gnu: r-bioccheck: Update to 1.10.1.

* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.10.1.
[propagated-inputs]: Remove "r-knitr" and "r-devtools".

gnu: r-tidyr: Update to 0.6.1.

* gnu/packages/statistics.scm (r-tidyr): Update to 0.6.1.
[propagated-inputs]: Add "r-tibble".

gnu: r-roxygen2: Update to 6.0.1.

* gnu/packages/statistics.scm (r-roxygen2): Update to 6.0.1.
[propagated-inputs]: Add "r-commonmark", "r-desc", "r-r6", and "r-xml2".

gnu: Add r-commonmark.

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

gnu: Add r-desc.

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

gnu: r-readr: Update to 1.1.0.

* gnu/packages/statistics.scm (r-readr): Update to 1.1.0.
[propagated-inputs]: Remove "r-curl".

gnu: r-tibble: Update to 1.3.0.

* gnu/packages/statistics.scm (r-tibble): Update to 1.3.0.
[propagated-inputs]: Remove "r-assertthat".

gnu: r-jsonlite: Update to 1.3.

* gnu/packages/web.scm (r-jsonlite): Update to 1.3.

gnu: ldc-bootstrap: Delete failing test.

* gnu/packages/ldc.scm (ldc-bootstrap)[arguments]: Delete failing test in
build phase.

gnu: guile-aspell: Switch to Guile 2.2.

* gnu/packages/guile.scm (guile-aspell)[inputs]: Replace GUILE-2.0 with
GUILE-2.2.

gnu: guile-aspell: Remove hard-coded "site/2.0" from $(guilesitedir).

* gnu/packages/guile.scm (guile-aspell)[arguments]: Remove
  #:configure-flags.  Add 'set-guilesitedir' phase.

gnu: guile-aspell: Update to 0.4.

* gnu/packages/guile.scm (guile-aspell): Update to 0.4.
[arguments] <#:phases>: Adjust 'set-libaspell-file-name' to new source
tree layout.

system: Support the --root option in 'guix system'.

Fixes <https://bugs.gnu.org/26271>.

* guix/scripts/system.scm (perform-action): Add #:gc-root parameter and
honor it.
(show-help): Document the --root option.
(%options): Add 'root'.
(process-action): Pass 'root' option to perform-action as #:gc-root.
* doc/guix.texi (Invoking guix system): Document '--root'.

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

build: Add and export procedure 'register-root*'.

* guix/scripts/build.scm (register-root*): Add and export it.

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

environment: Deal with single-entry search paths.

This is a followup to fcd75bdbfa99d14363b905afbf914eec20e69df8.

* guix/scripts/environment.scm (create-environment): Check whether
SEPARATOR is #f.

doc: Add "Documentation" section.

* doc/guix.texi (Documentation): New node.

profiles: Generate database file for man pages.

The mandb database file (index.db) is used by the "apropos" (whatis) or
"man -k" commands.  This change introduces a profile hook to generate
such database file.

* guix/profiles.scm (manual-database): New procedure.
(%default-profile-hooks): Add it.

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

build-system/python: 'package-with-explicit-python' uses 'package-mapping'.

* guix/build-system/python.scm (package-with-explicit-python)
[package-variant, cut?]: New procedures.
[transform]: Remove 'mlambdaq' form and input tuple handling.
Use 'package-mapping'.

packages: Add 'package-mapping' and base 'package-input-rewriting' on it.

* guix/packages.scm (package-mapping): New procedure.
(package-input-rewriting): Rewrite in terms of 'package-mapping'.
* tests/packages.scm ("package-mapping"): New test.
* doc/guix.texi (Defining Packages): Document it.

Revert "gnu: openexr: Add IlmBase include sub-directory to 'OpenEXR.pc'."

This reverts commit 01fe019166fe8a925b3bf3b489792b52b1b6ca7a,
which was unneeded because IlmBase is already listed as 'Requires'
in 'OpenEXR.pc'.