Add more missing (ice-9 format) imports.

* gnu/machine/ssh.scm: Import (ice-9 format).
* guix/scripts/graph.scm: Likewise.
* guix/scripts/system/search.scm: Likewise.
* guix/remote.scm: Likewise.

gnu: doctest: Update to 2.4.0.

* gnu/packages/check.scm (doctest): Update to 2.4.0.

gnu: asciidoc-py3: Update to 9.0.1.

* gnu/packages/documentation.scm (asciidoc-py3): Update to 9.0.1.

gnu: git: Update to 2.27.0.

* gnu/packages/version-control.scm (git): Update to 2.27.0.
[arguments]: Adjust xmlto substitution for upstream changes.

doc: cookbook: Fix encoding of "André".

This is a followup to f8945734a5abff69644284231cc47fb67456657b.

* doc/guix-cookbook.texi: Encode "André" as UTF-8, not ISO-8859-1.

gnu: mumble: Fix mumble-overlay.

The canonical mumble-overlay script searches for libmumble.so.1 in various
directories, none of which are relevant in Guix installations and
additionally does some work to match the architecture of the library to that
of the command that will be executed.
This work is unnecessary in Guix and only causes the script to fail, so we
instead just hardcode the path.

* gnu/packages/telephony.scm (mumble)[#:phases]: Add fix-mumble-overlay.

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

channels: Error out when the 'guix' channel lacks an introduction.

* guix/channels.scm (latest-channel-instance): Raise an error instead of
warning when 'guix is unauthenticated.
* tests/channels.scm ("latest-channel-instances, missing introduction for 'guix'"):
New test.

tests: Allow 'tests/git-authenticate.scm' to run when git/gpg is missing.

Fixes <https://bugs.gnu.org/42077>.
Reported by Jan Nieuwenhuizen <janneke@gnu.org>.

The typo was introduced in 7b06781a58326f251c4af6340379d68e3cb98adb.

* tests/git-authenticate.scm <top level>: Remove call to 'which'
around (gpg+git-available?).

processes: Write to $PAGER.

* guix/ui.scm (with-paginated-output-port): Export.
* guix/scripts/processes.scm (guix-processes): Use it instead of writing
directly to (current-output-port).

services: virtualization: Export hurd-vm-configuration accessors.

* gnu/services/virtualization.scm (hurd-vm-id, hurd-vm-options): Rename export
to ...
(hurd-vm-configuration-id, hurd-vm-configuration-options): ... these correct
accessor names.
(hurd-vm-configuration?, hurd-vm-configuration-os, hurd-vm-configuration-qemu,
hurd-vm-configuration-image, hurd-vm-configuration-disk-size,
hurd-vm-configuration-memory-size, hurd-vm-configuration-options,
hurd-vm-configuration-id, hurd-vm-configuration-net-options): Export record
predicate and accessors.

gnu: warzone2100: Update to 3.4.0.

* gnu/packages/games.scm (warzone2100): Update to 3.4.0.

gnu: emacs-elpher: Update to 2.9.1.

* gnu/packages/emacs-xyz.scm (emacs-elpher): Update to 2.9.1.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add emacs-libyaml.

* gnu/packages/emacs-xyz.scm (emacs-libyaml): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Remove rust-rustc-hash-1.0.

* gnu/packages/crates-io.scm (rust-rustc-hash-1.0): Remove variable.
(rust-hashbrown-0.5, rust-rusttype-0.8)
[arguments]: Replace rust-rustc-hash-1.0 with 1.1.

gnu: rust-bincode-1: Update to 1.3.1.

* gnu/packages/crates-io.scm (rust-bincode-1): Update to 1.3.1.

gnu: Rename rust-bincode-1.2 to rust-bincode-1.

