gnu: gnome-shell-extension-dash-to-dock: Update to 66.

* gnu/packages/gnome-xyz.scm (gnome-shell-extension-dash-to-dock):
Update to 66.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: python-argcomplete: Update to 1.10.3.

Co-authored-by: pimi <madalinionel.patrascu@mdc-berlin.de>
* gnu/packages/python-xyz.scm (python-argcomplete): Update to 1.10.3.
[arguments]: Patch completion script to keep tool references.
[inputs]: Add "grep" and "which".
[native-inputs]: Add "python-coverage", "python-flake8", "python-wheel", and
"fish".

gnu: vpnc-scripts: Use WRAP-SCRIPT.

* gnu/packages/vpn.scm (vpnc-scripts)[arguments]: Use WRAP-SCRIPT instead of
WRAP-PROGRAM.
[inputs]: Add guile.

gnu: qemu: Build with vde2 support.

* gnu/packages/virtualization.scm (qemu)[inputs]: Add vde2.
* gnu/packages/virtualization.scm (qemu-minimal)[inputs]: Remove vde2 from
  inherited inputs.

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

gnu: Add vde2.

* gnu/packages/networking.scm (vde2): New variable.

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

import: crate: Better handle license expressions.

* guix/import/crate.scm (%dual-license-rx): Removed function.
(crate->guix-package): Handle most of the multi-licensing cases.
* tests/crate.scm (licenses): Add tests for some licenses.

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

import: crate: Add recursive import test.

* tests/crate.scm (test-crate): Rename to...
(test-foo-crate): ... this.
(test-dependencies): Rename to...
(test-foo-dependencies): ... this.
(test-root-crate, test-root-dependencies, test-intermediate-1-crate)
(test-intermediate-1-dependencies, test-intermediate-2-crate)
(test-intermediate-2-dependencies, test-leaf-alice-crate)
(test-leaf-alice-dependencies, test-leaf-bob-crate)
(test-leaf-bob-dependencies): New variables.
("crate->guix-package"): Adjust accordingly.
("cargo-recursive-import"): New test.

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

import: utils: 'recursive-import' returns a list rather than a stream.

* guix/import/utils.scm (recursive-import): Remove 'list->stream' call.
* guix/scripts/import/cran.scm (guix-import-cran): Remove 'stream->list'
call.
* guix/scripts/import/crate.scm (guix-import-crate): Likewise.
* guix/scripts/import/elpa.scm (guix-import-elpa): Likewise.
* guix/scripts/import/gem.scm (guix-import-gem): Likewise.
* guix/scripts/import/hackage.scm (guix-import-hackage): Likewise.
* guix/scripts/import/opam.scm (guix-import-opam): Likewise.
* guix/scripts/import/pypi.scm (guix-import-pypi): Likewise.
* guix/scripts/import/stackage.scm (guix-import-stackage): Likewise.
* tests/gem.scm ("gem-recursive-import"): Likewise.
* tests/import-utils.scm ("recursive-import"): Likewise.

Co-authored-by: Brian Leung <bkleung89@gmail.com>

import: utils: 'recursive-import' returns packages in topological order.

* guix/import/utils.scm (topological-sort): New procedure.
(recursive-import): Rewrite to use it.
* tests/import-utils.scm ("recursive-import"): New test.
* guix/import/cran.scm (cran->guix-package): Always return two values.
* guix/scripts/import/cran.scm (guix-import-cran): Remove 'reverse' call
on 'cran-recursive-import' result.
* guix/scripts/import/crate.scm (guix-import-crate): Likewise.
* guix/scripts/import/elpa.scm (guix-import-elpa): Likewise.
* guix/scripts/import/gem.scm (guix-import-gem): Likewise.
* guix/scripts/import/hackage.scm (guix-import-hackage): Likewise.
* guix/scripts/import/opam.scm (guix-import-opam): Likewise.
* guix/scripts/import/pypi.scm (guix-import-pypi): Likewise.
* guix/scripts/import/stackage.scm (guix-import-stackage): Likewise.
* tests/gem.scm ("gem-recursive-import"): Change the order of package
expressions accordingly.

gnu: Add r-lintr.

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

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

gnu: Add r-cyclocomp.

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

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

gnu: Add r-xmlparsedata.

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

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

gnu: Add r-statcheck.

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

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

gnu: Deprecate kdevplatform package.

* gnu/packages/kde.scm (kdevplatform): Define as a deprecated alias
  for 'kdevelop`.

gnu: kdevelop: Update to 5.4.5.

