gnu: Add r-fpeek.

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

gnu: emacs: Load package descriptors from packages referenced by subdirs.el

* gnu/packages/aux-files/emacs/guix-emacs.el
(guix-emacs--non-core-load-path): New procedure.
(guix-emacs-autoload-packages): Use it here.
(guix-emacs-load-package-descriptors): New procedure.
* gnu/packages/emacs.scm (emacs)[install-site-start]: Install advice to run
‘guix-emacs-load-package-descriptors’.

build-system: emacs: Keep -pkg.el files.

Partly fixes <https://bugs.gnu.org/48331> -- package descriptions can now be
found in the install directory.

* guix/build/emacs-build-system.scm (%default-exclude): Remove "-pkg\\.el$".

gnu: emacs: Make DocView PDF work out of the box.

* gnu/packages/emacs.scm (emacs)[patch-program-file-names]: Add patches for
the programs “gs”, “dvipdf”, “ps2pdf” and “pdftotext”.
[inputs]: Add ghostscript and poppler.

gnu: emacs: Find real GVFS processes.

* gnu/packages/emacs.scm (emacs)[#:phases]<patch-program-file-names>: Expand
calls to “tramp-compat-process-running-p” so that Guix wrappers are also
matched.

gnu: Add valeronoi.

* gnu/packages/engineering.scm (valeronoi): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: st: Install terminfo files.

* gnu/packages/suckless.scm (st)[native-inputs]: Add ncurses.
[make-flags](TERMINFO): New flag.
[phases](inhibit-terminfo-install): Remove phase.

Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>

gnu: emacs-org: Preserve version information.

* gnu/packages/emacs-xyz.scm (emacs-org)[#:phases]: Prevent install phase from
deleting the version information.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: emacs-consult-notmuch: Update to 0.6.

* gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.6.

gnu: emacs-helm: Update to 3.8.2.

* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.2.

gnu: emacs-vertico: Update to 0.17.

* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.17.

gnu: python-ont-fast5-api: Update to 4.0.0.

* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0.
[source]: Remove bundled plugin binaries.
[arguments]: Install plugin from inputs.
[inputs]: Add vbz-compression.
[propagated-inputs]: Remove python-six; add python-packaging.

gnu: Add vbz-compression.

* gnu/packages/bioinformatics.scm (vbz-compression): New variable.

system: vm: Remove the vga argument.

* gnu/system/vm.scm (common-qemu-options): Remove the "-vga std" argument that
is the default since QEMU 2.2.

Suggested-by: Attila Lendvai <attila@lendvai.name>

guix system vm: Add --no-graphic CLI argument.

It configures QEMU to use the tty it was started in for IO (as opposed to
opening a separate graphical window).  This enables copy-pasting and
scrollback.  Exit QEMU with C-a x.

* gnu/system/vm.scm (system-qemu-image/shared-store-script): Also add the
'-nographic' QEMU argument when called with #:graphic? #false.
* guix/scripts/system.scm (system-derivation-for-action): Propagate
the #:graphic? keyword arg.
(perform-action): Add and propagate the #:graphic? keyword arg.
(show-help): Add --no-graphic CLI arg.
(%options): Process the new --no-graphic CLI arg.
(process-action): Feed in the CLI arg through the #:graphic? keyword arg.
* doc/guix.texi (Invoking guix system): Add example to combine guix system and
invoking the vm start script into one command.  Split the description of the
various options into separate paragraphs.  Add a paragraph to describe
--no-graphic.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>

gnu: cl-coalton: Update to 0.0.1-2.012f6c8.

* gnu/packages/lisp-xyz.scm (sbcl-coalton): Update to 0.0.1-2.012f6c8.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: cl-float-features: Update to 1.0.0-2.c1f86ae.

* gnu/packages/lisp-xyz.scm (sbcl-float-features): Update to 1.0.0-2.c1f86ae.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: ivar: Disable parallel tests.

* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.

gnu: Remove python2-biom-format.

There are no users of this variant, and the current version of biom-format
does not support Python 2.

* gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable.
(python-biom-format)[properties]: Remove field.

gnu: r-flowclust: Add gsl.

* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally
committed comment character.