* gnu/packages/crates-io.scm (rust-bincode-1.2): Rename to ...
(rust-bincode-1): ... this.
(rust-encoding-rs-0.8, rust-generic-array-0.14, rust-generic-array-0.13,
rust-parking-lot-0.10, rust-parking-lot-0.9, rust-parking-lot-0.8,
rust-parking-lot-0.7, rust-rand-0.5, rust-rand-isaac-0.2,
rust-rand-isaac-0.1, rust-rand-pcg-0.2, rust-rand-pcg-0.1,
rust-rand-xorshift-0.2, rust-rand-xorshift-0.1, rust-rand-xoshiro-0.4,
rust-rand-xoshiro-0.3, rust-serde-bytes-0.11, rust-smallvec-1,
rust-smallvec-0.6, rust-syntect-3.3, rust-uuid-0.7)[arguments]: Adjust accordingly.

gnu: Remove rust-bincode-1.1.

* gnu/packages/crates-io.scm (rust-bincode-1.1): Remove variable.
(rust-encoding-rs-0.8, rust-generic-array-0.13, rust-parking-lot-0.10,
rust-parking-lot-0.9, rust-parking-lot-0.8, rust-parking-lot-0.7,
rust-rand-0.5, rust-rand-isaac-0.2, rust-rand-isaac-0.1,
rust-rand-pcg-0.2, rust-rand-pcg-0.1, rust-rand-xorshift-0.2,
rust-rand-xorshift-0.1, rust-rand-xoshiro-0.4, rust-rand-xoshiro-0.3,
rust-serde-bytes-0.11, rust-smallvec-1, rust-smallvec-0.6,
rust-uuid-0.7) [arguments]: Replace rust-bincode-1.1 with 1.2.

gnu: rust-csv-core-0.1: Fix build.

* gnu/packages/crates-io.scm (rust-csv-core-0.1)[arguments]: Replace
rust-arrayvec-0.4 with 0.5 in cargo-development-inputs.

gnu: Rename rust-memchr-2.3 to rust-memchr-2.

* gnu/packages/crates-io.scm (rust-memchr-2.3): Rename to ...
(rust-memchr-2): ... this.
(rust-memchr-1.0): Inherit from rust-memchr-2.
(rust-aho-corasick-0.7, rust-aho-corasick-0.6, rust-bstr-0.2,
rust-csv-core-0.1, rust-futures-util-0.3, rust-futures-util-preview-0.3,
rust-grep-matcher-0.1, rust-ignore-0.4, rust-nom-5, rust-nom-4.2,
rust-odds-0.3, rust-pulldown-cmark-0.4, rust-regex-1, rust-regex-0.2,
rust-rusqlite-0.19, rust-tokio-0.2,
rust-aho-corasick-0.7, rust-aho-corasick-0.6, rust-bstr-0.2,
rust-csv-core-0.1, rust-futures-util-0.3, rust-futures-util-preview-0.3,
rust-grep-matcher-0.1, rust-ignore-0.4, rust-nom-5, rust-nom-4.2,
rust-odds-0.3, rust-pulldown-cmark-0.4, rust-regex-1, rust-regex-0.2,
rust-rusqlite-0.19, rust-tokio-0.2)[arguments]: Adjust accordingly.

gnu: Remove rust-memchr-2.2.

* gnu/packages/crates-io.scm (rust-memchr-2.2): Remove variable.
(rust-memchr-1.0): Inherit from rust-memchr-2.3.
(rust-aho-corasick-0.6, rust-bstr-0.2, rust-futures-util-0.3,
rust-futures-util-preview-0.3, rust-grep-matcher-0.1, rust-ignore-0.4,
rust-nom-5, rust-nom-4.2, rust-odds-0.3, rust-pulldown-cmark-0.4,
rust-regex-0.2, rust-rusqlite-0.19, rust-tokio-0.2)[arguments]: Use
rust-memchr-2.3 instead of rust-memchr-2.2.

gnu: Rename rust-unicase-2.6 to rust-unicase-2.

* gnu/packages/crates-io.scm (rust-unicase-2.6): Rename to ...
(rust-unicase-2): ... this.
(rust-unicase-1): Inherit from rust-unicase-2.
(rust-http-req-0.5, rust-phf-shared-0.8, rust-pulldown-cmark-0.4,
rust-rusqlite-0.19)[arguments]: Adjust accordingly.

gnu: Remove rust-unicase-2.4.

