branch core-updates updated (8d564b8 -> 0cf2b6f)

[guix-commits]

civodul pushed a change to branch core-updates
in repository guix.

      from  8d564b8   gnu: xyce: Use Bison 3.0.
      adds  3e27f47   gnu: Add emacs-skeletor.
      adds  ba567ca   gnu: dealii: Update to 9.1.1.
      adds  f805785   gnu: ubridge: Update to 0.9.16.
      adds  dcedcc7   gnu: youtube-viewer: Update to 3.5.8.
      adds  67e4abc   gnu: smu: Update to 1.5.
      adds  62b3a9b   gnu: smu: Don't use unstable tarball.
      adds  c5b4916   gnu: xtl: Update to 0.6.7.
      adds  aec6c09   gnu: xtensor: Update to 0.20.9.
      adds  3b1ccad   gnu: xtensor: Use HTTPS home page.
      adds  d49375c   gnu: z3: Update to 4.8.6.
      adds  21391f8   compile: Fix race condition on completion progress.
      adds  667c004   gnu: Add stapler.
      adds  f3575ad   gnu: r-ellipsis: Update to 0.3.0.
      adds  8fa7887   gnu: r-callr: Update to 3.3.2.
      adds  33194de   gnu: r-htmltable: Update to 1.13.2.
      adds  65ddcce   gnu: r-curl: Update to 4.2.
      adds  e85f050   gnu: r-recipes: Update to 0.1.7.
      adds  290c75f   gnu: r-tinytex: Update to 0.16.
      adds  9655b1d   gnu: r-ttr: Update to 0.23-5.
      adds  cd5d6e2   gnu: r-shinyace: Update to 0.4.1.
      adds  14c3e7b   gnu: r-sjmisc: Update to 2.8.2.
      adds  e7c8c68   gnu: r-raster: Update to 3.0-7.
      adds  f889a15   gnu: r-bayestestr: Update to 0.3.0.
      adds  6b28675   gnu: r-rcppannoy: Update to 0.0.13.
      adds  7c27558   gnu: r-rcpphnsw: Update to 0.2.0.
      adds  194c682   gnu: r-tidytree: Update to 0.2.8.
      adds  b9d9bc6   gnu: r-spdata: Update to 0.3.2.
      adds  bc9a839   gnu: r-sf: Update to 0.8-0.
      adds  4978222   gnu: r-spdep: Update to 1.1-3.
      adds  cbe42da   gnu: r-optparse: Update to 1.6.4.
      adds  4d86ea4   gnu: r-uwot: Update to 0.1.4.
      adds  446735d   gnu: r-parameters: Update to 0.2.0.
      adds  b1a112f   gnu: r-assertable: Update to 0.2.7.
      adds  76e8d07   gnu: r-mgcv: Update to 1.8-29.
      adds  ebf0b43   gnu: r-digest: Update to 0.6.21.
      adds  b2449a3   gnu: r-knitr: Update to 1.25.
      adds  a2b4039   gnu: r-microbenchmark: Update to 1.4-7.
      adds  2b953e0   gnu: r-devtools: Update to 2.2.1.
      adds  5199720   gnu: r-pkgconfig: Update to 2.0.3.
      adds  a416d68   gnu: r-lambda-r: Update to 1.2.4.
      adds  7d8986c   gnu: r-dt: Update to 0.9.
      adds  d0983f2   gnu: r-iranges: Update to 2.18.3.
      adds  272cb5a   gnu: r-rsamtools: Update to 2.0.1.
      adds  80004ec   gnu: r-rhtslib: Update to 1.16.2.
      adds  b0a5be0   gnu: r-mzr: Update to 2.18.1.
      adds  e0c6c18   gnu: r-gviz: Update to 1.28.3.
      adds  1333eb5   gnu: fc-host-tools: Update to 11.
      adds  2eefe1d   gnu: fc-host-tools: Improve description.
      adds  803f058   gnu: urlscan: Update to 0.9.4.
      adds  4c6d15c   gnu: libgnome-games-support: Update to 1.4.4.
      adds  2d8dca9   gnu: libgnome-games-support: Don't use NAME in source URI.
      adds  737e32a   gnu: libmanette: Update to 0.2.3.
      adds  f4a1de0   gnu: recode: Update to 3.7.6.
      adds  348d8e4   doc: Don't support a risky mix of Guix & Nix.
      adds  f99bc1a   gnu: gthumb: Update to 3.8.1.
      adds  7b6eabc   gnu: gpxsee: Update to 7.12.
      adds  a8f69a2   gnu: emacs-org-download: Update to 0.1.0-2.10c9d7c.
      adds  723fb01   gnu: emacs-dockerfile-mode: Update to 1.2-2.ed73e82.
      adds  beec3e3   gnu: emacs-docker: Update to 1.3.0.
      adds  7dd9f6e   gnu: emacs-mbsync: Update to 0.1.2-2.8f80c26.
      adds  1c2fb2a   gnu: emacs-mbsync: Update to 0.1.2-3.8f80c26.
      adds  44941fd   gnu: libssh: Update to 0.9.0.
      adds  a3af06a   offload: Include the port number in the machine lock file 
name.
      adds  ada9a19   daemon: Strictly respect timeouts for 'guix offload'.
      adds  569832d   gnu: gpodder: Update to 3.10.10.
      adds  de3896f   gnu: Add ell.
      adds  135b573   gnu: emacs-helm-company: Enable test.
      adds  0263366   gnu: emacs-hydra: Enable test.
      adds  52e62bb   gnu: emacs-prescient: Update to 3.3.
      adds  e038baf   gnu: emacs-tablist: Update to 1.0.
      adds  5510bb0   doc: Add a 'Upgrading Guix' section to the 'Installation' 
chapter.
      adds  9b98308   gnu: sbcl: Update to 1.5.7.
      adds  a799703   gnu: screenfetch: Update to 3.8.0-2.e7b94fc.
      adds  512c169   gnu: mame: Update to 0.214.
      adds  4a06bb3   gnu: perl-carp-clan: Update to 6.08.
      adds  b750a2c   gnu: emacs-dired-du: Update to 0.5.2.
      adds  2a86a18   gnu: emacs-dired-du: Use HTTPS home page.
      adds  e6e03f6   gnu: emacs-on-screen: Update to 1.3.3.
      adds  d485cdc   gnu: geocode-glib: Don't use NAME in source URI.
      adds  5754f0c   gnu: cogl: Don't use NAME in source URI.
      adds  84a1b00   gnu: libgee: Don't use NAME in source URI.
      adds  254cc3c   gnu: znc: Update to 1.7.5.
      adds  65de725   gnu: geocode-glib: Update to 3.26.1.
      adds  af96c41   gnu: Add xftwidth.
      adds  54c69ae   gnu: cogl: Update to 1.22.4.
      adds  4c2c5ae   gnu: libgee: Update to 0.20.2.
      adds  9e4a244   gnu: font-util: Update to 1.3.2.
      adds  0c80f7c   gnu: giac: Update to 1.5.0-65.
      adds  aa2441c   gnu: Remove deprecated "guile2.2-" packages.
      adds  7089f98   syscalls: 'define-as-needed' does not re-export local 
variables.
      adds  89a99d5   gnu: Add "guile3.0-" package variants.
      adds  2d74d42   gnu: emacs-org-ql: Update to 0.2.1.
      adds  18b3ba6   gnu: %default-extra-linux-options: Ensure namespaces are 
enabled in all linux-libre kernels.
      adds  2d03201   gnu: bubblewrap: Update to 0.3.3.
      adds  3bc7409   gnu: mcrl2: Update to 201908.0.
      adds  e03b912   gnu: Add mcrl2-minimal.
      adds  cab542c   gnu: emacs-compdef: Update to 0.2-2.67104a3.
      adds  8e5ffeb   gnu: Add emacs-handle.
      adds  8b4615a   ui: 'show-what-to-build' colorizes store file names.
      adds  43f7fd8   pull: Do not use '~*', which 'msgfmt' fails to interpret.
      adds  717b6ba   gnu: Add abcl.
       new  0cf2b6f   Merge branch 'master' into core-updates

