file-systems: Add 'file-system-mapping->bind-mount'.

* gnu/system/file-systems.scm (file-system-mapping->bind-mount): New
procedure.
* gnu/system/linux-container.scm (mapping->file-system): Remove.
(containerized-operating-system)[mapping->fs]: Use
'file-system-mapping->bind-mount' instead of 'mapping->file-system'.
* guix/scripts/environment.scm (launch-environment/container): Likewise.

gnu: guile-json: Texinfoify description.

* gnu/packages/guile.scm (guile-json)[description]: Use Texinfo markup.

gnu: gst-plugins-base: Fix build on 32bit.

* gnu/packages/patches/gst-plugins-base-fix-test-on-32bit.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gstreamer.scm (gst-plugins-base)[source]: Use it.

build: r-build-system: Use deterministic built date.

Fixes <http://bugs.gnu.org/25598>.

* guix/build/r-build-system.scm (install): Pass "--built-timestamp" option to
make build deterministic.

gnu: icedtea-8: Update to 3.3.0 [security fixes].

Fixes CVE-2016-{2183,5546,5547,5548,5549,5552} and
CVE-2017-{3231,3241,3252,3253,3260,3261,3272,3289}.

* gnu/packages/java.scm (icedtea-8): Update to 3.3.0.

gnu: emacs-with-editor: Update to 2.5.10.

* gnu/packages/emacs.scm (emacs-with-editor): Update to 2.5.10.

gnu: giac-xcas: Update to 1.2.3-19.

* gnu/packages/algebra.scm (giac-xcas): Update to 1.2.3-19.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

services: cuirass: Add load-path to cuirass configuration

* gnu/services/cuirass.scm (<cuirass-configuration>): Add load-path field.
(cuirass-shepherd-service): Honor it.
* doc/guix.texi (Continuous Integration): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: cuirass: Update to 0.0.1 revision 4.

* gnu/packages/ci.scm (cuirass): Update to 0.0.1 revision 4.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: joe: remove reference to WordStar.

* gnu/packages/text-editors.scm (joe)[description]: Remove WordStar reference.

gnu: reducelcs: Fix license.

* gnu/packages/maths.scm (reducelcs)[license]: Change to GPL3+.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>

gnu: httpd: Update to 2.4.25 [fixes CVE-2016-{0736,2161,5387,8743}].

* gnu/packages/web.scm (httpd): Update to 2.4.25.
[source]: Remove obsolete patch 'httpd-CVE-2016-8740.patch'.
* gnu/packages/patches/httpd-CVE-2016-8740.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: acme-client: Update to 0.1.16.

* gnu/packages/tls.scm (acme-client): Update to 0.1.16.

gnu: magit: Update to 2.10.1.

* gnu/packages/emacs.scm (magit): Update to 2.10.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

doc: Discuss encrypted swap space.

* doc/guix.texi (Preparing for Installation): Provide an example of how to
  set up (encrypted) swap space using a swap file.
  (operating-system Reference)[swap-devices]: Clarify that swap files are
  supported, too.
  (Mapped Devices): Explain how to use a mapped device with a swap file to
  encrypt swap space.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

doc: Clarify that 'guix pull' can't be easily rolled back.

* doc/guix.texi (Invoking guix pull): Clarify that 'guix pull' can't be
  easily rolled back.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

download: Add GNOME mirror.

* guix/download.scm (%mirrors): Add "https://download.gnome.org".

gnu: Add polkit-gnome.

* gnu/packages/polkit.scm (polkit-gnome): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add neomutt.

* gnu/packages/mail.scm (neomutt): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

services: Make 'static-networking' extensible.

This allows users to statically define several interfaces.

* gnu/services/networking.scm (<static-networking>)[provision]
[name-servers]: Add default values.
(static-networking-shepherd-service)
(static-networking-etc-files)
(static-networking-shepherd-services): New procedures.
(static-networking-service-type): Change to extend both
SHEPHERD-ROOT-SERVICE-TYPE and ETC-SERVICE-TYPE.
(static-networking-service): Remove default value of #:provision.
Implement using 'simple-service'.
* gnu/services/base.scm (%base-services): Replace
'static-networking-service' call with 'service' form.
* doc/guix.texi (Networking Services): Update documentation.

gnu: libevent: Skip tests that fail on 32bit.

* gnu/packages/patches/libevent-2.1-skip-failing-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/libevent.scm (libevent)[source]: Use it.

gnu: r-edger: Add r-statmod to inputs.

* gnu/packages/bioinformatics.scm (r-edger)[propagated-inputs]: Add r-statmod.

gnu: Add freeciv.

