gnu: Use PACKAGE/INHERIT in more places.

* gnu/packages/algebra.scm (fftwf, fftw-openmpi),
gnu/packages/audio.scm (ztoolkit-rsvg),
gnu/packages/bioinformatics.scm (python2-dendropy),
gnu/packages/boost.scm (boost-with-python2),
gnu/packages/check.scm (python2-mock, python2-pytest-mock),
gnu/packages/cups.scm (hplip-minimal),
gnu/packages/freedesktop.scm (libinput-minimal),
gnu/packages/gettext.scm (gnu-gettext),
gnu/packages/glib.scm (python2-pygobject),
gnu/packages/gnome.scm (gdl-minimal, libsoup-minimal, python2-pyatspi),
gnu/packages/groff.scm (groff-minimal),
gnu/packages/jami.scm (ffmpeg-jami),
gnu/packages/libcanberra.scm (libcanberra/gtk+-2),
gnu/packages/lirc.scm (python2-lirc),
gnu/packages/llvm.scm (clang-runtime-3.5),
gnu/packages/mpi.scm (java-openmpi, openmpi-thread-multiple),
gnu/packages/node.scm (libnode),
gnu/packages/onc-rpc.scm (libtirpc/hurd),
gnu/packages/python-compression.scm (bitshuffle-for-snappy),
gnu/packages/python-crypto.scm (python2-pycrypto, python2-cryptography)
(python2-cryptography, python2-m2crypto),
gnu/packages/python-web.scm (python2-html2text, python2-tornado)
(python2-terminado, python2-ndg-httpsclient, python2-websocket-client)
(python2-rauth, python2-url, python2-s3transfer),
gnu/packages/python-xyz.scm (python2-psutil, python2-serpent)
(python2-humanfriendly, python2-empy, python2-parse-type, python2-polib)
(python2-jsonschema, python2-pystache, python2-cython, python2-numpydoc)
(python2-ipyparallel, python2-traitlets, python2-dbus)
(python2-beautifulsoup4, python2-pep517, python2-flake8, python2-llfuse)
(python2-tlsh, python-file, python2-notebook, python-jupyter-console-minimal)
(python2-contextlib2, python2-promise, python2-anyjson, python2-amqp)
(python2-kombu, python2-billiard, python2-celery, python2-whoosh)
(python2-jellyfish, python-rope, ptpython-2, python2-binaryornot)
(python2-setproctitle, python2-argcomplete, python2-xopen, python2-isort)
(python2-radon, python2-rfc6555, python2-activepapers, python2-send2trash)
(python2-cloudpickle, python2-reparser),
gnu/packages/python.scm (python2-called-python),
gnu/packages/qt.scm (python2-sip, python-pyqt-without-qtwebkit, python2-pyqt)
(python-qscintilla, python-pyqt+qscintilla),
gnu/packages/scanner.scm (sane-backends),
gnu/packages/sdl.scm (guile3.0-sdl2),
gnu/packages/selinux.scm (checkpolicy, libselinux, libsemanage, secilc)
(python-sepolgen, policycoreutils),
gnu/packages/serialization.scm (lua5.1-libmpack, lua5.2-libmpack),
gnu/packages/simulation.scm (fenics),
gnu/packages/statistics.scm (python2-statsmodels),
gnu/packages/texinfo.scm (info-reader),
gnu/packages/wxwidgets.scm (wxwidgets-gtk2, wxwidgets-gtk2-3.1),
gnu/packages/xml.scm (xmlsec-nss),
gnu/packages/xorg.scm (uim-gtk, uim-qt),
guix/build-system/python.scm (package-with-explicit-python)
(strip-python2-variant): Use PACKAGE/INHERIT.

gnu: gvfs: Add 'lint-hidden-cve' property.

* gnu/packages/gnome.scm (gvfs)[properties]: New field, marking
CVE-2019-12447, CVE-2019-12448, and CVE-2019-12449 as fixed.

gnu: gnome-shell: Add 'lint-hidden-cve' property.

* gnu/packages/gnome.scm (gnome-shell)[properties]: New field, marking
CVE-2019-3820 as fixed.

gnu: qemu: Enable reproducible builds.

Fixes <https://issues.guix.gnu.org/47176>.  The solution was suggested by
bonzini on OFTC's #qemu channel.

* gnu/packages/virtualization.scm (qemu)[snippet]: Delete bundled meson copy.
[native-inputs]: Add meson-next.

gnu: Add meson-next.

