gnu: Add r-catterplots.

* gnu/packages/statistics.scm (r-catterplots): New variable.

gnu: Add salmon.

* gnu/packages/bioinformatics.scm (libstadenio-for-salmon,
spdlog-for-salmon, bwa-for-salmon, salmon): New variables.

gnu: Add sailfish.

* gnu/packages/bioinformatics.scm (sailfish): New variable.

gnu: Add libdivsufsort.

* gnu/packages/bioinformatics.scm (libdivsufsort): New variable.

gnu: Add libgff.

* gnu/packages/bioinformatics.scm (libgff): New variable.

gnu: orpheus: Fix build on aarch64-linux.

* gnu/packages/orpheus.scm (orpheus)[arguments]: Explicitly set the
build target when building on aarch64-linux.

gnu: python-kivy: Update to 1.10.0.

* gnu/packages/python.scm (python-kivy): Update to 1.10.0.
[arguments]: Remove custom "build" phase.

gnu: intel-gpu-tools: Use INVOKE.

* gnu/packages/admin.scm (intel-gpu-tools)[arguments]: Substitute INVOKE
for SYSTEM*.

gnu: intel-gpu-tools: Update to 1.21.

* gnu/packages/admin.scm (intel-gpu-tools): Update to 1.21.

gnu: libtorrent-rasterbar: Update to 1.1.6.

* gnu/packages/bittorrent.scm (libtorrent-rasterbar): Update to 1.1.6.

gnu: spice: Use HTTPS for spice-space.org home pages.

* gnu/packages/spice.scm (spice, spice-vdagent)[home-page]: Use HTTPS

gnu: spice-gtk: Update to 0.34.

* gnu/packages/spice.scm (spice-gtk): Update to 0.34.

gnu: babl: Update to 0.1.40.

* gnu/packages/gimp.scm (babl): Update to 0.1.40.

gnu: babl: Parameterise source URI.

* gnu/packages/gimp.scm (babl)[source]: Use VERSION-MAJOR+MINOR.

gnu: babl: Edit description.

* gnu/packages/gimp.scm (babl)[description]: Edit.

gnu: mktorrent: Update to 1.1.

* gnu/packages/bittorrent.scm (mktorrent): Update to 1.1.
[source, home-page]: Use new URI.

services: herd: 'with-shepherd' no longer leaves an open connection.

* gnu/services/herd.scm (with-shepherd): Use 'dynamic-wind' and close
CONNECTION at the end.

doc: No longer mention Wicd in OS examples.

* gnu/system/examples/desktop.tmpl,
gnu/system/examples/lightweight-desktop.tmpl: Mention NetworkManager
instead of Wicd.

services: Missing services are automatically instantiated.

This simplifies OS configuration: users no longer need to be aware of
what a given service depends on.

See the discussion at
<https://lists.gnu.org/archive/html/guix-devel/2018-01/msg00114.html>.

* gnu/services.scm (missing-target-error): New procedure.
(service-back-edges): Use it.
(instantiate-missing-services): New procedure.
* gnu/system.scm (operating-system-services): Call
'instantiate-missing-services'.
* tests/services.scm ("instantiate-missing-services")
("instantiate-missing-services, no default value"): New tests.
* gnu/services/version-control.scm (cgit-service-type)[extensions]: Add
FCGIWRAP-SERVICE-TYPE.
* gnu/tests/version-control.scm (%cgit-os): Remove NGINX-SERVICE-TYPE
and FCGIWRAP-SERVICE-TYPE instances.
* doc/guix.texi (Log Rotation): Remove 'mcron-service-type' in example.
(Miscellaneous Services): Remove 'nginx-service-type' and
'fcgiwrap-service-type' in Cgit example.

tests: Cgit test waits for /var/run/shepherd/socket.

Previously tests sometimes start before the shepherd was listening,
leading to test failures.

* gnu/tests/version-control.scm (run-cgit-test)[test]: Add "shepherd
socket ready" test.  Rename to two "service running" tests for clarity.