* gnu/packages/games.scm (freeciv): New variable.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>

gnu: Add zpaq.

* gnu/packages/compression.scm (zpaq): New variable.

download: Add ‘url-fetch/zipbomb’.

From this suggestion by Ludovic Courtès:
<http://lists.gnu.org/archive/html/guix-devel/2016-09/msg01983.html>

* guix/download.scm (url-fetch/zipbomb): New procedure.

download: url-fetch/tarball: Make ‘name’ truly optional.

* guix/download.scm (url-fetch/tarbomb): Fall back to ‘file-name’ if
‘name’ is #f, like the regular ‘url-fetch’ does.
* gnu/packages/bioinformatics.scm (muscle)[source]: Remove ‘file-name’.
* gnu/packages/engineering.scm (fastcap)[source]: Likewise.
* gnu/packages/scheme.scm (scmutils)[source]: Likewise.

gnu: Add nyx.

* gnu/packages/tor.scm (nyx): New variable.

gnu: tor: Use ‘license:’ prefix instead of #:select.

* gnu/packages/tor.scm (tor, torsocks, privoxy, onionshare)[license]:
Add prefix.

gnu: youtube-dl: Update to 2017.01.29.

* gnu/packages/video.scm (youtube-dl): Update to 2017.01.29.

gnu: python-stem: Update to 1.5.4.

* gnu/packages/python.scm (python-stem): Update to 1.5.4.

gnu: gstreamer: Update to 1.10.3.

* gnu/packages/gstreamer.scm (gstreamer): Update to 1.10.3.
(gst-plugins-base): Likewise.
(gst-plugins-good): Likewise.
(gst-plugins-bad): Likewise.
(gst-plugins-ugly): Likewise.
(gst-libav): Likewise.
(python-gst): Likewise.

gnu: xf86-video-intel: Update to 2.99.917-2-9fe04af.

* gnu/packages/xorg.scm (xf86-video-intel): Update to 2.99.917-2-9fe04af.

gnu: fio: Enable optional helper scripts.

* gnu/packages/benchmark.scm (fio)[arguments]: Add 'patch-paths' and
'wrap-python-scripts' phases.
[inputs]: Add GNUPLOT, PYTHON-2, PYTHON2-NUMPY and PYTHON2-PANDAS.

gnu: fio: Update to 2.17.

* gnu/packages/benchmark.scm (fio): Update to 2.17.

gnu: lftp: Update to 4.7.5.

* gnu/packages/ftp.scm (lftp): Update to 4.7.5.
[source]: Rearrange mirrors.

gnu: mumble: Update to 1.2.19.

* gnu/packages/telephony.scm (mumble): Update to 1.2.19.

gnu: xapian: Update to 1.4.3.

* gnu/packages/search.scm (xapian): Update to 1.4.3.

gnu: dtc: Update description to reference HOWTO.

* gnu/packages/u-boot.scm (dtc)[description]: Modify.

system: More 'file-append' instead of #~(string-append #$thing …).

* gnu/system/shadow.scm (<user-account>)[shell]: Use 'file-append'.
(%base-user-accounts): Likewise.
* gnu/system/grub.scm (%background-image): Likewise.

system: Create home directories once 'file-systems' is up.

Fixes <http://bugs.gnu.org/21108>.
Reported by Andy Patterson <ajpatter@uwaterloo.ca>
and Leo Famulari <leo@famulari.name>.

* gnu/build/activation.scm (activate-users+groups)[activate-user]: Pass
  #:create-home? #t iff CREATE-HOME? and SYSTEM?.
(activate-user-home): New procedure.
* gnu/system/shadow.scm (account-shepherd-service): New procedure.
(account-service-type)[extensions]: Add SHEPHERD-ROOT-SERVICE-TYPE
extension.
* gnu/tests/base.scm (run-basic-test)["home"]
["skeletons in home directories"]: New tests.
* gnu/tests/install.scm (%separate-home-os, %separate-home-os-source)
(%test-separate-home-os): New variables.

gnu: nginx: Update to 1.11.9.

* gnu/packages/web.scm (nginx): Update to 1.11.9.

gnu: mg: Upgrade to 20161005.

* gnu/packages/mg.scm (mg)[source]: Upgrade to 20161005.
[native-inputs]: Add pkg-config.
[inputs]: Add libbsd.
[arguments]: Use modify-phases.  Use #:make-flags rather than patching the
Makefile.  Install tutorial.
[description]:  Clarify relation to GNU Emacs.

gnu: Add JOE.

* gnu/packages/text-editors.scm (joe): New variable.

gnu: libevent: Update to 2.1.8 [security fixes].