* gnu/packages/build-tools.scm (meson-next): New variable.

gnu: mpg321: Fix CVE-2019-14247.

* gnu/packages/patches/mpg321-CVE-2019-14247.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/mp3.scm (mpg321)[source]: Apply it.

Signed-off-by: Léo Le Bouter <lle-bout@zaclys.net>
Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: varnish-modules: Update to 0.17.1 [fixes CVE-2021-28543].

* gnu/packages/web.scm (varnish-modules): Update to 0.17.1.

news: Add ‘de’ translation.

gnu: tor: Update to 0.4.5.7 [security fixes].

* gnu/packages/tor.scm (tor): Update to 0.4.5.7.

gnu: snakemake: Add missing inputs.

* gnu/packages/python-xyz.scm (snakemake)[propagated-inputs]: Add
python-nbformat, python-pulp, and python-toposort.

gnu: Add python-toposort.

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

gnu: Add python-pulp.

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

gnu: Add python-amply.

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

gnu: emacs-easy-kill: Update to 0.9.4.

* gnu/packages/emacs-xyz.scm (emacs-easy-kill): Update to 0.9.4.

gnu: emacs-leaf: Update to 4.4.0.

* gnu/packages/emacs-xyz.scm (emacs-leaf): Update to 4.4.0.

gnu: python-pikepdf: Update to 2.9.0.

* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.9.0.

gnu: asymptote: Update to 2.70.

* gnu/packages/plotutils.scm (asymptote): Update to 2.70.

gnu: b4: Fix setup.py version incompatibility.

* gnu/packages/version-control.scm (b4)[source]: Add snippet to not
require too specific of a version.

Reported-by: Kyle Meyer <kyle@kyleam.com>

gnu: libmemcached: Disable test suite.

* gnu/packages/databases.scm (libmemcached): Disable test suite.  Removing
trailing #t.
[phases]{fix-configure}: Remove useless group in pattern.
{disable-failing-tests}: Remove phase.
{build-and-install-html-doc}: Order after the build phase.
[home-page]: Please 'guix lint'.

Reported-by: Simon Tournier <zimon.toutoune@gmail.com>

gnu: hisat2: Update to 2.2.1.

* gnu/packages/bioinformatics.scm (hisat2): Update to 2.2.1.
[source]: Fetch from git repository on Github.
[arguments]: Add phase to build manual; remove trailing #t from other phases.
[native-inputs]: Remove unzip.
[home-page]: Update.
[inputs]: Add python-wrapper.

gnu: Remove MongoDB.

mongodb 3.4.10 has unpatched CVEs and mongodb 3.4.24 has some files in the
release tarball under the SSPL, therefore we cannot provide mongodb while
upholding to good security standards.

It turns out feff80cec3c97a3df2c20d300be12d67f79d4f22 was right since while
the main license file wasnt altered to SSPL, some files in the tree contain
SSPL headers.

* gnu/packages/databases.scm (go-gopkg.in-mgo.v2): Remove.
* gnu/packages/databases.scm (mongo-tools): Remove.
* doc/guix.texi (mongodb-service-type): Remove.
* gnu/tests/databases.scm (%test-mongodb, %mongodb-os, run-mongodb-test):
Remove.
* gnu/services/databases.scm (mongodb-configuration, mongodb-configuration?,
mongodb-configuration-mongodb, mongodb-configuration-config-file,
mongodb-configuration-data-directory, mongodb-service-type,
%default-mongodb-configuration-file, %mongodb-accounts, mongodb-activation,
mongodb-shepherd-service): Remove.
* gnu/packages/databases.scm (mongodb): Remove.

gnu: git: Fix git-manpages native input's hash.

This is a follow-up to commit ab9629b7c91ff7d6392a03512cfe442823267777.

* gnu/packages/version-control.scm (git)[native-inputs]: Fix git-manpages's
hash.

gnu: git: Update to 2.31.0.

* gnu/packages/version-control.scm (git): Update to 2.31.0.

gnu: python2-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].

* gnu/packages/python-web.scm (python2-urllib3)[base]: Base off of
python-urllib3/fixed.

gnu: python-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].

* gnu/packages/python-web.scm (python-urllib3/fixed): New variable.
(python-urllib3)[replacement]: Graft.

gnu: tmsu: Improve installation.

* gnu/packages/file-systems.scm (tmsu)[arguments]: Don't install go
source files. Install binary as tmsu instead of TMSU.

