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>

gnu: exfat-utils: Update to 1.2.6.

* gnu/packages/mtools.scm (exfat-utils): Update to 1.2.6.

gnu: fuse-exfat: Update to 1.2.6.

* gnu/packages/linux.scm (fuse-exfat): Update to 1.2.6.

build-system/python: 'package-with-explicit-python' uses 'eq?' memoization.

* guix/build-system/python.scm (package-with-explicit-python): Use
'mlambdaq' instead of 'mlambda'.  This does not change the <package>
graph and has no visible impact on performance.

gnu-maintenance: 'gnu-package?' uses 'eq?' memoization.

* guix/gnu-maintenance.scm (gnu-package?): Use 'mlambdaq' instead of
'mlambda'.

packages: Remove 'define-memoized/v' and use 'mlambdaq' instead.

* guix/packages.scm (define-memoized/v): Remove.
(package-transitive-supported-systems): Use 'mlambdaq' instead of
'define-memoized/v'.
(package-input-rewriting)[replace]: Likewise.

Use 'mlambda' instead of 'memoize'.

* gnu/packages.scm (find-newest-available-packages): Use 'mlambda'
instead of (memoize (lambda ...) ...).
* gnu/packages/bootstrap.scm (package-with-bootstrap-guile): Likewise.
* guix/build-system/gnu.scm (package-with-explicit-inputs)[rewritten-input]:
Likewise.
* guix/build-system/python.scm (package-with-explicit-python)[transform]:
Likewise.
* guix/derivations.scm (derivation->string): Likewise.
* guix/gnu-maintenance.scm (gnu-package?): Likewise.
* guix/modules.scm (module-file-dependencies): Likewise.
* guix/scripts/graph.scm (standard-package-set): Likewise.
* guix/scripts/lint.scm (official-gnu-packages*): Likewise.
* guix/store.scm (store-regexp*): Likewise.
* guix/utils.scm (location): Likewise.

Add (guix memoization).

* guix/combinators.scm (memoize): Remove.
* guix/memoization.scm: New file.
* Makefile.am (MODULES): Add it.
* gnu/packages.scm, gnu/packages/bootstrap.scm,
guix/build-system/gnu.scm, guix/build-system/python.scm,
guix/derivations.scm, guix/gnu-maintenance.scm,
guix/import/cran.scm, guix/import/elpa.scm,
guix/modules.scm, guix/scripts/build.scm,
guix/scripts/graph.scm, guix/scripts/lint.scm,
guix/store.scm, guix/utils.scm: Adjust imports accordingly.

doc: Fix typos.

Fixes a regression introduced in commit
f31f1acac2efb4bc6558b604a07b56f826423177.

Reported-by roptat on #guix.

* doc/guix.texi (Invoking guix build): Use "@@" instead of "@".

gnu: Add emacs-mu4e-alert.

* gnu/packages/emacs.scm (emacs-mu4e-alert): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>

gnu: Add emacs-alert.

* gnu/packages/emacs.scm (emacs-alert): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>

gnu: Add emacs-gntp.

* gnu/packages/emacs.scm (emacs-gntp): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>

gnu: Add emacs-log4e.

* gnu/packages/emacs.scm (emacs-log4e): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>

gnu: Add emacs-ht.

* gnu/packages/emacs.scm (emacs-ht): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>

gnu: tvtime: Update to 1.0.11.

* gnu/packages/tv.scm (tvtime): Update to 1.0.11.

gnu: manaplus: Update to 1.7.1.21.

* gnu/packages/games.scm (manaplus): Update to 1.7.1.21.

doc: Fix typos.

* doc/guix.texi: Use "@" for package specifications.

gnu: transmission-remote-cli: Superseded by tremc.

* gnu/packages/bittorrent.scm (transmission-remote-cli)[properties]: New field.

gnu: Add tremc.

* gnu/packages/bittorrent.scm (tremc): New variable.

doc: Clarify "Installing GuixSD in a VM".

* doc/guix.texi (Installing GuixSD in a VM): Mention decompressing the
installation image.

gnu: ldc: Add missing patches.

This is a followup to commit 2429dde57d8461cc8e51dbe6c9d47d795fe6fc9a.

* gnu/packages/patches/ldc-1.1.0-disable-dmd-tests.patch,
gnu/packages/patches/ldc-1.1.0-disable-phobos-tests.patch: New files.

doc: Fix networking instructions in "Installing GuixSD in a VM".

This is a followup to commit c8b543741f422ecf41e7635c6a1c40b3bd55947a.

* doc/guix.texi (Installing GuixSD in a VM): Fix typo.

gnu: assword: Wrap with the GObject typelib of GTK+.

Fixes <https://debbugs.gnu.org/25457>.

