--enable-nsec"          "--enable-nsec3"
-                               "--enable-tsig"          "--enable-caching"
-                               ;; NSID is a rarely-used debugging aid, that also
-                               ;; causes the build to fail. Just disable it.
-                               "--disable-nsid")))
+                               "--enable-tsig"          "--enable-caching")))
     (home-page "http://www.yadifa.eu/")
     (synopsis "Authoritative DNS name server")
     (description "YADIFA is an authoritative name server for the @dfn{Domain
@@ -486,14 +483,14 @@ Extensions} (DNSSEC).")
 (define-public knot
   (package
     (name "knot")
-    (version "2.5.2")
+    (version "2.5.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://secure.nic.cz/files/knot-dns/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1sgmw8k9qccc7bgxbwrvahdinj1bjq90iza55rxj199mxsj72ri8"))
+                "13lxxnnw0v7s0q648grz87bwlfwjh5sfbj1qax7jdklalqqy52np"))
               (modules '((guix build utils)))
               (snippet
                '(begin
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 75122af8b3..43de130574 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -2514,6 +2514,35 @@ number.")
 @code{org-mode} to be rendered as UTF-8 characters.")
     (license license:gpl3+)))
 
+(define-public emacs-org-pomodoro
+  (package
+    (name "emacs-org-pomodoro")
+    (version "2.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/lolownia/org-pomodoro/archive/"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1jalsggw3q5kvj353f84x4nl04a5vmq07h75ggppy1627lb31zm4"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-alert" ,emacs-alert)))
+    (home-page "https://github.com/lolownia/org-pomodoro")
+    (synopsis "Pomodoro technique for org-mode")
+    (description "@code{emacs-org-pomodoro} adds very basic support for
+Pomodoro technique in Emacs org-mode.
+
+Run @code{M-x org-pomodoro} for the task at point or select one of the
+last tasks that you clocked time for.  Each clocked-in pomodoro starts
+a timer of 25 minutes and after each pomodoro a break timer of 5
+minutes is started automatically.  Every 4 breaks a long break is
+started with 20 minutes.  All values are customizable.")
+    (license license:gpl3+)))
+
 (define-public emacs-org-trello
   (package
     (name "emacs-org-trello")
@@ -2586,14 +2615,14 @@ package provides a light and a dark variant.")
 (define-public emacs-ahungry-theme
   (package
     (name "emacs-ahungry-theme")
-    (version "1.3.0")
+    (version "1.4.0")
     (source
      (origin (method url-fetch)
              (uri (string-append "https://elpa.gnu.org/packages/ahungry-theme-"
                                  version ".tar"))
              (sha256
               (base32
-               "1p2zaq0s4bbl5cx6wyab24wamw7m0mysb0v47dqjmnvfc25z84rq"))))
+               "1n8k12mfn01f20j0pyd7ycj77x0y3a008xc94frklaaqjc0v26s4"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/ahungry/color-theme-ahungry")
     (synopsis "Ahungry color theme for Emacs")
diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index 866db9687c..b62ab5f6f5 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -327,7 +327,7 @@ Libraries stack (eo, evas, ecore, edje, emotion, ethumb and elementary).")
 (define-public edi
   (package
     (name "edi")
-    (version "0.5.0")
+    (version "0.5.1")
     (source
       (origin
         (method url-fetch)
@@ -335,7 +335,7 @@ Libraries stack (eo, evas, ecore, edje, emotion, ethumb and elementary).")
                             "download/v" version "/edi-" version ".tar.bz2"))
         (sha256
          (base32
-          "1l90x1bw82a0df6r11wd55qizhi99gg0qcljwxga606ahy6ycnkn"))))
+          "0k0ymi9ilhkypqb9pniv365kh3jgbl2g2k0ylvsmisn2jhbqk49a"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 04ae70b07a..748b59c9e1 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -70,7 +70,8 @@
        ("miniupnpc" ,miniupnpc)
        ("openssl" ,openssl)
        ("protobuf" ,protobuf)
-       ("qtbase" ,qtbase)))
+       ;; TODO Build with the modular Qt.
+       ("qt" ,qt)))
     (arguments
      `(#:configure-flags
         (list
diff --git a/gnu/packages/flashing-tools.scm b/gnu/packages/flashing-tools.scm
index f25c25fbfb..127fc795a3 100644
--- a/gnu/packages/flashing-tools.scm
+++ b/gnu/packages/flashing-tools.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017 Jonathan Brielmaier <jonathan.brielmaier@web.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -82,6 +83,37 @@ network/graphics/storage controller cards, and various other
 programmer devices.")