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

gnu: glances: Update to 3.1.6.

* gnu/packages/python-xyz.scm (glances): Update to 3.1.6.

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

syscalls: mounts: Fix a matching bug.

On some systems, the columns in /proc/self/mountinfo look like this:

23 28 0:21 / /proc rw,nosuid,nodev,noexec,relatime shared:11 - proc proc rw

Before this change, the mounts procedure was written with the assumption that
the type and source could always be found in columns 8 and 9, respectively.
However, the proc(5) man page explains that there can be zero or more optional
fields starting at column 7 (e.g., "shared:11" above), so this assumption is
false in some situations.

* guix/build/syscalls.scm (mounts): Update the match pattern to use ellipsis
to match zero or more optional fields followed by a single hyphen.  Remove the
trailing ellipsis, since multiple ellipses are not allowed in the same level.
The proc(5) man page indicates that there are no additional columns, so it is
probably OK to match an exact number of columns at the end like this.

Revert some commits that caused `guix pull` to fail.

This reverts commits 821e6439212f8e94580674eaaff2ce6752cd3b18 through
8f9fd9b70c7bf166d96a4b1dc8b427f8cdf040b5.

Specifically, these commits caused the build failure of
guix-package-cache.drv like this:

------
(repl-version 0 1 1)
Generating package cache for '/gnu/store/vyz7q26kxxd4z70m24rkkqqhaizdla7g-profile'...
(exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (r-biobase)) (value #f))

gnu: r-biocparallel: Build reproducibly.

* gnu/packages/bioconductor.scm (r-biocparallel)[arguments]: Add phase
"make-reproducible".

gnu: r-delayedarray: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here...
* gnu/packages/bioconductor.scm (r-delayedarray): ...to here.

gnu: r-rsamtools: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...to here.

gnu: r-biostrings: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-biostrings): Move from here...
* gnu/packages/bioconductor.scm (r-biostrings): ...to here.

gnu: r-biocparallel: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here...
* gnu/packages/bioconductor.scm (r-biocparallel): ...to here.

gnu: r-biomart: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.

gnu: r-annotationdbi: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here...
* gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.

gnu: r-biobase: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-biobase): Move from here...
* gnu/packages/bioconductor.scm (r-biobase): ...to here.

gnu: r-genomicranges: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here...
* gnu/packages/bioconductor.scm (r-genomicranges): ...to here.

gnu: r-xvector: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-xvector): Move from here...
* gnu/packages/bioconductor.scm (r-xvector): ...to here.

gnu: r-limma: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-limma): Move from here...
* gnu/packages/bioconductor.scm (r-limma): ...to here.

gnu: dbus-c++: Fix command name in description.

* gnu/packages/glib.scm (dbus-c++)[description]: Fix command prefix in
description, and mention the second command installed as well.

news: Add news entry about changes to the QEMU binfmt service.

* etc/news.scm: Add entry.

gnu: qemu: Update to 5.2.0.

* gnu/packages/virtualization.scm (qemu): Update to 5.2.0.
[source]: Re-indent and break long lines, to appease 'guix lint'.
[arguments]{disable-unusable-tests}: Adjust for the new Meson build
system.  Remove patching for a test workaround that has been resolved in
5.2.0.
{patch-test-shebangs, patch-/bin/sh-references}: Combine into...
{patch-embedded-shebangs}: ... this new phase.  Patch the SHELL variable in
the Makefile.
{fix-optionrom-makefile}: New phase.
{install-user-static}: Adjust as the binaries are now symbolic links pointing to their
actual build path.
[native-inputs]: Add ninja.
* gnu/packages/patches/qemu-build-info-manual.patch: Update patch.

Co-authored-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>

services/qemu-binfmt: Use the F flag and the static output of QEMU.

Fixes <https://issues.guix.gnu.org/36117>.

Before this change, the 'binfmt_misc' entries registered for QEMU would not be
usable in container contexts outside of guix-daemon (without manually bind
mounting file names).

For example:

$ docker run --rm arm32v7/debian true
standard_init_linux.go:207: exec user process caused "no such file or directory"

After this change, any container can make use of the QEMU binfmt_misc
registrations, as their corresponding QEMU static binaries are fully
pre-loaded by the kernel.