* gnu/packages/password-utils.scm (assword)[inputs]: Add 'gtk+'.
[arguments]: Add 'wrap-assword' phase.

gnu: python-xdo: Hardcode the path of 'libxdo.so'.

* gnu/packages/python.scm (python-xdo)[arguments]: Add 'patch-libxdo-path'
phase.

gnu: python-xdo: Add 'python-six' to 'propagated-inputs'.

* gnu/packages/python.scm (python-xdo)[propagated-inputs]: New field.

gnu: gtksourceview-2: Adjust inputs.

Fixes <https://debbugs.gnu.org/25537>.

* gnu/packages/gtk.scm (gtksourceview-2): Move 'shared-mime-info' and
'xorg-server' to 'native-inputs'.  Move 'gtk+-2' to 'propagated-inputs'.

gnu: Add ldc@1.1.0-beta6.

* gnu/packages/ldc.scm (ldc-1.1.0-beta6, ldc-beta): New variables.
* gnu/packages/patches/ldc-1.1.0-disable-dmd-tests.patch: New file.
* gnu/packages/patches/ldc-1.1.0-disable-phobos-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add them.

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

tests: Adjust pypi test to recent importer change.

This is a followup to 2f977d92d3ae517788d3dee98f63680ca149aa1a.

* tests/pypi.scm ("pypi->guix-package"): Don't expect 'python-setuptools' in
'propagated-inputs'.
("pypi->guix-package, wheels"): Likewise.

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

doc: Add missing Upstart command for the binary installation.

Fixes <http://bugs.gnu.org/25551>.
Reported by Jason Self <jason@bluehome.net>.

* doc/guix.texi (Binary Installation): Add 'initctl
reload-configuration' command for Upstart.

doc: Add 'cups-configuration' example with 'hplip'.

* doc/guix.texi (Printing Services): Add example with 'hplip'.

packages: Add 'package-upstream-name' and use it.

* guix/packages.scm (package-upstream-name): New procedure.
* guix/gnu-maintenance.scm (gnu-package?, ftp-server/directory)
(latest-release*, latest-gnome-release)
(latest-kde-release): Use it instead of the inline expression.

import: github: Better tolerate unexpected file extensions.

* guix/import/github.scm (find-extension): Add ".tbz".
(updated-github-url): When 'find-extension' returns #f, use "" for EXT.

gnu-maintenance: 'gnu-package?' ignores invalid URLs.

* guix/gnu-maintenance.scm (gnu-package?)[gnu-home-page?]: Add '>>'
threading macro and use it.

gnu: emacs-emms: Add 'upstream-name' property.

* gnu/packages/emacs.scm (emms)[properties]: New field.

gnu-maintenance: GNU updater handles gnu.org-hosted Emacs packages.

* guix/gnu-maintenance.scm (pure-gnu-package?): If an "emacs-" package
matches 'gnu-hosted?', return true.
(gnu-hosted?): New procedure.

gnu-maintenance: Honor 'upstream-name' property in GNU updater.

* guix/gnu-maintenance.scm (gnu-package?): Honor the 'usptream-name'
property of PACKAGE.
(ftp-server/directory): Likewise.

gnu: offlineimap: Update to 7.0.13.

* gnu/packages/mail.scm (offlineimap): Update to 7.0.13.

gnu: btrfs-progs: Update to 4.9.1.

* gnu/packages/linux.scm (btrfs-progs): Update to 4.9.1.

Update .mailmap entries for ng0.

* .mailmap: Update entries for ng0.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>

gnu: extremetuxracer: Update to 0.7.4.

* gnu/packages/games.scm (extremetuxracer): Update to 0.7.4.

gnu: linux-libre: Update to 4.9.6.

* gnu/packages/linux.scm (%linux-libre-version, %linux-libre-hash)
(linux-libre): Update to 4.9.6.

gnu: linux-libre@4.4: Update to 4.4.45.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.45.

gnu: pius: Update to 2.2.3.

* gnu/packages/gnupg.scm (pius): Update to 2.2.3.
[source]: Switch back to using the tarball release.
[arguments]: End 'set-gpg-file-name' phase on #t.

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

gnu: kakoune: Move reproducibility substitution to source snippet.

* gnu/packages/text-editors.scm (kakoune)[arguments]: Move substitution to ...
[source]: ... here.

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

gnu: openssl-next: Update to 1.1.0d [fixes CVE-2017-{3730, 3731, 3732}].

* gnu/packages/tls.scm (openssl-next): Update to 1.1.0d.

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

gnu: openssl: Replace with openssl-1.0.2k [security fixes].

Fix CVE-2016-7055 and CVE-2017-{3731,3732}.

* gnu/packages/tls.scm (openssl)[replacement]: New field.
(openssl-1.0.2k): New variable.
(openssl-next)[replacement]: New field.

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