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 doc/guix.texi                                      |  51 ++++---
 gnu/local.mk                                       |   3 +-
 gnu/packages/admin.scm                             |   7 +-
 gnu/packages/algebra.scm                           |  10 +-
 gnu/packages/bioinformatics.scm                    |  23 ++--
 gnu/packages/cpp.scm                               |   4 +-
 gnu/packages/cran.scm                              |  88 ++++++------
 gnu/packages/emacs-xyz.scm                         | 147 ++++++++++++++++-----
 gnu/packages/embedded.scm                          |  26 ++--
 gnu/packages/emulators.scm                         |   8 +-
 gnu/packages/games.scm                             |   4 +-
 gnu/packages/gnome.scm                             |  35 +++--
 gnu/packages/gnupg.scm                             |  10 +-
 gnu/packages/gpodder.scm                           |   8 +-
 gnu/packages/gps.scm                               |   6 +-
 gnu/packages/guile-xyz.scm                         |  29 ++--
 gnu/packages/guile.scm                             |  17 ++-
 gnu/packages/java.scm                              |  66 ++++++++-
 gnu/packages/linux.scm                             |  48 +++++++
 gnu/packages/lisp.scm                              |   4 +-
 gnu/packages/mail.scm                              |   5 +-
 gnu/packages/markup.scm                            |  19 +--
 gnu/packages/maths.scm                             |  26 ++--
 gnu/packages/messaging.scm                         |   4 +-
 gnu/packages/networking.scm                        |   4 +-
 gnu/packages/patches/abcl-fix-build-xml.patch      |  50 +++++++
 gnu/packages/patches/dealii-mpi-deprecations.patch |  28 ----
 gnu/packages/patches/mame-rapidjson-fix.patch      |  37 ------
 gnu/packages/pdf.scm                               |  44 +++++-
 gnu/packages/perl.scm                              |   5 +-
 gnu/packages/ssh.scm                               |   7 +-
 gnu/packages/statistics.scm                        |  35 ++---
 gnu/packages/textutils.scm                         |   8 +-
 gnu/packages/tls.scm                               |   5 +-
 gnu/packages/video.scm                             |   4 +-
 gnu/packages/virtualization.scm                    |   7 +-
 gnu/packages/xdisorg.scm                           |  42 ++++++
 gnu/packages/xorg.scm                              |   5 +-
 guix/build/compile.scm                             |   9 +-
 guix/scripts/offload.scm                           |   3 +-
 guix/scripts/pull.scm                              |   2 +-
 guix/ui.scm                                        |  40 ++++--
 nix/libstore/build.cc                              |   2 +-
 43 files changed, 642 insertions(+), 343 deletions(-)
 create mode 100644 gnu/packages/patches/abcl-fix-build-xml.patch
 delete mode 100644 gnu/packages/patches/dealii-mpi-deprecations.patch
 delete mode 100644 gnu/packages/patches/mame-rapidjson-fix.patch