* gnu/services/virtualization.scm (<qemu-platform>): Define using
'define-record-type*'.
[flags]: New field, which defaults to "F" (fix binary).
(%i386, %i486, %alpha, %arm, %armeb, %sparc, %sparc32plus, %ppc, %ppc64)
(%ppc64le, %m68k, %mips, %mipsel, %mipsn32, %mipsn32el, %mips64, %mips64el)
(%riscv32, %riscv64, %sh4, %sh4eb, %s390x, %aarch64, %hppa): Adjust.
(qemu-binfmt-guix-chroot): Remove variable.
(qemu-binfmt-service-type): Remove the qemu-binfmt-guix-chroot extension.
* gnu/services/qemu-binfmt (qemu-platform->binfmt):  Use the static output of
QEMU.
* doc/contributing.texi (Submitting Patches): Update doc.
* doc/guix.texi (Virtualization Services): Update doc.

gnu: qemu: Add a static output.

The static output is equivalent to what other distributions commonly package
as 'qemu-user-static'.

* gnu/packages/virtualization.scm (qemu)[outputs]: Add a static output.
[phases]{configure}: Configure the main build as an out-of-source build.  Move
all configure flags to ...
[configure-flags]: ... here.  The options explicitly enabling optional
features are removed; the configure script does a good job at enabling all the
features available based on the inputs present and this allows reusing the
flags in variant packages such as qemu-minimal.
{configure-user-static, build-user-static, install-user-static}: New phases.
{patch-test-shebangs}: New phase, extracted from the configure phase.
[native-inputs]: Add glib-static, pcre:static and zlib:static.
(qemu-minimal)[arguments]: Reuse the configure-flags argument.  Rewrite to use
match instead of cond.

gnu: Add glib-static.

* gnu/packages/glib.scm (glib-static): New variable.

gnu: qemu: Fix indentation and remove trailing #t.

* gnu/packages/virtualization.scm (qemu): Fix indentation and remove
trailing #t, appeasing 'guix lint'.

gnu: r-seurat: Fix build.

This is a follow-up to commit e4d4046999304a3693da80cf0fdfe5fd5753b2b7

* gnu/packages/cran.scm (r-seurat)[arguments]: Patch NAMESPACE file.

gnu: xterm: Fix uxterm in pure environments.

* gnu/packages/xorg.scm (xterm)[arguments]: Add a 'patch-file-names
phase.

gnu: sudo: Update to 1.9.6p1.

* gnu/packages/admin.scm (sudo): Update to 1.9.6p1.

gnu: ibus-libpinyin: Update to 1.12.0.

* gnu/packages/ibus.scm (ibus-libpinyin): Update to 1.12.0.
[arguments]: Enable opencc; include setup files on PYTHONPATH; override
PYTHONPATH instead of prefixing.
[inputs]: Add opencc; remove python-pyxdg.
[license]: Change to GPLv3+.

gnu: libpinyin: Update to 2.6.0.

* gnu/packages/ibus.scm (libpinyin): Update to 2.6.0.

gnu: r-genomicfeatures: Update to 1.42.2.

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.

gnu: r-delayedarray: Update to 0.16.2.

* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.

gnu: r-scater: Update to 1.18.6.

* gnu/packages/bioconductor.scm (r-scater): Update to 1.18.6.

gnu: r-cytoml: Update to 2.2.2.

* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.2.2.
[inputs]: Add zlib.

gnu: r-diffbind: Update to 3.0.14.

* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.14.

gnu: r-reportingtools: Update to 2.30.2.

* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.30.2.

gnu: r-genomeinfodb: Update to 1.26.4.

* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.4.

gnu: r-deseq2: Update to 1.30.1.

* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.30.1.

gnu: alacritty: Use more packaged rust libraries.

* gnu/packages/terminals.scm (alacritty)[arguments]: Move
rust-bitflags-1, rust-dirs-2, rust-libc-0.2, rust-unicode-width-0.1,
rust-winapi-0.3 from cargo-inputs ...
[inputs]: ... to here.

gnu: rust-dirs-2: Adapt for new build system.

* gnu/packages/crates-io.scm (rust-dirs-2)[inputs]: Add rust-cfg-if-0.1,
rust-dirs-sys-0.3.

gnu: rust-dirs-sys-0.3: Adapt for new build system.

* gnu/packages/crates-io.scm (rust-dirs-sys-0.3)[inputs]: Add
rust-cfg-if-0.1, rust-libc-0.2, rust-redox-users-0.3, rust-winapi-0.3.

gnu: rust-lazy-static-1: Adapt for new build system.

