gnu: calibre: Update to 2.58.0.

* gnu/packages/ebook.scm (calibre): Update to 2.58.0.

gnu: python-pyqt: Use 'modify-phases'.

* gnu/packages/qt.scm (python-pyqt)[arguments]: Use 'modify-phases'.

gnu: python-pyqt: Update to 5.6.

* gnu/packages/qt.scm (python-pyqt, python2-pyqt): Update to 5.6.
(python-pyqt)[native-inputs]: Remove qt, add qtbase.
(python2-pyqt)[native-inputs]: Remove qt, add qtbase.

gnu: python-sip: Use 'modify-phases'.

* gnu/packages/qt.scm (python-sip)[arguments]: Use 'modify-phases'.

gnu: python-sip: Update to 4.18.

* gnu/packages/qt.scm (python-sip, python2-sip): Update to 4.18.

gnu: Add emacs-cider.

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

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

gnu: znc: Update to 1.6.3.

* gnu/packages/messaging.scm (znc): Update to 1.6.3.

gnu: services: Add dicod-service.

* gnu/services/dict.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* doc/guix.texi (Various Services): Document it.

gnu: ntp: Update to 4.2.8p8 [fixes CVE-2016-{4953, 4954, 4955, 4956, 4957}].

* gnu/packages/ntp.scm (ntp): Update to 4.2.8p8.

gnu: ntp: Add HTTPS URL.

This works around an HTTP -> HTTPS redirection.

* gnu/packages/ntp.scm (ntp)[source]: Add HTTPS URL.

services: urandom-seed: Refresh seed at boot.

* gnu/services/base.scm (urandom-seed-shepherd-service): Refresh the random
seed unconditionally at boot. Ensure directory structure for %random-seed-file
exists when shutting down.
(%urandom-seed-activation): Remove variable.
(urandom-seed-service-type): Remove deleted variable from list of extensions.

gnu: krona-tools: Correct paths used internally.

* gnu/packages/web.scm (krona-tools)[arguments]: Add 'check' phase.
Correct paths used internally.

profiles: 'profile-derivation' now honors #:system.

Fixes <http://bugs.gnu.org/23682>.
Reported by Ander GM <anthk@openmailbox.org>.

* guix/profiles.scm (profile-derivation): Pass #:system to
'gexp->derivation'.
* tests/guix-environment.sh: Add 'guix environment -s' test.

gnu: Add Wireshark.

* gnu/packages/networking.scm (wireshark): New variable.

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

gnu: Use full SHA1 commit ids.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu, mosaik,
  smithlab-cpp, piranha): Use full SHA1 commit ids.
* gnu/packages/ci.scm (hydra): Likewise.
* gnu/packages/compression.scm (sfarkxtc): Likewise.
* gnu/packages/emacs.scm (emacs-ob-ipython): Likewise.
* gnu/packages/games.scm (mars, emulation-station): Likewise.
* gnu/packages/gnunet.scm (guile-gnunet): Likewise.
* gnu/packages/music.scm (non-sequencer): Likewise.
* gnu/packages/version-control.scm (git-flow, git-test-sequence): Likewise.
* gnu/packages/xorg.scm (xf86-video-intel): Likewise.

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

doc: Mention the 'ip' command.

Suggested by Alex Kost <alezost@gmail.com>.

* doc/guix.texi (Preparing for Installation): Mention 'ip'.

gnu: Add qtbase.

* gnu/packages/qt.scm (qtbase): New variable.

Co-authored by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add emacs-helm.

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

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

gnu: lirc: Update to 0.9.4.

* gnu/packages/lirc.scm (lirc): Update to 0.9.4.
[arguments]: Add 'patch-lirc-make-devinput' and 'patch-doc/Makefile.in'
phases.
[inputs]: Add 'libusb-compat' and 'linux-libre-headers'.

gnu: Add python-twisted and python2-twisted.

* gnu/packages/python.scm (python-twisted, python2-twisted): New variables.