* gnu/packages/algebra.scm (giac): Update to 1.6.0-25.
[native-inputs]: Add hevea.

* gnu/services/xorg.scm (gdm-pam-service): Mark pam_gdm.so optional.

* gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support for custom URIs.

* gnu/packages/gnome.scm (eolie): Update to 0.9.99.

* gnu/packages/nano.scm (nano): Update to 5.3.

* gnu/packages/ftp.scm (filezilla)[native-inputs]: Add cppunit.

* gnu/packages/ftp.scm (libfilezilla)[arguments]: Add ‘--disable-static’
to #:configure-flags.

* gnu/packages/ftp.scm (libfilezilla): Update to 0.24.1.
[native-inputs]: Add gettext-minimal.
[inputs]: Add gnutls.
(filezilla): Update to 3.50.0.

* gnu/packages/ci.scm (cuirass): Update to 0.0.1-51.cb2c4e3.

* gnu/packages/tex.scm (texlive-fpl): New variable.

* gnu/packages/lisp-xyz.scm (sbcl-xmls, cl-xmls, ecl-xmls): New variables.

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

* gnu/packages/lisp-xyz.scm (sbcl-lambda-fiddle, cl-lambda-fiddle,
  ecl-lambda-fiddle): New variables.

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

* gnu/packages/entr.scm (entr)[arguments]: Use CC-FOR-TARGET.
Use INPUTS instead of WHICH.
[inputs]: Add non-native bash and coreutils packages.

* gnu/packages/entr.scm (entr): Update to 4.6.

* gnu/packages/hardware.scm (ddcutil): Update to 0.9.9.

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

Remove emacs-org-contrib's dependency on SuperCollider by extracting
ob-sclang.el into its own package.

* gnu/packages/emacs-xyz.scm (emacs-org-contrib)[source]: Add snippet
that deletes ob-sclang.el.
[propagated-inputs]: Remove emacs-scel.
(emacs-ob-sclang): New variable.

* gnu/packages/emacs-xyz.scm (emacs-geiser): Update to 0.12.

* gnu/packages/tex.scm (texlive-mathpazo)[inherit]: Add directory.

This brings Python 3 support & fixes building against goffice@0.10.48.

* gnu/packages/gnome.scm (gnumeric): Update to 1.12.48.
[inputs]: Replace python-2 and python2-gobject with python and
python-pygobject, respectively.

* gnu/packages/perl.scm (perl-digest-md5): Update to 2.58.
[arguments]: Remove field.

* gnu/packages/dns.scm (knot)[source]: Snip out bundled libbpf sources.
[arguments]: Add ‘--enable-xdp=auto’ to #:configure-flags.
Add a ‘link-missing-libbpf-dependency’ phase.
[inputs]: Add libbpf and libelf.

* gnu/packages/dns.scm (knot)[arguments]: Fix a typo in
the #:configure-flags.

* gnu/packages/dns.scm (knot)[source]: Apply patch from upstream that
helps ensure the "test_net_shortwrite" test suite can complete
regardless of platform or configuration.
* gnu/packages/patches/knot-test_net_shortwrite-ensure-connection.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>

* gnu/packages/dns.scm (knot)[arguments]: Add "build-info" and
"install-info" phases.
[native-inputs]: Add texinfo and python-sphinx.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>

* gnu/packages/dns.scm (knot)[inputs]: Add nghttp2:lib.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>

This reverts commit 2fb12dd1, which
causes the 'svn export' command to fail with:

svn: E155000: Destination directory exists; please remove the directory
or use --force to overwrite

* gnu/packages/tex.scm (texlive-mathpazo): New variable.

* gnu/packages/vim.scm (vim): Update to 8.2.1805.

* gnu/packages/linux.scm (pipewire): Update to 0.3.13.

* gnu/packages/language.scm (praat): Update to 6.1.26.

* gnu/packages/terminals.scm (libtsm)[source]: Snip xkbcommon-keysyms.h.

* gnu/packages/terminals.scm (libtsm)[inputs]: Move check & libxkbcommon
from here…
[native-inputs]: …to here.

* gnu/packages/games.scm (stockfish): Update to 12.
[inputs]: Add fetching of the official neural network file.
[arguments]: Add phase 'copy-net to copy this file and embed it.

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

* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.4.

* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.3.

* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.1.

* gnu/packages/bioconductor.scm (r-bgx): Update to 1.54.1.

* gnu/packages/bioconductor.scm (r-xcms): Update to 3.10.2.

* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.12.5.