* gnu/packages/kde.scm(kdevelop): Update to 5.4.5, use qt-build-sytem.
  [native-inputs]: Move shared-mime-info from …
  [inputs] … here; Remove kconfig, kdevplatform, libepoxy; Add apr, apr-util,
  astyle, attica, boost, kconfigwidgets, kservice, libkomparediff2,
  oxygen-icons, qtquickcontrols2, sonnet, subversion; structure and sort list
  of inputs.
  [arguments] Disable tests.  <phases>: Base on phases from qt-build-system.
  {wrap-executable}: Remove.  {add-include-path}: New phase.  {check} Keep it..

gnu: kdevelop-pg-qt: Update to 2.2.0.

* gnu/packages/kde.scm(kdevelop-pg-qt): Update to 2.2.0.

gnu: nss: Fix CVE-2019-11745 via graft.

* gnu/packages/patches/nss-CVE-2019-11745.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/nss.scm (nss/fixed): New variable.
(nss)[replacement]: Add field.

gnu: enchive: Update to 3.5.

* gnu/packages/crypto.scm (enchive): Update to 3.5.
[source]: Replace url-fetch with git-fetch.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: libraft: Update to 0.9.11.

* gnu/packages/cluster.scm (libraft): Update to 0.9.11.
[arguments]: Enable libuv I/O backend. Add phase to skip some tests.
[inputs]: Add libuv.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: xf86-video-intel: Update to 2.99.917-15.f66d395.

* gnu/packages/xorg.scm (xf86-video-intel): Update to 2.99.917-15.f66d395.

gnu: Remove duplicate copyright line.

* gnu/packages/kde.scm: Remove duplicate copyright.

gnu: strace: Update to 5.4.

* gnu/packages/linux.scm (strace): Update to 5.4.

gnu: shadow: Update to 4.8.

* gnu/packages/admin.scm (shadow): Update to 4.8.

gnu: OpenAL: Update home page.

* gnu/packages/audio.scm (openal)[source, home-page]: Use HTTPS.

gnu: OpenAL: Update to 1.20.0.

* gnu/packages/audio.scm (openal): Update to 1.20.0.
[arguments]: Adjust for renamed files.
[native-inputs]: Remove.

gnu: re2: Update to 2019-12-01.

* gnu/packages/regex.scm (re2): Update to 2019-12-01.

gnu: dav1d: Update to 0.5.2.

* gnu/packages/video.scm (dav1d): Update to 0.5.2.

gnu: frei0r-plugins: Update to 1.7.0.

* gnu/packages/video.scm (frei0r-plugins): Update to 1.7.0.
[native-inputs]: Remove LIBTOOL, AUTOCONF and AUTOMAKE.
[arguments]: Remove 'autotools' phase.  Add 'patch-Makefile' phase.

gnu: libsoup: Update to 2.68.3.

* gnu/packages/gnome.scm (libsoup): Update to 2.68.3.

gnu: elogind: Update to 241.4.

* gnu/packages/freedesktop.scm (elogind): Update to 241.4.

gnu: git: Update to 2.24.1 [security fixes].

Includes fixes for CVE-2019-1348, CVE-2019-1349, CVE-2019-1350,
CVE-2019-1351, CVE-2019-1352, CVE-2019-1353, CVE-2019-1354,
CVE-2019-1387, and CVE-2019-19604.

* gnu/packages/version-control.scm (git): Update to 2.24.1.
[native-inputs]: Update git-manpages accordingly.

gnu: cgit: Update git-source to 2.18.2 [security-fixes].

Includes fixes for CVE-2019-1348, CVE-2019-1349, CVE-2019-1350,
CVE-2019-1351, CVE-2019-1352, CVE-2019-1353, CVE-2019-1354,
and CVE-2019-1387

* gnu/packages/version-control.scm (cgit)[inputs]: Update git-source
to 2.18.2.

profiles: Use 'getpwuid' when $USER and $LOGNAME are undefined.

Reported by YOANN P <yoann_mac_donald@hotmail.com>.

* guix/profiles.scm (%profile-directory): Fall back to 'getpwuid' when
"USER" and "LOGNAME" are undefined.

pack: Clarify the /bin/sh requirement for Singularity.

* guix/scripts/pack.scm (squashfs-image)[symlinks*]: New variable.
[build]: Use it instead of SYMLINKS.
(guix-pack): Emit a warning and a hint when "bash" and "bash-minimal"
are missing and PACK-FORMAT is 'squashfs.
* doc/guix.texi (Invoking guix pack): Document the /bin/sh requirement
for Singularity.

gnu: qps: Update to 2.0.0.