* gnu/packages/crates-io.scm (rust-unicase-2.4): Remove variable.
(rust-unicase-1): Inherit from rust-unicase-2.6.
(rust-http-req-0.5, rust-pulldown-cmark-0.4, rust-rusqlite-0.19)
[arguments]: Use rust-unicode-2.6.

gnu: rust-typenum-1: Update to 1.12.0.

* gnu/packages/crates-io.scm (rust-typenum-1): Update to 1.12.0.

gnu: Rename rust-typenum-1.10 to rust-typenum-1.

* gnu/packages/crates-io.scm (rust-typenum-1.10): Rename to ...
(rust-typenum-1): ... this.
(rust-generic-array-0.14, rust-generic-array-0.13, rust-nalgebra-0.18)
[arugments]: Adjust accordingly.

gnu; Add go-minisign.

* gnu/packages/crypto.scm (go-minisign): New variable.

gnu: Add rust-minisign.

* gnu/packages/crypto.scm (rust-minisign): New variable.

gnu: Add rust-scrypt-0.3.

* gnu/packages/crates-io.scm (rust-scrypt-0.3): New variable.
(rust-scrypt-0.2): Inherit from rust-scrypt-0.2.

gnu: Add rust-pbdkdf2-0.4.

* gnu/packages/crates-io.scm (rust-pbkdf2-0.4): New variable.
(rust-pbkdf2-0.3): Inherit from rust-pbkdf2-0.4.

gnu: Add rust-hmac-0.8.

* gnu/packages/crates-io.scm (rust-hmac-0.8): New variable.
(rust-hmac-0.7): Inherit from rust-hmac-0.8.

gnu: rust-sha2-asm-0.5: Update to 0.5.4.

* gnu/packages/crates-io.scm (rust-sha2-asm-0.5): Update to 0.5.4.

gnu: rust-sha2-0.8: Update to 0.8.2.

* gnu/packages/crates-io.scm (rust-sha2-0.8): Update to 0.8.2.
[arguments]: Remove rust-cc-1.0 from cargo-development-inputs.

gnu: Add rust-sha2-0.9.

* gnu/packages/crates-io.scm (rust-sha2-0.9): New variable.
(rust-sha2-0.8): Inherit from rust-sha2-0.9.

gnu: Add rust-md-5-0.9.

* gnu/packages/crates-io.scm (rust-md-5-0.9): New variable.
(rust-md-5-0.8): Inherit from rust-md-5-0.9.

gnu: Add rust-block-buffer-0.8.

* gnu/packages/crates-io.scm (rust-block-buffer-0.8): New variable.

gnu: rust-sha-1-0.8: Update to 0.8.2.

* gnu/packages/crates-io.scm (rust-sha-1-0.8): Update to 0.8.2.
[arguments]: Don't skip build. Add rust-libc-0.2 to cargo-inputs.
Replace rust-hex-literal-0.2 with 0.1 in cargo-development-inputs.

gnu: rust-sha1-asm-0.4: Don't skip build.

* gnu/packages/crates-io.scm (rust-sha1-asm-0.4)[arguments]: Don't skip
build. Move rust-cc-1.0 from cargo-development-inputs to cargo-inputs.

gnu: Add rust-sha-1-0.9.

* gnu/packages/crates-io.scm (rust-sha-1-0.9): New variable.
(rust-sha-1-0.8): Inherit from rust-sha-1-0.9.

gnu: rust-block-buffer-0.7: Don't skip build.

* gnu/packages/crates-io.scm (rust-block-buffer-0.7)[arguments]: Don't
skip build.

gnu: Add rust-block-buffer-0.9.

* gnu/packages/crates-io.scm (rust-block-buffer-0.9): New variable.
(rust-block-buffer-0.7): Inherit from rust-block-buffer-0.9.

gnu: Add rust-digest-0.9.

* gnu/packages/crates-io.scm (rust-digest-0.9): New variable.
(rust-digest-0.8): Inherit from rust-digest-0.9.

gnu: Add rust-crypto-mac-0.8.