* gnu/packages/libevent.scm (libevent): Update to 2.1.8.
[inputs]: Change 'python-wrapper' to 'python-2'. Move 'which' to ...
[native-inputs]: ... here. New field.
(libevent-2.0): New variable.
* gnu/packages/patches/libevent-2.1-dns-tests.patch,
  gnu/packages/patches/libevent-2.0-evdns-fix-remote-stack-overread.patch
  gnu/packages/patches/libevent-2.0-evdns-fix-searching-empty-hostnames.patch
  gnu/packages/patches/libevent-2.0-evutil-fix-buffer-overflow.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/gnuzilla.scm (icecat)[inputs]: Change 'libevent' to 'libevent-2.0'.

lint: Use the "@" syntax for versioned packages in warnings.

* guix/scripts/lint.scm (emit-warning): Use the "@" syntax.

gnu: mdadm: Update to 4.0.

* gnu/packages/linux.scm (mdadm): Update to 4.0.
[arguments]: Add "CC=gcc" to #:make-flags.

gnu: parallel: Update to 20170122.

* gnu/packages/parallel.scm (parallel): Update to 20170122.

gnu: kbd: Update to 2.0.4.

* gnu/packages/linux.scm (kbd): Update to 2.0.4.

gnu: gdb: Update to 7.12.1.

* gnu/packages/gdb.scm (gdb): Update to 7.12.1.

gnu: xcalc: Update to 1.0.6.

* gnu/packages/xorg.scm (xcalc): Update to 1.0.6.

system: Introduce 'file-systems' Shepherd service.

* gnu/services/base.scm (file-system-shepherd-services): New procedure.
(file-system-service-type): Use it as the SHEPHERD-ROOT-SERVICE-TYPE
extension.
(user-processes-service-type): Change to take a single 'grace-delay'
parameter.
(user-processes-service): Remove 'file-systems' parameter.  Pass
GRACE-DELAY as the only value for the service.
* gnu/system.scm (essential-services): Adjust accordingly.

file-systems: Do not read superblocks past the end of a device.

Fixes <http://bugs.gnu.org/25573>.
Reported by Alex Kost <alezost@gmail.com>.

* gnu/build/file-systems.scm (seek*): New procedure.
(read-superblock): Use it instead of 'seek' and ensure it returns
OFFSET.

gnu: Add r-rhdf5.

gnu: Add r-tximport.

gnu: Add ocaml-bin-prot.

* gnu/packages/ocaml.scm (ocaml-bin-prot): New variable.

gnu: Add ocaml-js-build-tools.

* gnu/packages/ocaml.scm (ocaml-js-build-tools): New variable.

gnu: Add ocaml-oasis.

* gnu/packages/ocaml.scm (ocaml-oasis): New variable.

gnu: Add ocaml-fileutils.

* gnu/packages/ocaml.scm (ocaml-fileutils): New variable.

gnu: Add ocaml-expect.

* gnu/packages/ocaml.scm (ocaml-expect): New variable.

gnu: Add ocaml-pcre.

* gnu/packages/ocaml.scm (ocaml-pcre): New variable.

gnu: Add ocaml-batteries.

* gnu/packages/ocaml.scm (ocaml-batteries): New variable.

gnu: Add omake.

* gnu/packages/ocaml.scm (omake): New variable.
* gnu/packages/patches/omake-fix-non-determinism.patch: New file.
* gnu/local.mk (dist_patch_DATA): New patch.

gnu: Add ocamlify.

* gnu/packages/ocaml.scm (ocamlify): New variable.

gnu: Add ocaml-base64.

* gnu/packages/ocaml.scm (ocaml-base64): New variable.

gnu: Add xinetd.

* gnu/packages/web.scm (xinetd): New variable.
* gnu/packages/patches/xinetd-CVE-2013-4342.patch,
gnu/packages/patches/xinetd-fix-fd-leak.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add patches.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: Add neovim.

* gnu/packages/vim.scm (neovim): New variable.

gnu: Add lua5.2-lpeg.

* gnu/packages/lua.scm (lua5.2-lpeg): New variable.

gnu: Add lua5.2-bitop.

* gnu/packages/lua.scm (lua5.2-bitop): New variable.

gnu: Add lua5.2-libmpack.

* gnu/packages/serialization.scm (lua5.2-libmpack): New variable.

gnu: Add lua-libmpack.

* gnu/packages/serialization.scm (lua-libmpack): New variable.

gnu: Add libmpack.

* gnu/packages/serialization.scm (libmpack): New variable.

gnu: gmsh: Update to 2.16.0

* gnu/packages/maths.scm (gmsh): Update to 2.16.0

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: bundler: Update to 1.14.3.