* gnu/packages/crates-io.scm (rust-lazy-static-1)[inputs]: Add
rust-spin-0.5.

gnu: alacritty: Use packaged rust-wayland-client.

* gnu/packages/terminals.scm (alacritty)[arguments]: Remove
rust-wayland-client-0.28 from cargo-inputs. In custom
'add-absolute-library-references remove substitutions for
rust-wayland-client.
[inputs]: Add rust-wayland-client-0.28.

gnu: rust-glutin-0.26: Adapt for new build system.

* gnu/packages/crates-graphics.scm (rust-glutin-0.26)
[arguments]: Don't skip build. Remove rust-wayland-client-0.28 from
cargo-inputs.
[inputs]: Add rust-wayland-client-0.28, rust-wayland-egl-0.28.

gnu: rust-winit-0.24: Adapt for new build system.

* gnu/packages/crates-graphics.scm (rust-winit-0.24)[arguments]: Move
rust-wayland-client-0.28 from cargo-inputs ...
[inputs]: ... to here.

gnu: rust-wayland-server-0.28: Adapt for new build system.

* gnu/packages/crates-graphics.scm (rust-wayland-server-0.28)
[arguments]: Don't skip build. Remove rust-wayland-commons-0.28,
rust-wayland-scanner-0.28, rust-wayland-sys-0.28 from cargo-inputs.
[inputs]: Add rust-bitflags-1, rust-downcast-rs-1, rust-lazy-static-1,
rust-libc-0.2, rust-nix-0.18, rust-parking-lot-0.18, rust-scoped-tls-1,
rust-wayland-commons-0.28, rust-wayland-scanner-0.28,
rust-wayland-sys-0.28.
(rust-wayland-server-0.23): Adjust accordingly.

gnu: rust-wayland-scanner-0.28: Adapt for new build system.

* gnu/packages/crates-graphics.scm (rust-wayland-scanner-0.28):
[arguments]: Don't skip build. Remove cargo-inputs.
[inputs]: Add rust-proc-macro2-1, rust-quote-1, rust-xml-rs-0.8.
(rust-wayland-scanner-0.23): Adjust accordingly.

gnu: rust-wayland-protocols-0.28: Adapt for new build system.

* gnu/packages/crates-graphics.scm (rust-wayland-protocols-0.28)
[arguments]: Don't skip build. Remove everything from cargo-inputs
except rust-bitflags-1.
[inputs]: Add rust-bitflags-1, rust-wayland-client-0.28,
rust-wayland-commons-0.28, rust-wayland-scanner-0.28,
rust-wayland-server-0.28.
(rust-wayland-protocols-0.23): Adjust accordingly.

gnu: rust-wayland-egl-0.28: Adapt for new build system.

* gnu/packages/crates-graphics.scm (rust-wayland-egl-0.28)
[arguments]: Don't skip build. Remove cargo-inputs.
[inputs]: Add rust-wayland-client-0.28, rust-wayland-sys-0.28.
[native-inputs]: Add pkg-config.

gnu: rust-wayland-cursor-0.28: Adapt for new build system.

* gnu/packages/crates-graphics.scm (rust-wayland-cursor-0.28)
[arguments]: Don't skip build. Remove rust-wayland-client-0.28 from
cargo-inputs.
[inputs]: Add rust-nix-0.18, rust-wayland-client-0.28, rust-xcursor-0.3.

gnu: rust-wayland-client-0.28: Adapt for new build system.

* gnu/packages/crates-graphics.scm (rust-wayland-client-0.28)
[arguments]: Don't skip build. Remove rust-wayland-commons-0.28,
rust-wayland-scanner-0.28, rust-wayland-sys-0.28 from cargo-inputs.
[inputs]: Add rust-bitflags-1, rust-downcast-rs-1, rust-libc-0.2,
rust-nix-0.18, rust-scoped-tls-1, rust-wayland-commons-0.28,
rust-wayland-scanner-0.28, rust-wayland-sys-0.28.
(rust-wayland-client-0.23): Adjust accordingly.

gnu: rust-wayland-commons-0.28: Adapt for new build system.

* gnu/packages/crates-graphics.scm (rust-wayland-commons-0.28)
[arguments]: Don't skip build. Remove rust-wayland-sys-0.28 from
cargo-inputs.
[inputs]: Add rust-nix-0.18, rust-once-cell-1, rust-smallvec-1,
rust-wayland-sys-0.28.
(rust-wayland-commons-0.23): Adjust accordingly.

gnu: rust-libloading-0.6: Update to 0.6.7.