* gnu/packages/crates-io.scm (rust-crypto-mac-0.8): New variable.
(rust-crypto-mac-0.7): Inherit from rust-crypto-mac-0.8.

gnu: rust-generic-array-0.13: Don't skip build.

* gnu/packages/crates-io.scm (rust-generic-array-0.13)[arguments]: Don't
skip build.
(rust-generic-array-0.12)[arguments]: Same.

gnu: Add rust-generic-array-0.14.

* gnu/packages/crates-io.scm (rust-generic-array-0.14): New variable.
(rust-generic-array-0.13): Inherit from rust-generic-array-0.14.

gnu: Add rust-subtle-2.

* gnu/packages/crates-io.scm (rust-subtle-2): New variable.
(rust-subtle-1.0): Inherit from rust-subtle-2.

gnu: rust-block-padding-0.1: Don't skip build.

* gnu/packages/crates-io.scm (rust-block-padding-0.1)[arguments]: Don't
skip build.

gnu: Add rust-block-padding-0.2.

* gnu/packages/crates-io.scm (rust-block-padding-0.2): New variable.
(rust-block-padding-0.1): Inherit from rust-block-padding-0.2.

gnu: Add rust-cpuid-bool-0.1.

* gnu/packages/crates-io.scm (rust-cpuid-bool-0.1): New variable.

gnu: Add rust-opaque-debug-0.3.

* gnu/packages/crates-io.scm (rust-opaque-debug-0.3): New variable.
(rust-opaque-debug-0.2): Inherit from rust-opaque-debug-0.3.

.gitignore: Ignore 'etc/committer.scm'.

* .gitignore: Add '/etc/committer.scm'.

doc: Add progress display in 'dd' command lines.

* doc/guix.texi (System Installation): Adjust 'dd' command line to
display progress …
(System Configuration): … same here.

doc: cookbook: Update entry about getting substitutes through Tor.

* doc/guix-cookbook.texi (Getting substitutes from Tor): Update
section warning to mention the use of torsocks when pulling.

services: Add rshiny service.

* gnu/services/science.scm: New file.
(<rshiny-configuration>): New record.
(rshiny-shepherd-service-type): New variable.
* doc/guix.texi (Miscellaneous Services): Document it.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

gnu: emacs-nov-el: Update to 0.3.1.

* gnu/packages/emacs-xyz.scm (emacs-nov-el): Update to 0.3.1.

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

gnu: emacs-nov-el: Use version tag instead of commit.

* gnu/packages/emacs-xyz.scm (emacs-nov-el): Remove let binding and associated
comment; correct indentation.
[source]: Use version tag as commit identifier now that upstream has restored
this information.

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

gnu: r-qtl2: Update synopsis, description.

* gnu/packages/bioinformatics.scm (r-qtl2)[synopsis]: Use upstream's
synopsis.
[description]: Same.

gnu: r-qtl2: Update to 0.22-8.

* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-8.
[source]: Download from cran.

gnu: Add rust-scrypt-0.2.

* gnu/packages/crates-io.scm (rust-scrypt-0.2): New variable.

gnu: Add rust-pbkdf2-0.3.

* gnu/packages/crates-io.scm (rust-pbkdf2-0.3): New variable.

gnu: Add rust-hmac-0.7.

* gnu/packages/crates-io.scm (rust-hmac-0.7): New variable.

gnu: Add rust-md-5-0.8.

* gnu/packages/crates-io.scm (rust-md-5-0.8): New variable.

gnu: Add rust-md5-asm-0.4.

* gnu/packages/crates-io.scm (rust-md5-asm-0.4): New variable.

gnu: emacs-idris-mode: Update to 1.0.

* gnu/packages/emacs-xyz.scm (emacs-idris-mode): Update to 1.0.
[description]: Mention compatibility with Idris 1.

gnu: r-fpc: Update to 2.2-7.

* gnu/packages/statistics.scm (r-fpc): Update to 2.2-7.

gnu: r-openssl: Update to 1.4.2.

* gnu/packages/statistics.scm (r-openssl): Update to 1.4.2.
[native-inputs]: Add r-knitr.

gnu: r-roxygen2: Update to 7.1.1.

