Fixes <https://bugs.gnu.org/41993>.
Reported by Kurt I <gitlabcanada@runbox.com>.

* gnu/packages/video.scm (ffmpeg)[inputs]: Conditionally add RAV1E.
[arguments]: Adjust #:configure-flags accordingly.

The "image-root" derivation output is used as a temporary directory that is
passed to GNU Xorriso later on. By merging the creation of this directory and
the production of an ISO image, we can get rid of the derivation.

* gnu/system/image.scm (system-iso9660-image): Merge "image-root" and
"iso9660-image" derivations so that we spare an extra derivation.

* gnu/packages/vpn.scm (xl2tpd)[arguments]: Substitute hardcoded pppd path
instead of trying to set CFLAGS variable.

But keep version 2.4.1 around for packages that still need it and for python2
support.

* gnu/packages/graph.scm (python-plotly): Update to 4.8.1.
[source]: Use git-fetch so that tests are also included.
[arguments]: Enable tests.
[home-page]: Follow redirect.
(python-plotly-2.4.1): New variable.
(python2-plotly): Inherit from python-plotly-2.4.1.
* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on
python-plotly-2.4.1.

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

From 27ec21904f769c1e8114f767972d9037e1e9f68a Mon Sep 17 00:00:00 2001
From: Pierre Langlois <pierre.langlois@gmx.com>
Date: Thu, 18 Jun 2020 00:58:02 +0200
Subject: [PATCH 4/5] gnu: Add python-xarray.

* gnu/package/python-science.scm (python-xarray): New variable.

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

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

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

But also keep version 0.25.3 around for packages requiring an earlier
versions, as well as version 0.24.2 for a version with python2.

* gnu/packages/python-science.scm (python-pandas): Update to 1.0.5.
[arguments]: Adapt 'patch-which phase.  Add new 'prepare-x phase.  Do not
delete tests that depend on "moto", they are skipped automatically.
[propagated-inputs]: Add python-jinja2.
[inputs]: Add xsel and xclip.
[native-inputs]: Add xorg-server-for-tests so we can test clipboard support.
(python-pandas-0.24): New variable.
(python2-pandas): Inherit from python-pandas-0.25.
* gnu/packages/bioinformatics.scm (python-biom-format)[propagated-inputs]:
Switch to python-pandas-0.25.

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

And make sure python-deeptools's tests are running.

* gnu/packages/bioinformatics.scm (python-deeptools): Fetch source using git.
[native-inputs]: Add python-mock and python-nose.
(deeptools): Mark as deprecated.

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

* gnu/packages/guile.scm (guile-3.0/libgc-7): Inherit from GUILE-3.0.3.

Until now, we'd call (nar-sha256 file) unconditionally.  Thus, if FILE
was a directory, we would traverse it for no reason, and then call
'deduplicate' on FILE, which would again traverse it.

This change also removes redundant (mkdir-p store) calls from the loop,
and avoids 'lstat' calls by using 'scandir*'.

* guix/store/deduplication.scm (deduplicate): Add named loop.  Move
'mkdir-p' outside the loop.  Use 'scandir*' instead of 'scandir'.  Do
not call 'nar-sha256' when FILE has type 'directory.

* guix/build/compile.scm (optimization-options): Use '-O1' for the
simple case.

* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.6.3.

* gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): Update to 0.5.

* gnu/packages/radio.scm (js8call)[inputs]: Use regular hamlib.

* gnu/packages/radio.scm (wsjtx-hamlib): Update to 2.2.1.
  [arguments]: Add a 'fix-tests' phase.
  (wsjtx): Update to 2.2.1.

* gnu/packages/geo.scm (qgis)[arguments]: Disable a few more failing tests.

* gnu/packages/bioconductor.scm (r-rgreat): New variable.

* gnu/packages/crates-io.scm (rust-libc-0.2)[arguments]: Don't skip
build.

* gnu/packages/crates-io.scm (rust-libc-0.2): Update to 0.2.71.

* gnu/packages/crates-io.scm (rust-rayon-1.3): Rename to rust-rayon-1.
(rust-criterion-0.3, rust-criterion-0.2, rust-gimli-0.18,
rust-hashbrown-0.5, rust-indexmap-1.3, rust-jpeg-decoder-0.1,
rust-nasm-rs-0.1, rust-scroll-0.9, rust-syn-1.0, rust-syn-0.15)
[arguments]: Adjust accordingly.
* gnu/packages/gnome.scm (librsvg-next)[arguments]: Same.
* gnu/packages/rust-apps.scm (tokei)[arguments]: Same.
* gnu/packages/video.scm (rav1e)[arguments]: Same.

* gnu/packages/crates-io.scm (rust-rayon-1.1): Remove variable.
(rust-criterion-0.2, rust-gimli-0.18, rust-hashbrown-0.5,
rust-jpeg-decoder-0.1, rust-scroll-0.9, rust-syn-0.15)
[arguments]: Replace rust-rayon-1.1 with 1.3.

* gnu/packages/crates-io.scm (rust-rayon-core-1.7): Rename to
rust-rayon-core-1.
(rust-criterion-0.2, rust-rayon-1.3, rust-rayon-1.1, rust-rayon-0.8)
[arguments]: Adjust accordingly.

* gnu/packages/crates-io.scm (rust-rayon-core-1.5): Remove variable.
(rust-criterion-0.2, rust-rayon-1.1) [arguments]: Replace
rust-rayon-core-1.5 with 1.7.

* gnu/packages/sequoia.scm (sequoia)[arguments]: Move unquote next to
the expression it applies to.