     (license gpl2)))
 
+(define-public 0xffff
+  (package
+    (name "0xffff")
+    (version "0.7")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (string-append "https://github.com/pali/0xffff/archive/"
+                          version ".tar.gz"))
+      (file-name (string-append "0xFFFF" version ".tar.gz" ))
+      (sha256
+       (base32
+        "1g4032c81wkk37wvbg1dxcqq6mnd76y9x7f2crmzqi6z4q9jcxmj"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("libusb",libusb-0.1))) ; doesn't work with libusb-compat
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)) ; no configure
+       #:make-flags (list (string-append "PREFIX=" %output))
+       #:tests? #f)) ; no 'check' target
+    (home-page "https://github.com/pali/0xFFFF")
+    (synopsis "Flash FIASCO images on Maemo devices")
+    (description
+     "The Open Free Fiasco Firmware Flasher (0xFFFF) is a flashing tool
+for FIASCO images.  It supports generating, unpacking, editing and
+flashing of FIASCO images for Maemo devices.  Use it with care.  It can
+brick your device.")
+    (license gpl3+)))
+
 (define-public avrdude
   (package
     (name "avrdude")
diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index ceadbe1c39..51073eff9f 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -472,24 +472,7 @@ variants.")
               (sha256
                (base32
                 "1mkmxq8g2hjcglb3zajfqj20r4r88l78ymsp2xyl5yav8w3f7dz4"))))
-    (build-system trivial-build-system)
-    (arguments
-     `(#:modules ((guix build utils))
-       #:builder
-       (begin
-         (use-modules (guix build utils))
-         (let ((PATH (string-append (assoc-ref %build-inputs "tar")  "/bin:"
-                                    (assoc-ref %build-inputs "gzip") "/bin"))
-               (font-dir (string-append (assoc-ref %outputs "out")
-                                        "/share/fonts/wenquanyi/")))
-           (setenv "PATH" PATH)
-           (mkdir-p font-dir)
-           (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
-           (chdir "wqy-zenhei")
-           (install-file "wqy-zenhei.ttc" font-dir)))))
-    (native-inputs
-     `(("gzip" ,gzip)
-       ("tar" ,tar)))
+    (build-system font-build-system)
     (home-page "http://wenq.org/wqy2/")
     (synopsis "CJK font")
     (description
@@ -516,23 +499,7 @@ ko (Korean) locales for @code{fontconfig}.")
               (sha256
                (base32
                 "0gi1yxqph8xx869ichpzzxvx6y50wda5hi77lrpacdma4f0aq0i8"))))
-    (build-system trivial-build-system)
-    (arguments
-     `(#:modules ((guix build utils))
-       #:builder
-       (begin
-         (use-modules (guix build utils))
-         (let ((PATH (string-append (assoc-ref %build-inputs "tar")  "/bin:"
-                                    (assoc-ref %build-inputs "gzip") "/bin"))
-               (font-dir (string-append (assoc-ref %outputs "out")
-                                        "/share/fonts/wenquanyi")))
-           (mkdir-p font-dir)
-           (setenv "PATH" PATH)
-           (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
-           (install-file "wqy-microhei/wqy-microhei.ttc" font-dir)))))
-    (native-inputs
-     `(("gzip" ,gzip)
-       ("tar" ,tar)))
+    (build-system font-build-system)
     (home-page "http://wenq.org/wqy2/")
     (synopsis "CJK font")
     (description
@@ -594,7 +561,7 @@ languages, plus Greek and Cyrillic.")
 (define-public font-gnu-unifont
   (package
     (name "font-gnu-unifont")
-    (version "10.0.04")
+    (version "10.0.05")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -602,7 +569,7 @@ languages, plus Greek and Cyrillic.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "150p79rq4rzb4pbg2dwcz93k1chzzvm0l0nwh60spw19nfyrxj0p"))))
+                "07sajc32l2knnz6gmd81zxjhcxq8xr6r2kf42wig56vj05s3d1cb"))))
     (build-system gnu-build-system)
     (outputs '("out" ; TrueType version
                "pcf" ; PCF (bitmap) version
diff --git a/gnu/packages/gforth.scm b/gnu/packages/forth.scm
index b2a67ce58c..6d66faf5d6 100644
--- a/gnu/packages/gforth.scm
+++ b/gnu/packages/forth.scm
@@ -17,7 +17,7 @@
 ;;; You should have received a copy of the GNU General Public License
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
-(define-module (gnu packages gforth)
+(define-module (gnu packages forth)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 67f6c55017..dabe951da8 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -380,7 +380,7 @@ support.")
 (define-public tiled
   (package
     (name "tiled")
-    (version "1.0.1")
+    (version "1.0.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/bjorn/tiled/archive/v"
@@ -388,7 +388,7 @@ support.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1y75jmpcf2lv8s3g9v3ghnrwvs2fc4ni7nx74csaylg1g04cwlq7"))))
+                "134xi74xajh38rj1qhmc4x1zmncfdmqb01axnkxh6zs3qz0rxp93"))))
     (build-system gnu-build-system)
     (inputs
      `(("qtbase" ,qtbase)
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index a7f697ece4..2dec9a3951 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm