* guix/import/cran.scm (cran-guix-name, cran-recursive-import): New
procedures.
(recursive-import): Remove procedure.
* guix/import/utils.scm (guix-name, recursive-import): New procedures.
* guix/scripts/import/cran.scm (guix-import-cran): Use
'cran-recursive-import' procedure.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.107.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.136.

Synchronise with upstream README.

* gnu/packages/ruby.scm (ruby-asciidoctor)[description]: Add PDF.

* gnu/packages/admin.scm (inxi)[synopsis]: Fix typo.
[description]: Use @code{}.

* gnu/packages/engineering.scm (libngspice): Update to 28.

* gnu/packages/engineering.scm (libngspice): Use a more standard
(C-locale) date format when forging timestamps.

* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Substitute
INVOKE for SYSTEM*.

* gnu/packages/firmware.scm (seabios)[arguments]: Return #t from
the ‘install’ phase.

This adds ~3.6 MiB (3.6%) to gnuastro's now-103.9 MiB closure.

* gnu/packages/astronomy.scm (gnuastro)[inputs]: Add libtiff and zlib.

* gnu/packages/xml.scm (xmlsec): Update to 1.2.26.

* gnu/packages/xdisorg.scm (xcalib): Update to 0.10.
[home-page]: Switch to new upstream.
[source]: Use GIT-FETCH.  Add xcalib-update-man-page.patch.
[build-system]: Switch to CMAKE-BUILD-SYSTEM.
[arguments]: Remove the old build system's arguments.
[inputs]: Add libxrandr.

* gnu/packages/web.scm (perl-net-http): Update to 6.18.

* gnu/packages/web.scm (perl-cgi): Update to 4.38.

* gnu/packages/engineering.scm (qucs)[arguments]<#:phases>[patch-bootstrap]:
New phase.

* gnu/packages/engineering.scm (qucs-s): Update to 0.0.20.
[arguments]: Modify patch-paths phase to work with version 0.0.20.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

* gnu/packages/maths.scm (lapack-3.5): Delete package.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

* gnu/packages/engineering.scm (xyce-serial): Update to 6.8.
[inputs]: Replace lapack-3.5 with lapack.
* gnu/packages/engineering.scm (xyce-prallel):
[arguments]: Update configure flags to work with 6.8 version.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

* gnu/packages/engineering.scm (trilinos-serial-xyce): Update to 12.12.1.
[arguments]: Add delete-tribits phase.
[inputs]: Replace lapack-3.5 with lapack.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

* gnu/packages/engineering.scm (libngspice): Update to 27.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

* gnu/packages/engineering.scm (qucs): Add TODO comment.
[source]: Use git commit b4f27d9.
[native-inputs]: Add autoconf, automake, flex and bison.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.6.0.
[source]: Fetch from bioconductor.
[native-inputs]: Remove r-knitr.
[propagated-inputs]: Add r-biocgenerics, r-biostrings, r-cowplot, r-dbi,
r-ggseqlogo, r-knitr, r-pheatmap, r-proxy, r-rsqlite, and r-s4vectors.

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

* gnu/packages/vulkan.scm (vulkan-icd-loader): New variable.

* gnu/packages/firmware.scm (ovmf)[arguments]: Change custom 'build-ia32
phase to replace 'build. Remove unneeded substitutions in 'configure,
'build and 'build-x64. Shorten 'build and 'build-x64 phases.

* gnu/packages/bioinformatics.scm (star): Update to 2.6.0c.
[source]: Fetch from git.

* gnu/packages/patches/libreoffice-icu.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/libreoffice.scm (libreoffice): Update to 6.0.5.1.
[source]: Add patch.
[inputs]: Add libepubgen and libqxp.
[arguments]: Adjust "prepare-src" phase.

* gnu/packages/libreoffice.scm (orcus): Update to 0.13.4.

* gnu/packages/libreoffice.scm (ixion): Update to 0.13.0.

* gnu/packages/libreoffice.scm (libqxp): New variable.

* gnu/packages/libreoffice.scm (libepubgen): New variable.

* gnu/packages/patches/opensmtpd-fix-crash.patch: New patch.
* gnu/packages/mail.scm (opensmtpd)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.

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

The old downloads.ghostscript.com returns a bogus 200 response, while
the new home page lists a different source.

Reported by Gábor Boskovits <boskovits@gmail.com>.

* gnu/packages/image.scm (jbig2dec)[source, home-page]: Update URIs.

* gnu/packages/scribus.scm (scribus)[arguments]: Re-introduce fix for
  "ImportError: No module named _sysconfigdata_nd".

* gnu/packages/games.scm (colobot): Update to 0.1.11.1-alpha.
[native-inputs]: Update "colobot-data" and "colobot-music" to 0.1.11.1-alpha.

* gnu/packages/scribus.scm (scribus)[inputs]: Add "libzmf".

* gnu/packages/scribus.scm (scribus): Update to 1.5.4.
[source]: Remove patches.
[arguments]: Remove `patch-source' phase.

* gnu/packages/emulators.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.
* gnu/packages/games.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.
* gnu/packages/video.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.
* gnu/packages/vulkan.scm (vulkan-loader): Rename from 'vulkan-icd-loader' to
'vulkan-loader'. Update URL and hash.
* gnu/packages/wine.scm: Change references from 'vulkan-icd-loader' to
'vulkan-loader'.

* gnu/packages/video.scm (you-get): Update to 0.4.1077.