* gnu/packages/crates-io.scm (rust-libloading-0.6): Update to 0.6.
[arguments]: Replace rust-cfg-if-0.1 with 1.
[inputs]: Add rust-cfg-if-1, rust-winapi-0.3.

gnu: dlib-0.4: Update to 0.4.2.

* gnu/packages/crates-io.scm (rust-dlib-0.4): Update to 0.4.2.
[arguments]: Replace rust-libloading-0.5 with 0.6.
[inputs]: Add rust-libloading-0.6.

gnu: rust-proc-macro2-1: Adapt for new build system.

* gnu/packages/crates-io.scm (rust-proc-macro2-1)[inputs]: Add
rust-unicode-xid-0.2.

gnu: rust-winapi-0.3: Adjust for new build system.

* gnu/packages/crates-io.scm (rust-winapi-0.3)[inputs]: Add
rust-winapi-i686-pc-windows-gnu, rust-winapi-x86-64-pc-windows-gnu.

gnu: rust-pkg-config-0.3: Hardcode location of pkg-config.

* gnu/packages/crates-io.scm (rust-pkg-config-0.3)[arguments]: Add phase
to hardcode location of pkg-config binary.

gnu: rust-pkg-config-0.3: Update to 0.3.19.

* gnu/packages/crates-io.scm (rust-pkg-config-0.3): Update to 0.3.19.

gnu: rust-wayland-sys-0.28: Adapt for new build system.

* gnu/packages/crates-graphics.scm (rust-wayland-sys-0.28)[arguments]:
Don't skip build. Add phase to refer explicitly to wayland libraries.
[inputs]: Add rust-dlib-0.4, rust-lazy-static-1, rust-libc-0.2,
rust-pkg-config-0.3.
[propagated-inputs]: Add wayland.
(rust-wayland-sys-0.23): Adjust accordingly.

gnu: rust-quote-1: Update to 1.0.9.

* gnu/packages/crates-io.scm (rust-quote-1): Update to 1.0.9.

build-system/cargo: Don't clobber packaged crates while building.

This fixes an issue where two packages share a common dependent.

* guix/build/cargo-build-system.scm (unpack-rust-crates): Only copy rust
crates into the target directory if there isn't one already there with
the same name.

gnu: r-variantannotation: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here...
* gnu/packages/bioconductor.scm (r-variantannotation): ...to here.

gnu: r-edger: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-edger): Move from here...
* gnu/packages/bioconductor.scm (r-edger): ...to here.

gnu: r-genomeinfodb: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.

gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.

gnu: r-iranges: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-iranges): Move from here...
* gnu/packages/bioconductor.scm (r-iranges): ...to here.

gnu: r-s4vectors: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-s4vectors): Move from here...
* gnu/packages/bioconductor.scm (r-s4vectors): ...to here.

gnu: r-bioccheck: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here...
* gnu/packages/bioconductor.scm (r-bioccheck): ...to here.

gnu: r-grohmm: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-grohmm): Move from here...
* gnu/packages/bioconductor.scm (r-grohmm): ...to here.

gnu: r-biocstyle: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-biocstyle): Move from here...
* gnu/packages/bioconductor.scm (r-biocstyle): ...to here.

gnu: r-biocviews: Move to (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-biocviews): Move from here...
* gnu/packages/bioconductor.scm (r-biocviews): ...to here.

gnu: r-rsqlite: Update to 2.2.4.

* gnu/packages/statistics.scm (r-rsqlite): Update to 2.2.4.

gnu: r-rcpparmadillo: Update to 0.10.2.2.0.

* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.10.2.2.0.

gnu: r-formatr: Update to 1.8.

* gnu/packages/statistics.scm (r-formatr): Update to 1.8.
[native-inputs]: Add r-knitr.

gnu: r-survival: Update to 3.2-9.

* gnu/packages/statistics.scm (r-survival): Update to 3.2-9.

gnu: r-textshaping: Update to 0.3.2.

* gnu/packages/cran.scm (r-textshaping): Update to 0.3.2.

gnu: r-mlr3tuning: Update to 0.8.0.

* gnu/packages/cran.scm (r-mlr3tuning): Update to 0.8.0.

gnu: r-bbotk: Update to 0.3.1.

* gnu/packages/cran.scm (r-bbotk): Update to 0.3.1.