gnu: dino: Use new package style.

* gnu/packages/messaging.scm (dino)[arguments]: Convert to list of
G-Expressions.
[native-inputs, inputs]: Drop labels.

gnu: Add kaidan.

* gnu/packages/messaging.scm (kaidan): New variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

gnu: bitmask: Update to 0.21.11.

* gnu/packages/vpn.scm (bitmask)[version]: Update to 0.21.11.
[inputs]: Add qtsvg.

gnu: sbcl-nhooks: Update to 1.1.1.

* gnu/packages/lisp-xyz.scm (sbcl-nhooks): Update to 1.1.1.

gnu: gdm: Use regular check.

* gnu/packages/gnome.scm (gdm)[native-inputs]: Replace check-0.14 with check.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

gnu: iodine: Use regular check.

* gnu/packages/networking.scm (iodine)[native-inputs]: Replace check-0.14 with
check.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

gnu: libsbml: Use regular check.

* gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Replace check-0.14
with check.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

gnu: edi: Use regular check.

* gnu/packages/enlightenment.scm (edi)[native-inputs]: Replace check-0.14 with
check.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

gnu: burp: Use regular check.

* gnu/packages/backup.scm (burp)[native-inputs]: Replace check-0.14 with
check.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

gnu: libsigrokdecode: Use regular check.

* gnu/packages/electronics.scm (libsigrokdecode)[native-inputs]: Replace
check-0.14 with check.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

gnu: recutils: Use regular check.

* gnu/packages/databases.scm (recutils)[native-inputs]: Replace check-0.14
with check.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

gnu: curl: Skip failing test on x86-32.

* gnu/packages/curl.scm (curl-7.84.0)[arguments]<#:phases>: When running on
x86-32, add a phase to skip test 3026 “curl_global_init thread-safety”.

gnu: ibus-anthy: Modernize arguments.

* gnu/packages/ibus.scm (ibus-anthy)[arguments]: Convert to list of
G-Expressions.

gnu: ibus-anthy: Archaize wrapper.

This is a follow-up to 39b118776bbbaed049f8bcafa27bde30d9d0b2f6, which
applied the wrong modernization metaphors.  For more information, see
<https://issues.guix.gnu.org/52576#16>.

* gnu/packages/ibus.scm (ibus-anthy)[#:phases]<wrap-programs>: Refer to
outputs by assoc-ref.

tests: Adjust 'guix graph' test to latest OCaml changes.

* tests/graph.scm ("reverse bag DAG"): Adjust to latest OCaml changes by
looking at dune/ocaml-camomile/ocaml-utop.

profiles: Do not repeat entries in 'manifest' file.

Fixes <https://issues.guix.gnu.org/55499>.
Reported by Ricardo Wurmus <rekado@elephly.net>.

With this change, the manifest file created for:

  guix install r r-seurat r-cistopic r-monocle3 r-cicero-monocle3 r-assertthat

goes from 5.7M to 176K.  Likewise, on this profile, wall-clock time of:

  GUIX_PROFILING=gc guix package -I

goes from 0.7s to 0.1s, with heap usage going from 55M to 9M.

* guix/profiles.scm (manifest->gexp)[optional]: New procedure.
[entry->gexp]: Turn into a monadic procedure.  Return a 'repeated' sexp
if ENTRY was already visited before.
Adjust caller accordingly.  Bump manifest version.
(sexp->manifest)[sexp->manifest-entry]: Turn into a monadic procedure.
Add case for 'repeated' nodes.  Add each entry to the current state
vhash.
Add clause for version 4 manifests.
[sexp->manifest-entry/v3]: New procedure, with former
'sexp->manifest-entry' code.
* tests/profiles.scm ("deduplication of repeated entries"): New test.
* guix/build/profiles.scm (manifest-sexp->inputs+search-paths)[let-fields]:
New macro.
Use it.  Expect version 4.  Add clause for 'repeated' nodes.

tests: Augment profile collision test.

* tests/profiles.scm ("collision of propagated inputs"): Check the
parents of ENTRY1 and ENTRY2.

services: openssh: Listen on IPv6 only when IPv6 is supported.

Fixes <https://issues.guix.gnu.org/56327>.
Reported by André Batista <nandre@riseup.net>.

* gnu/services/ssh.scm (openssh-shepherd-service)[ipv6-support?]: New
variable.
Use it in 'start' method.

upstream: 'guix refresh -u' no longer stops when upstream info is lacking.

Fixes <https://issues.guix.gnu.org/56338>.

