gnu: r-knitrbootstrap: Update to 1.0.3.

* gnu/packages/statistics.scm (r-knitrbootstrap): Update to 1.0.3.
[native-inputs]: Add r-knitr.

Change-Id: Ic049e0c898f7c6a258796a59d87972fc9e0a6ff3

gnu: r-nmf: Update to 0.27.

* gnu/packages/bioconductor.scm (r-nmf): Update to 0.27.

Change-Id: I85f44258abaaceeef6d20e3b3f29512560f5efbb

gnu: whoogle-search: Update to 0.8.4.

* gnu/packages/python-web.scm (whoogle-search): Update to 0.8.4.
[propagated-inputs]: Add python-validators.

Change-Id: I4543808d662e7e946c8a398b28ca963e75d4bfd1
Signed-off-by: Christopher Baines <mail@cbaines.net>

gnu: clojure-tools: Update to 1.11.1.1200.

* gnu/packages/clojure.scm (clojure-tools): Update to 1.11.1.1200.

Change-Id: Ifcd272ab679c5a8634167cfd289ca6719c36bbdb
Signed-off-by: Christopher Baines <mail@cbaines.net>

gnu: execline: Correct symlink permissions on the hurd.

* gnu/packages/skarnet.scm (execline)[arguments]: Patch tools/install.sh
umask.

Change-Id: I1e5d2497e1fd2ad8a39a5e1ca1c3c409968204a8

build-system: perl: Accept Gexps for #:module-build-flags.

Matching the change in 2d40e6f7ab04ec367a9a7fc1af3daa507fb60d3c otherwise the
cross build derivations are broken, as was the case for emacs-pde.

* guix/build-system/perl.scm (perl-cross-build) [module-build-flags]: Accept
gexps.

Change-Id: I2dc85bc50bc077581e3abfc5baaedc6487118192

gnu: Add python-pdbfixer.

* gnu/packages/bioinformatics.scm (python-pdbfixer): New variable.

Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: nvc: Update to 1.11.3.

* gnu/packages/fpga.scm (nvc): Update to 1.11.3.
[inputs]: Add zstd.

Change-Id: I7347a047a559c15beec75bfe5feb0b15a6cc5584

gnu: patool: Update to 2.1.1.

* gnu/packages/patool.scm (patool): Update to 2.1.1.

Change-Id: I86a5e93b10e377a6705c3b7f4a822d8d54f66483

gnu: patool: Fix build.

* gnu/packages/patool.scm (patool): Fix build.
[build-system]: Swap to pyproject-build-system.
[arguments] <#:test-flags>: Disable failing tests.

Change-Id: I53ccec4b39bfae6649bfd715fdb2158b2f7a33e1

gnu: vale: Remove package labeles.

* gnu/packages/textutils.scm (vale) [native-inputs]: Remove labeles.

Change-Id: Id6ac7bcf26b90291b2ec9de18cde8078f6f8f115

gnu: Deprecate the go-github-com-errata-ai-vale variable.

* gnu/packages/ipfs.scm (go-github-com-errata-ai-vale): Rename to "vale".
(go-github-com-errata-ai-vale): Define as deprecated by "vale".

Change-Id: I3c715a36295cd52e36b16e99f39455b7ad961743

gnu: packages: textuitils: Sort use-module alphabetically.

* gnu/packages/textutils.scm: Sort use-module alphabetically to ease
maintenance.

Change-Id: Ia698a0b3e137ce2fc2f68d0206d209649acdad5e

gnu: moe: Update to 1.14.

* gnu/packages/moe.scm (moe): Update to 1.14.

Change-Id: I176ec1a3a2505a4e50426863282dbc73815ae904
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: gama: Update to 2.28.

* gnu/packages/gps.scm (gama): Update to 2.28.

Change-Id: I5e74bf81e158970559e4937c9563578eae253241
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: wlr-randr: Update to 0.4.0.

* gnu/packages/wm.scm (wlr-randr): Update to 0.4.0.

Change-Id: I3a04bf965c4ec098268c9ac4a1328c6ca575cf9e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: mupdf: Update to 1.23.9.

* gnu/packages/pdf.scm (mupdf): Update to 1.23.9.

Change-Id: Id67767304d33a09df8cea7b91111729d0bc99366
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: dos2unix: Update to 7.5.2.

* gnu/packages/textutils.scm (dos2unix): Update to 7.5.2.

Change-Id: I8b27da05c0780fe942fe19f00766cd2772c66bc0
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: fheroes2: Update to 1.0.11.

* gnu/packages/games.scm (fheroes2): Update to 1.0.11.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: syncthing: Update to 1.27.2.

* gnu/packages/syncthing.scm (syncthing): Update to 1.27.2.

Change-Id: Ifc6af7a518d4dfc75e42889de1a0873cdcbdfaaf
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>