* gnu/packages/ruby.scm (bundler): Update to 1.14.3.

gnu: tor: Add hardening configure-flags.

* gnu/packages/tor.scm (tor)[arguments]: Add '--enable-expensive-hardening',
'enable-gcc-hardening', '--enable-linker-hardening' to configure-flags.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

tests: Really skip /var/run/utmpx test when needed.

* tests/syscalls.scm: Change 'test-ski' to 'test-skip'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: tcpdump: Update to 4.9.0 [security fixes].

Fixes CVE-2016-{7922,7923,7924,7925,7926,7927,7928,7929,7930,7931,7932,7933
7934,7935,7936,7937,7938,7939,7940,7973,7974,7975,7983,7984,7985,7986,7992,7993,
8574,8575} and CVE-2017-{5202,5203,5204,5205,5341,5342,5482,5483,5484,5485,
5486}.

* gnu/packages/admin.scm (tcpdump): Update to 4.9.0.
[source]: Add alternate URL and set the file-name.

gnu: libpcap: Update to 1.8.1.

* gnu/packages/admin.scm (libpcap): Update to 1.8.1.

gnu: bitlbee: Update to 3.5.1 [security fixes].

* gnu/packages/messaging.scm (bitlbee): Update to 3.5.1.
[source]: Remove patches.
(%bitlbee-buddy-nick-change-patch): Remove.
(%bitlbee-always-use-nicks-patch): Remove.

gnu: Add rocksdb.

* gnu/packages/databases.scm (rocksdb): New variable.

gnu: xauth: Update to 1.0.10.

* gnu/packages/xorg.scm (xauth): Update to 1.0.10.

gnu: re2: Update to 2017-01-01.

* gnu/packages/regex.scm (re2): Update to 2017-01-01.
[arguments]: End 'delete-static-library' phase on #t.

gnu: ghc-8: Update to 8.0.2.

* gnu/packages/haskell.scm (ghc-8): Update to 8.0.2.
  [arguments]: Remove #:modules, #:imported-modules and phase
  configure-testsuite.
* gnu/packages/patches/ghc-dont-pass-linker-flags-via-response-files.patch:
  New file.
* gnu/local.mk (dist_patch_DATA): Add it.

gnu: Add reducelcs.

* gnu/packages/maths.scm (reducelcs): New variable.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>

maint: Fix invalid calls to 'info'.

* HACKING <Contributing>: Remove name of the manual from the item argument.
* README <Installation>: Likewise.

gnu: Add r-bsgenome-hsapiens-1000genomes-hs37d5.

* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
  New variable.

gnu: Add light.

* gnu/packages/linux.scm (light): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

environment: Fix setting writable? on networking related files

* guix/scripts/environment.scm (launch-environment/container): Include the
  file name in the call to string=? when deciding if the file should be
  writable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add font-awesome.

* gnu/packages/fonts.scm (font-awesome): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add opencascade-oce.

* gnu/packages/maths.scm (opencascade-oce): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

store: Add 'add-data-to-store'.

* guix/serialization.scm (write-bytevector): New procedure.
(write-string): Rewrite in terms of 'write-bytevector'.
* guix/store.scm (write-arg): Add 'bytevector' case.
(add-data-to-store): New procedure, from former 'add-text-to-store'.
(add-text-to-store): Rewrite in terms of 'add-data-to-store'.
* tests/store.scm ("add-data-to-store"): New test.

gnu: Add catimg.

* gnu/packages/image-viewers.scm (catimg): New variable.

Signed-off-by: Kei Kebreau <kei@openmailbox.org>

gnu: Add dub.

* gnu/packages/ldc.scm (dub): New variable.

gnu: khal: Update to 0.9.1.

* gnu/packages/calendar.scm (khal): Update to 0.9.1.

doc: Fix typo.

* doc/guix.texi (ocaml-build-system): Replace ocaml with OCaml.

doc: Document ocaml-build-system.

* doc/guix.texi (Build Systems) [ocaml-build-system]: New definition.

gnu: emacs-org: Update to 20170124.

* gnu/packages/emacs.scm (emacs-org): Update to 20170124.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: wireshark: Update to 2.2.4.

* gnu/packages/networking.scm (wireshark): Update to 2.2.4.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: asymptote: Update to 2.39

* gnu/packages/plotutils.scm (asymptote): Update to 2.39.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: vim: Update to 8.0.0257.

* gnu/packages/vim.scm (vim): Update to 8.0.0257.

gnu: Add GNU Freetalk.

* gnu/packages/messaging.scm (freetalk): New variable.

Signed-off-by: Mathieu Lirzin <mthl@gnu.org>