Starting from 53b9c27aa59bebf955f0aa24fef60a101480ef5c, 'guix refresh -u'
would stop upon the first failure to determine upstream releases.  This
fixes that.

* guix/upstream.scm (package-update): Warn rather than update.

gnu: Add luppp.

* gnu/packages/music.scm (luppp): New variable.

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

gnu: Add fabla.

* gnu/packages/music.scm (fabla): New variable.

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

gnu: sorcer: Update to 1.1.3-1.cc7f6f5.

* gnu/packages/music.scm (sorcer): Update to 1.1.3-1.cc7f6f5.
[source]: Fetch with git; remove generated C++ file.
[native-inputs]: Replace faust with faust-0.9.67.

This update fixes the building of the package.

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

gnu: Add faust-0.9.67.

* gnu/packages/audio.scm (faust-0.9.67): New variable.

gnu: linux-libre 5.4: Update to 5.4.202.

* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.202.
(linux-libre-5.4-pristine-source): Update hash.

gnu: linux-libre 5.10: Update to 5.10.127.

* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.127.
(linux-libre-5.10-pristine-source): Update hash.

gnu: linux-libre 5.15: Update to 5.15.51.

* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.51.
(linux-libre-5.15-pristine-source): Update hash.

gnu: linux-libre: Update to 5.18.8.

* gnu/packages/linux.scm (linux-libre-5.18-version): Update to 5.18.8.
(linux-libre-5.18-pristine-source): Update hash.

gnu: dezyne: Update to 2.15.3.

* gnu/packages/dezyne.scm (dezyne)[source]: Update to 2.15.3.

gnu: mcrl2: Update to 202206.0.

* gnu/packages/patches/mcrl2-fix-1687.patch,
gnu/packages/patches/mcrl2-fix-counterexample.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/maths.scm (mcrl2): Update to 202206.0 and use them.

gnu: Add python-ikarus.

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

tests: Add sanitizer test.

* tests/records.scm ("define-record-type* & sanitize without default
value"): New test.

image: Add sanitizers for 'format' and 'partition-table-type'.

This allows common mistakes to be diagnosed early.

* gnu/image.scm (define-set-sanitizer): New macro.
(validate-image-format, validate-partition-table-type): New sanitizers.
(<image>)[format, partition-table-type]: Add 'sanitize' property.

image: Raise an error when an image lacks a bootable partition.

* gnu/system/image.scm (find-root-partition): Raise an error when 'find'
returns #f.

image: Avoid use of the deprecated 'gpt' option of genimage.

* gnu/system/image.scm (system-disk-image)[genimage-type-options]: Use
'partition-table-type' instead of the deprecated 'gpt' option.

image: Add default value for partition initializer.

Previously, the default value would lead to a wrong-type-to-apply crash.

* gnu/system/image.scm (system-disk-image)[image-builder]: When
'partition-initializer' returns #f, fall back to
INITIALIZE-ROOT-PARTITION.
* gnu/tests/base.scm (run-root-unmount-test)[test-image]: Remove
'initializer' field of partition.
* gnu/image.scm (<partition>)[initializer]: Add comment.

image: 'system-image' throws when given an incorrect image format.

Previously 'system-image' would return *unspecified* in that case,
leading to a wrong-type-arg error crash down the road.

* gnu/system/image.scm (system-image): Add 'else' clause.

services: root-file-system: Cleanly unmount upon shutdown.

Fixes <https://issues.guix.gnu.org/56209>.
Reported by angry rectangle <angryrectangle@cock.li>.

* gnu/packages/admin.scm (shepherd-0.9)[modules, snippet]: New fields.
* gnu/services/base.scm (%root-file-system-shepherd-service): In 'stop'
method, remove 'call-with-blocked-asyncs'.  When 'mount' throws to
'system-error, call (@ (fibers) sleep) and try again.
* gnu/tests/base.scm (run-root-unmount-test): New procedure.
(%test-root-unmount): New variable.

file-systems: Add 'cleanly-unmounted-ext2?'.

* gnu/build/file-systems.scm (ext2-superblock-cleanly-unmounted?)
(cleanly-unmounted-ext2?): New procedures.

gnu: texlive-fmtcount: Add proper 'license' value.

This is a followup to df5e07c16d2d4e72423f0e8c6b5b53c7020bc77a.

* gnu/packages/tex.scm (texlive-fmtcount)[license]: New field.

services: nginx: Add support for extra content in upstream blocks.

I'm looking at this as I'd like to use the keepalive functionality.