* gnu/packages/statistics.scm (r-roxygen2): Update to 7.1.1.
[native-inputs]: Add r-knitr.

gnu: r-directlabels: Update to 2020.6.17.

* gnu/packages/cran.scm (r-directlabels): Update to 2020.6.17.
[native-inputs]: Add r-knitr.

gnu: r-rgdal: Update to 1.5-12.

* gnu/packages/cran.scm (r-rgdal): Update to 1.5-12.

gnu: r-flexdashboard: Update to 0.5.2.

* gnu/packages/cran.scm (r-flexdashboard): Update to 0.5.2.
[source]: Delete minified JavaScript files in a snippet.

gnu: r-rcppparallel: Update to 5.0.2.

* gnu/packages/cran.scm (r-rcppparallel): Update to 5.0.2.

gnu: r-emmeans: Update to 1.4.8.

* gnu/packages/cran.scm (r-emmeans): Update to 1.4.8.

gnu: r-raster: Update to 3.3-7.

* gnu/packages/cran.scm (r-raster): Update to 3.3-7.

gnu: r-sjlabelled: Update to 1.1.6.

* gnu/packages/cran.scm (r-sjlabelled): Update to 1.1.6.

gnu: r-officer: Update to 0.3.12.

* gnu/packages/cran.scm (r-officer): Update to 0.3.12.

gnu: r-ggpubr: Update to 0.4.0.

* gnu/packages/cran.scm (r-ggpubr): Update to 0.4.0.

gnu: r-renv: Update to 0.11.0.

* gnu/packages/cran.scm (r-renv): Update to 0.11.0.

gnu: r-jsonlite: Update to 1.7.0.

* gnu/packages/cran.scm (r-jsonlite): Update to 1.7.0.
[native-inputs]: Add r-knitr.

gnu: r-scater: Update to 1.16.2.

* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.2.

gnu: r-biocviews: Update to 1.56.1.

* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.1.

gnu: r-dexseq: Update to 1.34.1.

* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.1.

gnu: dropbear: Update to 2020.80 [fix for CVE-2018-20685].

* gnu/packages/ssh.scm (dropbear): Update to 2020.80.

gnu: lxqt: Update to 0.15.0.

* gnu/packages/lxqt.scm
(libstatgrab): Update to 0.92.
(lxqt-build-tools): Update to 0.7.0.
(libqtxdg): Update to 3.5.0.
(liblxqt): Update to 0.15.1.
(libsysstat): Update to 0.4.3.
(lxqt-about): Update to 0.15.0.
(lxqt-admin): Update to 0.15.0.
(lxqt-config): Update to 0.15.0.
(lxqt-globalkeys): Update to 0.15.0.
(lxqt-notificationd): Update to 0.15.0.
(lxqt-openssh-askpass): Update to 0.15.0.
(lxqt-panel): Update to 0.15.1.
(lxqt-policykit): Update to 0.15.0.
(lxqt-powermanagement): Update to 0.15.0.
(lxqt-qtplugin): Update to 0.15.1.
(lxqt-runner): Update to 0.15.0.
(lxqt-session): Update to 0.15.0.
(lxqt-sudo): Update to 0.15.0.
(lxqt-themes): Update to 0.15.0.
(libfm-qt): Update to 0.15.1.
(pcmanfm-qt): Update to 0.15.1.
(compton-conf): Update to 0.15.0.
(lximage-qt): Update to 0.15.0.
(obconf-qt): Update to 0.15.0.
(pavucontrol-qt): Update to 0.15.0.
(qps): Update to 2.1.0.
(qps)[inputs]: Add kwindowsystem, liblxqt and libqtxdg.
(qtermwidget): Update to 0.15.0.
(qterminal): Update to 0.15.0.
(screengrab): Update to 2.0.1.
(lxqt-archiver): Update to 0.2.0.
(lxqt-archiver)[origin]: Use tarball release.
(lxqt-connman-applet): Update to 0.15.0.
(lxqt-connman-applet)[arguments]: Add new patch phase.