* gnu/packages/lxqt.scm (qps): Update to 2.0.0.

Signed-off-by: Brett Gilio <brettg@posteo.net>

gnu: gajim: Fix search for translations.

Fixes <https://bugs.gnu.org/38558>.

* gnu/packages/messaging.scm (gajim)[arguments]: Wrap executables in
XDG_DATA_DIRS.

gnu: Add kjumpingcube.

* gnu/packages/games.scm (kjumpingcube): New variable.

gnu: Add ksquares.

* gnu/packages/games.scm (ksquares): New variable.

gnu: Add kreversi.

* gnu/packages/games.scm (kreversi): New variable.

gnu: Add knavalbattle.

* gnu/packages/games.scm (knavalbattle): New variable.

gnu: Add kollision.

* gnu/packages/games.scm (kollision): New variable.

gnu: Add ksnakeduel.

* gnu/packages/games.scm (ksnakeduel): New variable.

gnu: Add killbots.

* gnu/packages/games.scm (killbots): New variable.

gnu: Add bovo.

* gnu/packages/games.scm (bovo): New variable.

gnu: Add kspaceduel.

* gnu/packages/games.scm (kspaceduel): New variable.

gnu: Add kapman.

* gnu/packages/games.scm (kapman): New variable.

gnu: Add lskat.

* gnu/packages/games.scm (lskat): New variable.

gnu: Add kubrick.

* gnu/packages/games.scm (kubrick): New variable.

gnu: Add kigo.

* gnu/packages/games.scm (kigo): New variable.

gnu: Add kiriki.

* gnu/packages/games.scm (kiriki): New variable.

gnu: Add palapeli.

* gnu/packages/games.scm (palapeli): New variable.

gnu: Add ksirk.

* gnu/packages/games.scm (ksirk): New variable.

gnu: Add granatier.

* gnu/packages/games.scm (granatier): New variable.

gnu: Add bomber.

* gnu/packages/games.scm (bomber): New variable.

gnu: Add knetwalk.

* gnu/packages/games.scm (knetwalk): New variable.

gnu: Add kblackbox.

* gnu/packages/games.scm (kblackbox): New variable.

gnu: Add kfourinline.

* gnu/packages/games.scm (kfourinline): New variable.

gnu: Add kdiamond.

* gnu/packages/games.scm (kdiamond): New variable.

gnu: Add kgoldrunner.

* gnu/packages/games.scm (kgoldrunner): New variable.

gnu: Add klines.

* gnu/packages/games.scm (klines): New variable.

gnu: Add ksudoku.

* gnu/packages/games.scm (ksudoku): New variable.

gnu: Add kblocks.

* gnu/packages/games.scm (kblocks): New variable.

gnu: Add kbounce.

* gnu/packages/games.scm (kbounce): New variable.

gnu: Add konquest.

* gnu/packages/games.scm (konquest): New variable.

gnu: Add kmines.

* gnu/packages/games.scm (kmines): New variable.

gnu: Add kbreakout.

* gnu/packages/games.scm (kbreakout): New variable.

gnu: Add kajongg.

* gnu/packages/games.scm (kajongg): New variable.

gnu: Add kshisen.

* gnu/packages/games.scm (kshisen): New variable.

gnu: Add kmahjongg.

* gnu/packages/games.scm (kmahjongg): New variable.

gnu: Add libkmahjongg.

* gnu/packages/kde-misc.scm (libkmahjongg): New variable.

gnu: Add kolf.

* gnu/packages/games.scm (kolf): New variable.

Co-Authored-By: Hartmut Goebel <h.goebel@crazy-compilers.com>

gnu: Add picmi.

* gnu/packages/games.scm (picmi): New variable.

gnu: Add ktuberling.

* gnu/packages/games.scm (ktuberling): New variable.

gnu: Add libkdegames.

* gnu/packages/kde.scm (libkdegames): New variable.

gnu: libwnck-2: Adjust for changes in inherited package.

This is a followup to d3b406969a0916fed8f7dc7c094de9d523ac12c9.

* gnu/packages/gnome.scm (libwnck-2)[build-system]: Override with
gnu-build-system.
[native-inputs]: Add field to exclude GLIB and GOBJECT-INTROSPECTION.

Signed-off-by: Kei Kebreau <kkebreau@posteo.net>

gnu: gnupg: Update to 2.2.19.

