packages: Reintroduce 'find-newest-available-packages'.

This is a followup to e2a903c807ccacec5925f197ce26f626060e1953.

* gnu/packages.scm (find-newest-available-packages): New procedure.

gnu: php: Disable failing tests on armhf.

* gnu/packages/php.scm (php)[arguments]: Disable failing tests on armhf.

gnu: reptyr: Enable support for aarch64-linux.

* gnu/packages/screen.scm (reptyr)[supported-systems]: Mark
aarch64-linux as supported.

gnu: Add emacs-link-hint.

* gnu/packages/emacs-xyz.scm (emacs-link-hint): New variable.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

gnu: dropbear: Don't use unstable tarball.

* gnu/packages/screen.scm (dropbear)[source]: Use GIT-FETCH and
GIT-FILE-NAME.

gnu: dropbear: Update to 2019.78.

* gnu/packages/ssh.scm (dropbear): Update to 2019.78.

gnu: reptyr: Update to 0.7.0.

* gnu/packages/screen.scm (reptyr): Update to 0.7.0.
[source]: Remove patch.
[arguments]: Add bash completion directory name.
* gnu/packages/patches/reptyr-fix-gcc-7.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: dvdisaster: Use archived source and home page.

* gnu/packages/cdrom.scm (dvdisaster)[source, home-page]:
Use archive.org mirror.

gnu: emacs-dired-hacks: Update to 0.0.1-1.2c12345.

* gnu/packages/emacs-xyz.scm (emacs-dired-hacks): Update to 0.0.1-1.2c12345.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

gnu: gzdoom: Limit supported architectures.

* gnu/packages/games.scm (gzdoom)[supported-systems]: New field.

gnu: Add r-a4.

* gnu/packages/bioconductor.scm (r-a4): New variable.

gnu: Add r-a4base.

* gnu/packages/bioconductor.scm (r-a4base): New variable.

gnu: Add r-a4reporting.

* gnu/packages/bioconductor.scm (r-a4reporting): New variable.

gnu: Add r-a4preproc.

* gnu/packages/bioconductor.scm (r-a4preproc): New variable.

gnu: Add r-a4classif.

* gnu/packages/bioconductor.scm (r-a4classif): New variable.

gnu: Add r-a4core.

* gnu/packages/bioconductor.scm (r-a4core): New variable.

gnu: Add r-annaffy.

* gnu/packages/bioconductor.scm (r-annaffy): New variable.

gnu: Add r-mlinterfaces.

* gnu/packages/bioconductor.scm (r-mlinterfaces): New variable.

gnu: Add r-mpm.

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

gnu: Add r-mlbench.

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

gnu: Add r-threejs.

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

gnu: Add r-gbm.

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

gnu: Add r-ggvis.

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

gnu: Add r-rda.

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

gnu: Add r-pamr.

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

gnu: Add r-varselrf.

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

gnu: ogre: Don't use unstable tarball.

* gnu/packages/graphics.scm (ogre)[source]: Download using git-fetch.

gnu: googletest: Don't use unstable tarball.

* gnu/packages/check.scm (googletest)[source]: Download using git-fetch.
* gnu/packages/crypto.scm (encfs)[arguments]: Adjust accordingly.
* gnu/packages/gnucash.scm (gnucash)[arguments]: Same.
* gnu/packages/terminals.scm (eternalterminal)[arguments]: Same.
* gnu/packages/graphics.scm (ogre)[arguments]: Same. Remove now
unnecessary custom 'pre-build phase.

gnu: hpcguix-web: Fix indentation.

* gnu/packages/web.scm (hpcguix-web): Fix indentation.

gnu: emacs-emmet-mode: Don't use unstable tarball.

* gnu/packages/emacs-xyz.scm (emacs-emmet-mode)[source]: Download using
git-fetch.

gnu: emacs-tablist: Don't use unstable tarball.

* gnu/packages/emacs-xyz.scm (emacs-tablist)[source]: Download using
git-fetch.

gnu: emacs-mmm-mode: Update to 0.5.7.

* gnu/packages/emacs-xyz.scm (emacs-mmm-mode): Update to 0.5.7.

gnu: emacs-mmm-mode: Remove unnecessary phase.

* gnu/packages/emacs-xyz.scm (emacs-mmm-mode)[arguments]: Remove
unnecessary 'autogen phase.

gnu: emacs-mmm-mode: Don't use unstable tarball.

* gnu/packages/emacs-xyz.scm (emacs-mmm-mode)[source]: Don't use
unstable tarball.

gnu: emacs-google-maps: Don't use unstable tarball.

* gnu/packages/emacs-xyz.scm (emacs-google-maps)[source]: Download using
git-fetch.

gnu: emacs-direnv: Don't use unstable tarball.

* gnu/packages/emacs-xyz.scm (emacs-direnv)[source]: Download using
git-fetch.

gnu: emacs-calfw: Don't use unstable tarball.