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

gnu: libtiff: Use HTTPS.

* gnu/packages/image.scm (libtiff)[source]: Use HTTPS.

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

packages: Recognize SHA3 and BLAKE2s for 'content-hash'.

* guix/packages.scm (build-content-hash): Add 'sha3-256', 'sha3-512',
and 'blake2s-256'.
* tests/packages.scm ("package-source-derivation, origin, sha3-512"):
New test.

daemon: Recognize SHA3 and BLAKE2s.

* nix/libutil/hash.hh (HashType): Add htSHA3_256, htSHA3_512, and
htBLAKE2s_256.
* nix/libutil/hash.cc (parseHashType, printHashType): Recognize them.
* tests/store.scm ("add-to-store"): Test these algorithms.

daemon: Remove OpenSSL hash compatibility wrappers.

* nix/libutil/hash.cc (struct Ctx): Copy from gcrypt-hash.hh.
(start, update, finish): Use gcrypt functions directly instead of
OpenSSL-like wrappers.
* nix/libutil/gcrypt-hash.cc, nix/libutil/gcrypt-hash.hh,
nix/libutil/md5.h, nix/libutil/sha1.h, nix/libutil/sha256.h,
nix/libutil/sha512.h: Remove.
* nix/local.mk (libutil_a_SOURCES, libutil_headers): Adjust
accordingly.

daemon: Map directly to gcrypt hash functions.

* nix/libutil/hash.hh (HashType): Map directly to GCRY_MD_ values.
(md5HashSize, sha1HashSize, sha256HashSize, sha512HashSize): Remove.
* nix/libutil/hash.cc (Hash::Hash): Use 'gcry_md_get_algo_dlen'.

bash completion: Complete 'guix environment' properly.

* etc/completion/bash/guix (_guix_complete): Add case for "guix environment".

gnu: Add autofs.

* gnu/packages/file-systems.scm (autofs): New public variable.

Co-authored-by: Oleg Pykhalov <go.wigust@gmail.com>

gnu: python-setproctitle: Fix indentation.

* gnu/packages/python-xyz.scm (python-setproctitle): Re-indent.

gnu: python-setproctitle: Fix build.

* gnu/packages/python-xyz.scm (python-setproctitle)[arguments]:
Add ‘--embed’ to $PYCONFIG.

gnu: Add r-shapforxgboost.

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

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

gnu: Add emacs-browse-kill-ring.

* gnu/packages/emacs-xyz.scm (emacs-browse-kill-ring): New variable.

gnu: x265: Update to 3.4.

* gnu/packages/patches/x265-arm-flags.patch: Update patch.
* gnu/packages/video.scm (x265): Update to 3.4.
[arguments]: Remove obsolete substitution.  Disable the newly-added assembly
optimizations on AArch64, as they are not implemented for all targets we build.

gnu: libcyaml: Remove unused input.

* gnu/packages/web.scm (libcyaml)[native-inputs]: Remove GIT.

gnu: ilmbase: Update to 2.5.2.

* gnu/packages/patches/ilmbase-fix-test-arm.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/graphics.scm (ilmbase): Update to 2.5.2.
[source](patches): Remove 'ilmbase-fix-test-arm.patch'.
(openexr)[arguments]: Really increase test timeout, as the previous fix was
ineffective.

gnu: libzip: Update to 1.7.1.

* gnu/packages/compression.scm (libzip): Update to 1.7.1.

gnu: exempi: Delete the static library.

* gnu/packages/freedesktop.scm (exempi)[arguments]: Add phase to delete libexempi.a.

gnu: exempi: Update to 2.5.2.

* gnu/packages/freedesktop.scm (exempi): Update to 2.5.2.

gnu: python-gevent: Update to 20.6.2.

* gnu/packages/python-xyz.scm (python-gevent): Update to 20.6.2.
(python2-gevent)[native-inputs]: Add PYTHON2-SELECTORS2.

gnu: python-greenlet: Update to 0.4.16.

* gnu/packages/python-xyz.scm (python-greenlet): Update to 0.4.16.