* gnu/packages/crates-io.scm (rust-regex-1.3): Rename to rust-regex-1.
(rust-ansi-term-0.12, rust-bindgen-0.52, rust-bindgen-0.51,
rust-bindgen-0.50, rust-bindgen-0.37, rust-bindgen-0.49, rust-clap-2,
rust-compiletest-rs-0.3, rust-console-0.9, rust-console-0.7,
rust-docopt-1.1, rust-env-logger-0.7, rust-env-logger-0.6,
rust-env-logger-0.5, rust-gimli-0.18, rust-globset-0.4,
rust-grep-cli-0.1, rust-grep-matcher-0.1, rust-grep-regex-0.1,
rust-grep-searcher-0.1, rust-ignore-0.4, rust-lalrpop-0.17,
rust-lalrpop-util-0.17, rust-locale-config-0.3, rust-localeconfig-0.2,
rust-nom-5, rust-nom-4.2, rust-once-cell-1.2, rust-proptest-0.9,
rust-proptest-0.8, rust-pulldown-cmark-0.4, rust-regex-automata-0.1,
rust-rusqlite-0.19, rust-scan-fmt-0.2, rust-syn-1.0, rust-syn-0.15,
rust-ucd-parse-0.1, rust-version-sync-0.8) [arguments]: Adjust accordingly.
* gnu/packages/gnome.scm (librsvg-next)[arguments]: Same.
* gnu/packages/rust-apps.scm (fd, ripgrep, tokei, rust-cargo-c)
[arguments]: Same.
* gnu/packages/sequoia.scm (sequoia)[arguments]: Same.

* gnu/packages/crates-io.scm (rust-regex-1.1): Remove variable.
(rust-bindgen-0.50, rust-bindgen-0.49, rust-clap-2,
rust-compiletest-rs-0.2, rust-console-0.7, rust-docopt-1.1,
rust-env-logger-0.7, rust-env-logger-0.6, rust-env-logger-0.5,
rust-gimli-0.18, rust-globset-0.4, rust-grep-cli-0.1,
rust-grep-matcher-0.1, rust-grep-regex-0.1, rust-grep-searcher-0.1,
rust-ignore-0.4, rust-nom-5, rust-nom-4.2, rust-once-cell-1.2,
rust-proptest-0.9, rust-proptest-0.8, rust-pulldown-cmark-0.4,
rust-regex-automata-0.1, rust-rusqlite-0.19, rust-syn-0.15,
rust-ucd-parse-0.1, rust-version-sync-0.8) [arguments]: Replace
rust-regex-1.1 with 1.3.
* gnu/packages/rust-apps.scm (ripgrep)[arguments]: Same.

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

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

* gnu/packages/crates-io.scm (rust-gettext-sys-0.19): New variable.

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

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

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

* gnu/packages/crates-io.scm (rust-section-testing-0.0): New variable.

* gnu/packages/crates-io.scm (rust-tempfile-3.1): Rename to ...
(rust-tempfile-3): .. this.
(rust-cairo-rs-0.8, rust-cairo-rs-0.7, rust-cc-1.0,
rust-compiletest-rs-0.3, rust-filetime-0.2, rust-gdk-pixbuf-sys-0.9,
rust-gio-sys-0.9, rust-git2-0.11, rust-glib-0.9, rust-glib-0.8,
rust-glib-sys-0.9, rust-gobject-sys-0.9, rust-handlebars-2.0,
rust-lscolors-0.6, rust-native-tls-0.2, rust-nix-0.15, rust-nix-0.14,
rust-no-panic-0.1, rust-pango-sys-0.9, rust-pangocairo-0.10,
rust-proptest-0.9, rust-proptest-0.8, rust-rustdoc-stripper-0.1,
rust-rustls-0.16, rust-rusty-fork-0.2, rust-sourcefile-0.1,
rust-tiff-0.2, rust-tokio-0.2, rust-tokio-fs-0.1, rust-tokio-uds-0.2,
rust-wayland-client-0.23, rust-wayland-client-0.21, rust-xattr-0.2)
[arguments]: Adjust accordingly.
* gnu/packages/rust-apps.scm (rust-cbindgen, tokei)[arguments]: Same.
* gnu/packages/sequoia.scm (sequoia)[arguments]: Same.
* gnu/packages/terminals.scm (alacritty)[arguments]: Same.

* gnu/packages/crates-io.scm (rust-tempfile-3.0): Remove variable.
(rust-compiletest-rs-0.3, rust-filetime-0.2, rust-handlebars-2.0,
rust-nix-0.15, rust-nix-0.14, rust-proptest-0.9, rust-proptest-0.8,
rust-rustls-0.16, rust-rusty-fork-0.2, rust-tiff-0.2, rust-tokei-fs-0.1,
rust-tokio-uds-0.2, rust-xattr-0.2) [arguments]: Replace
rust-tempfile-3.0 with 3.1.
* gnu/packages/rust-apps.scm (tokei)[arguments]: Same.

* gnu/packages/crates-io.scm (rust-proptest-0.9): Update to 0.9.
[arguments]: Don't skip build. In cargo-inputs replace rust-rand-0.4
with 0.6, rust-rand-chacha-0.2 with 0.1, rust-rand-xorshift-0.2 with 0.1.

* gnu/packages/statistics.scm (r-zoo): Move this variable from here...
* gnu/packages/cran.scm (r-zoo): ...to here.

* gnu/packages/statistics.scm (r-directlabels): Move this variable from here...
* gnu/packages/cran.scm (r-directlabels): ...to here.

* gnu/packages/statistics.scm (r-boruta): Move this variable from here...
* gnu/packages/cran.scm (r-boruta): ...to here.

* gnu/packages/statistics.scm (r-boruta)[description]: Fix indentation, add
line breaks, and complete the first sentence fragment.