gnu: expect: Update to 5.45.3.

* gnu/packages/tcl.scm (expect): Update to 5.45.3.

gnu: deutex: Update to 5.1.0.

* gnu/packages/games.scm (deutex): Update to 5.1.0.

doc: Clarify treatment of the root account.

* doc/guix.texi (operating-system Reference): Clarify the situation of
UID 0.

guix gc: '--verify=foo' is reported as an error.

Fixes <https://bugs.gnu.org/29761>.
Reported by Martin Castillo <castilma@uni-bremen.de>.

* guix/scripts/gc.scm (argument->verify-options): New procedure.
(%options) ["verify"]: Adjust to use it.
* tests/guix-gc.sh: Add test.

gnu: emacspeak: Update to 47.0.

* gnu/packages/emacs.scm (emacspeak): Update to 47.0.
[source]: Remove snippet.
[arguments]: Set SHELL environment variable.

gnu: rsync: Patch CVE-2017-{16548,17433,17434}.

* gnu/packages/rsync.scm (rsync)[source]: Add patches.
[properties]: Mark CVE-2017-15994 as not relevant.
* gnu/packages/patches/rsync-CVE-2017-16548.patch,
gnu/packages/patches/rsync-CVE-2017-17433.patch,
gnu/packages/patches/rsync-CVE-2017-17433-fix-tests.patch,
gnu/packages/patches/rsync-CVE-2017-17434-pt1.patch,
gnu/packages/patches/rsync-CVE-2017-17434-pt2.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register them.

gnu: psm: Update home page URL.

* gnu/packages/linux.scm (psm)[home-page]: Update.
[source](uri): Use it.

gexp: 'computed-file' has a new #:guile parameter.

* guix/gexp.scm (<computed-file>)[guile]: New field.
(computed-file): Add #:guile.
(computed-file-compiler): Honor 'guile'.

gnu: Fix ambiguous 'zip' reference.

* gnu/packages/photo.scm: Hide 'zip' from (srfi srfi-1).

ui: Non-zero exit for compound '&message' and '&error-location' conditions.

* guix/ui.scm (call-with-error-handling): When both 'message?' and
'error-location?' are true, add call to 'exit'.

system: examples: Add a template for BeagleBone Black.

* gnu/system/examples/beaglebone-black.tmpl: New file.
* Makefile.am (EXAMPLES): Add it.
* gnu/system/install.scm (/etc/configuration-files): Add it.

gnu: claws-mail: Update to 3.16.0.

* gnu/packages/mail.scm (claws-mail): Update to 3.16.0.

services: nginx: Allow to add raw content to the server blocks.

* doc/guix.texi (Web Services): Document 'raw-content'.
* gnu/services/web.scm (<nginx-server-configuration>)[raw-content]: New field.
(emit-nginx-server-config): Add it.

services: nginx: Replace 'http-port' and 'https-port' with 'listen'.

* doc/guix.texi (Web Services, Version Control Services): Update accordingly.
* gnu/services/certbot.scm (certbot-nginx-server-configurations): Likewise.
* gnu/services/version-control.scm (%cgit-configuration-nginx): Likewise.
* gnu/services/web.scm (<nginx-server-configuration>,
emit-nginx-server-config): Likewise.
* gnu/tests/version-control.scm (%cgit-configuration-nginx,
%git-nginx-configuration): Likewise.
* gnu/tests/web.scm (%nginx-servers, %php-fpm-nginx-server-blocks): Likewise.

gnu: r-seurat: Update to 2.1.0.

* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.1.0.
[propagated-inputs]: Add r-diffusionmap, r-dtw, r-ggjoy, r-hmisc, r-ica,
r-mass, r-matrix, r-nmf, r-plotly, r-sdmtools, r-tidyr; remove r-plyr,
r-rcppeigen, r-fastica.

gnu: Add r-diffusionmap.

* gnu/packages/graph.scm (r-diffusionmap): New variable.

gnu: Add r-ggjoy.

* gnu/packages/cran.scm (r-ggjoy): New variable.

gnu: Add r-ggridges.

* gnu/packages/cran.scm (r-ggridges): New variable.

gnu: Add r-scatterplot3d.

* gnu/packages/cran.scm (r-scatterplot3d): New variable.

gnu: Add r-sdmtools.

* gnu/packages/cran.scm (r-sdmtools): New variable.