* gnu/packages/emacs-xyz.scm (emacs-calfw)[source]: Download using
git-fetch.

gnu: emacs-autothemer: Don't use unstable tarball.

* gnu/packages/emacs-xyz.scm (emacs-autothemer)[source]: Download using
git-fetch.

gnu: emacs-ag: Don't use unstable tarball.

* gnu/packages/emacs-xyz.scm (emacs-ag)[source]: Download using
git-fetch.

gnu: font-open-dyslexic: Don't use unstable tarball.

* gnu/packages/fonts.scm (font-open-dyslexic)[source]: Download using
git-fetch.

gnu: font-google-material-design-icons: Don't use unstable tarball.

* gnu/packages/fonts.scm (font-google-material-design-icons)[source]:
Download using git-fetch.

gnu: font-tamzen: Don't use unstable tarball.

* gnu/packages/fonts.scm (font-tamzen)[source]: Download using
git-fetch.
[native-inputs]: Remove gzip, tar.
[arguments]: Adjust build accordingly.

gnu: font-fira-sans: Don't use unstable tarball.

* gnu/packages/fonts.scm (font-fira-sans)[source]: Download using
git-fetch.

gnu: font-adobe-source-han-sans: Don't use unstable tarball.

* gnu/packages/fonts.scm (font-adobe-source-han-sans)[source]: Download
using git-fetch.
[native-inputs]: Remove gzip, tar.
[arguments]: Adjust build accordingly.

gnu: r-geometry: Update to 0.4.1.

* gnu/packages/cran.scm (r-geometry): Update to 0.4.1.
[propagated-inputs]: Fix typo.

gnu: r-feather: Update to 0.3.3.

* gnu/packages/cran.scm (r-feather): Update to 0.3.3.

gnu: Add emacs-relint.

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

gnu: Add emacs-zones.

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

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

gnu: Add r-clusterprofiler.

* gnu/packages/bioconductor.scm (r-clusterprofiler): New variable.

gnu: Add r-enrichplot.

* gnu/packages/bioconductor.scm (r-enrichplot): New variable.

gnu: Add r-dose.

* gnu/packages/bioconductor.scm (r-dose): New variable.

gnu: Add r-ggraph.

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

gnu: Add r-europepmc.

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

gnu: Add r-ggforce.

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

gnu: Add r-urltools.

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

gnu: Add r-polyclip.

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

gnu: Add r-tweenr.

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

gnu: Add r-triebeard.

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

gnu: Add r-ggplotify.

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

gnu: Add r-farver.

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

gnu: Add r-gridgraphics.

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

gnu: Add r-do-db.

* gnu/packages/bioconductor.scm (r-do-db): New variable.

gnu: Add r-fgsea.

* gnu/packages/bioconductor.scm (r-fgsea): New variable.

gnu: Add r-msigdbr.

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

gnu: Add r-xkcd.

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

gnu: Add r-extrafont.

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

gnu: Add r-extrafontdb.

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

gnu: Add r-rttf2pt1.

* gnu/packages/cran.scm (r-rttf2pt1): New variable.

gnu: emacs-debbugs: Update to 0.17.

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

refresh: Update the source code URL.

Reported by Tobias Geerinckx-Rice <me@tobias.gr>
in <https://bugs.gnu.org/35010>.

* guix/upstream.scm (update-package-source): Take 'source' instead of
'version' as the second argument.
[update-expression]: Change to take 'replacements', a list of
replacement pairs.
Compute OLD-URL and NEW-URL and replace the dirname of the OLD-URL with
that of NEW-URL.
* guix/scripts/refresh.scm (update-package): Adjust call to
'update-package-source' accordingly.

upstream: 'package-update' returns the <upstream-source> object.

Fixes a regression introduced in
abd4d6b33dba4de228e90ad15a8efb456fcf7b6e, where CHANGES would no longer
be a thunk.

Reported by Ricardo Wurmus.

* guix/upstream.scm (package-update/url-fetch): Return SOURCE as the
third value instead of CHANGES.
* guix/scripts/refresh.scm (update-package): Adjust accordingly.

gnu: Add r-xyz.

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

scripts: Skip 'guix pull' suggestion when running code from a checkout.

* guix/scripts.scm (warn-about-old-distro): Do not warn when
GUIX_UNINSTALLED is set.

vm: Ask QEMU for more RAM in the VM that makes ISO9660 images.

* gnu/system/vm.scm (iso9660-image): Pass #:memory-size to
'expression->derivation-in-linux-vm'.

services: Deprecate 'xfce-desktop-service'.