* gnu/packages/gnupg.scm (gnupg): Update to 2.2.19.

gnu: Add r-qtl2.

* gnu/packages/bioinformatics.scm (r-qtl2): New variable.

gnu: terminology: Update to 1.6.0.

* gnu/packages/enlightenment.scm (terminology): Update to 1.6.0.

gnu: efl: Update to 1.23.3.

* gnu/packages/enlightenment.scm (efl): Update to 1.23.3.

tests: processes: Skip tests if running with binfmt.

* tests/processes.scm (binfmt-misc?): New procedure,
(test-assert*): new procedure that skips the test if binfmt-misc? returns

gnu: python-xmltodict: Adjust indentation.

* gnu/packages/xml.scm (python-xmltodict): Correct indentation in the source block.

gnu: python-xmltodict: Update to 0.12.0.

* gnu/packages/xml.scm (python-xmltodict): Update to 0.12.0.

gnu: Add lemonbar.

* gnu/packages/wm.scm (lemonbar): New variable.

Co-authored-by: Brett Gilio <brettg@posteo.net>
Signed-off-by: Brett Gilio <brettg@posteo.net>

gnu: emacs-prop-menu: Use git-reference.

* gnu/packages/emacs-xyz.scm (emacs-prop-menu)[source]: Use git-reference
  instead of url-fetching from MELPA stable.

gnu: emacs-php-mode: Update to 1.22.1.

* gnu/packages/emacs-xyz.scm (emacs-php-mode): Update to 1.22.1.

gnu: emacs-php-mode: Use git-reference.

* gnu/packages/emacs-xyz.scm (emacs-php-mode)[source]: Use git-reference
  instead of url-fetching from MELPA stable.

gnu: emacs-org-noter: Update to 1.4.1.

* gnu/packages/emacs-xyz.scm (emacs-org-noter): Update to 1.4.1.

gnu: emacs-org-noter: Use git-reference.

* gnu/packages/emacs-xyz.scm (emacs-org-noter)[source]: Use git-reference
  instead of url-fetching from MELPA stable.

gnu: delft-icon-theme: Fix broken icons.

* gnu/packages/gnome-xyz (delft-icon-theme): Inherit from Adwaita instead of
  using the (non-existing) GNOME theme.

Signed-off-by: Brett Gilio <brettg@posteo.net>

gnu: tor: Update to 0.4.2.5.

* gnu/packages/tor.scm (tor): Update to 0.4.2.5.

gnu: python-dbusmock: Adjust indentation.

* gnu/packages/python-xyz.scm (python-dbusmock): Correct indentation in
  affected regions.

gnu: python-language-server: Update to 0.31.2.

* gnu/packages/python-xyz.scm (python-language-server): Update to 0.31.2.

gnu: python-jsonrpc-server: Update to 0.3.2.

* gnu/packages/python-xyz.scm (python-jsonrpc-server): Update to 0.3.2.

gnu: Add python-ujson.

* gnu/packages/python-xyz.scm (python-ujson): New variable.

gnu: shepherd: Use Guile with the finalization crash bug-fix.

Fixes <https://bugs.gnu.org/37757>.
Reported by Jesse Gibbons <jgibbons2357@gmail.com>.

* gnu/packages/admin.scm (shepherd)[native-inputs, inputs]: Use
GUILE-2.2/BUG-FIX instead of GUILE-2.2.

gnu: guile: Add 2.2.6-1 with a finalization crash bug-fix.

* gnu/packages/patches/guile-finalization-crash.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/guile.scm (guile-2.2/bug-fix): New variable.

gnu: i2pd: Update to 2.29.0.

* gnu/packages/i2p.scm (i2pd): Update to 2.29.0.
  [arguments]: Disable x25519 test in the 'check' phase.

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

gnu: websocketpp: Add patch for Boost >= 1.70.

* gnu/packages/patches/websocket-fix-for-boost-1.70.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/web.scm (websocketpp): Use it.

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

gnu: bitcoin-abc: Update to 0.20.7.

* gnu/packages/finance.scm (bitcoin-abc): Update to 0.20.7.
  [native-inputs]: Add autoconf, automake and libtool.
  [inputs]: Add qrencode and zlib.
  [arguments]: Remove fix-tests phase.

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

gnu: r-metap: Update to 1.2.

* gnu/packages/cran.scm (r-metap): Move this from here...
* gnu/packages/bioconductor.scm (r-metap): ...to here and update to 1.2.
[propagated-inputs]: Add r-mutoss and r-tfisher.