* gnu/services/desktop.scm (xfce-desktop-service-type)[default-value]
[description]: New fields.
(xfce-desktop-service): Deprecate.
* gnu/system/examples/desktop.tmpl: Use the (service …) form.
* gnu/installer/services.scm (%desktop-environments): Add TODO comment.
* doc/guix.texi (Desktop Services): Adjust accordingly, and fix spelling
of "Xfce" throughout.

services: Deprecate 'gnome-desktop-service'.

* gnu/services/desktop.scm (gnome-desktop-service-type)[default-value]:
New field.
(gnome-desktop-service): Deprecate.
* gnu/installer/services.scm (%desktop-environments): Use the (service …)
form for GNOME.
* gnu/system/examples/desktop.tmpl: Likewise.
* doc/guix.texi (Desktop Services): Adjust accordingly.

installer: Use the (service …) form for MATE.

* gnu/installer/services.scm (%desktop-environments): Use
'mate-desktop-service-type' for MATE.

installer: Ask for confirmation before formatting partitions.

* gnu/installer/newt/page.scm (run-confirmation-page): New procedure.
* gnu/installer/newt/partition.scm (draw-formatting-page): Call it.

installer: Produce an 'initrd-modules' field if needed.

* gnu/installer/parted.scm (root-user-partition?): New procedure.
(bootloader-configuration): Use it.
(user-partition-missing-modules, initrd-configuration): New procedures.
(user-partitions->configuration): Call 'initrd-configuration'.o
* gnu/installer.scm (not-config?): Rename to...
(module-to-import?): ... this.  Add cases to exclude non-installer and
non-build (gnu …) modules.
(installer-program)[installer-builder]: Add GUIX to the extension list.

installer: Emit 'bootloader' field before 'swap-devices'.

* gnu/installer/parted.scm (user-partitions->configuration): Move
'bootloader' section above 'swap-devices'.

gnu: Add emacs-webfeeder.

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

gnu: trim-galore: Add pigz.

* gnu/packages/bioinformatics.scm (trim-galore)[inputs]: Add pigz.
[arguments]: Embed reference to pigz.

gnu: trim-galore: Fix test for Python.

* gnu/packages/bioinformatics.scm (trim-galore)[arguments]: Replace
"configure" phase to skip ill-advised test for Python.

gnu: hdf-java: Adjust indentation.

* gnu/packages/maths.scm (hdf-java): Adjust indentation.

gnu: hdf-java: Fix build.

* gnu/packages/maths.scm (hdf-java)[arguments]: Fix copying from automake;
substitute embedded hdf5 version number.

gnu: hdf-java: Use INVOKE.

* gnu/packages/maths.scm (hdf-java)[arguments]: Unconditionally return #T from
build phases.

gnu: r-rhdf5lib: Update to 1.4.3.

* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.3.

gnu: r-genomicfeatures: Update to 1.34.7.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.7.

gnu: r-hdf5r: Update to 1.1.1.

* gnu/packages/cran.scm (r-hdf5r): Update to 1.1.1.

gnu: r-caret: Update to 6.0-82.

* gnu/packages/statistics.scm (r-caret): Update to 6.0-82.

gnu: r-gtable: Update to 0.3.0.

* gnu/packages/statistics.scm (r-gtable): Update to 0.3.0.

gnu: grantlee: Delete broken tests.

* gnu/packages/qt.scm (grantlee)[arguments]: Add phase "delete-broken-tests".

gnu: Add adanaxis-mush and adanaxisgpl.

* gnu/packages/games.scm (adanaxis-mush, adanaxisgpl): New variables.

gnu: qjackctl: Re-enable xunique.

Version 0.5.6 of qjackctl appears to have fixed the xunique
bug that was causing X hanging when using tiling window managers.

See https://github.com/rncbc/qjackctl/blob/d54a1da43fa197da04d676a110f36a1d4c062252/ChangeLog#L9

* gnu/packages/audio.scm (qjackctl)[arguments]: Remove "--disable-xunique"
from configure-flags.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: python-django-overextends: Use INVOKE.

* gnu/packages/django.scm (python-django-overextends)[arguments]: Use INVOKE.

gnu: python-django-contact-form: Use INVOKE.

* gnu/packages/django.scm (python-django-contact-form)[arguments]: Use INVOKE.

gnu: fritzing: Update to 0.9.3b.

* gnu/packages/engineering.scm (fritzing): Update to 0.9.3b.
[source]: Fetch from git.
[arguments]: Use INVOKE and adjust configure phase.
[inputs]: Add libgit2; fetch fritzing-parts-db via git.

gnu: ldc: Use INVOKE.

* gnu/packages/dlang.scm (ldc)[arguments]: Use INVOKE.

gnu: ldc-bootstrap: Use INVOKE.

* gnu/packages/dlang.scm (ldc-bootstrap)[arguments]: Use INVOKE and
unconditionally return #T from build phase.

gnu: open-adventure: Use INVOKE.

* gnu/packages/games.scm (open-adventure)[arguments]: Use INVOKE.