* gnu/services/web.scm (nginx-upstream-configuration-extra-content): New
procedure.
(emit-nginx-upstream-config): Include the extra-content if applicable.
* doc/guix.texi (NGINX): Document this.

gnu: grip: Update to 4.6.1.

* gnu/packages/python-web.scm (grip): Update to 4.6.1.
(arguments): Use a gexp.

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

services: guix: Support guix-build-coordinator parallel hooks.

* gnu/services/guix.scm (guix-build-coordinator-configuration-parallel-hooks):
New procedure.
(make-guix-build-coordinator-start-script): Accept and use #:parallel-hooks.
(guix-build-coordinator-shepherd-services): Pass parallel-hooks to
make-guix-build-coordinator-start-script.
* doc/guix.texi (Guix Build Coordinator): Document this new field.

gnu: guix-build-coordinator: Update to 0-55.23504e0.

* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-55.23504e0.

gnu: Add r-sungeo.

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

gnu: Add r-measurements.

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

gnu: Add r-cartogram.

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

gnu: Add r-automap.

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

gnu: Add r-gstat.

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

gnu: Add r-spacetime.

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

gnu: Add r-antiprofiles.

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

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

gnu: Add r-annmap.

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

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

gnu: Add r-anf.

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

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

gnu: Add r-anaquin.

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

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

gnu: opensbi: Update to 1.1.

* gnu/packages/firmware.scm (make-opensbi-package): Update to 1.1.

gnu: itstool: Update home page.

* gnu/packages/glib.scm (itstool)[home-page]: Use HTTPS and remove defunct
subdomain.

gnu: cURL: Replace with 7.84.0 [security fixes].

This fixes CVE-2022-22576, CVE-2022-27774, CVE-2022-27775, CVE-2022-27776,
CVE-2022-27781, and CVE-2022-27782.

* gnu/packages/curl.scm (curl)[replacement]: New field.
(curl-7.84.0): New private variable.

gnu: cURL: Update source URI.

* gnu/packages/curl.scm (curl)[source](uri): Follow redirect.

gnu: Add sketch.

* gnu/packages/lisp-xyz.scm (cl-sketch, ecl-sketch, sbcl-sketch): New variables.

gnu: Add cl-sdl2-ttf.

* gnu/packages/lisp-xyz.scm (cl-sdl2-ttf, ecl-sdl2-ttf, sbcl-sdl2-ttf): New variables.

gnu: Add cl-sdl2-image.

* gnu/packages/lisp-xyz.scm (cl-sdl2-image, ecl-cl-sdl2-image,
sbcl-cl-sdl2-image): New variables.

gnu: Add cl-geometry.

* gnu/packages/lisp-xyz.scm (cl-geometry, ecl-cl-geometry, sbcl-cl-geometry):
New variables.

gnu: Add cl-trees.

* gnu/packages/lisp-xyz.scm (cl-trees, ecl-cl-trees, sbcl-cl-trees): New variables.

gnu: Add glkit.

* gnu/packages/lisp-xyz.scm (cl-glkit, ecl-glkit, sbcl-glkit): New variables.

gnu: Add sdl2kit.

* gnu/packages/lisp-xyz.scm (cl-sdl2kit, ecl-sdl2kit, sbcl-sdl2kit): New variables.

gnu: Add mathkit.

* gnu/packages/lisp-xyz.scm (cl-mathkit, ecl-mathkit, sbcl-mathkit): New
variables.

gnu: Add sb-cga.

* gnu/packages/lisp-xyz.scm (cl-sb-cga, ecl-sb-cga, sbcl-sb-cga): New variables.

gnu: sbcl: Enable sb-gmp, sb-mpfr and install shared library.

* gnu/packages/lisp.scm (sbcl)[inputs]: Add gmp, mpfr.
[arguments]: Fix shared library makefile.
Fix contrib references to gmp and mpfr.
Add phase to build shared library.
Add phase to install shared library.

gnu: Add physical-quantities.

* gnu/packages/lisp-xyz.scm (cl-physical-quantities, ecl-physical-quantities,
sbcl-physical-quantities): New variables.

gnu: Add parseq.

* gnu/packages/lisp-xyz.scm (cl-parseq, ecl-parseq, sbcl-parseq): New variables.

gnu: Add slot-extra-options.

* gnu/packages/lisp-xyz.scm (cl-slot-extra-options, ecl-slot-extra-options,
sbcl-slot-extra-options): New variables.

gnu: sbcl-parachute: Update to 20210920.

* gnu/packages/lisp-check.scm (sbcl-parachute): Update to 20210920.

gnu: Add polymorphic-functions.

* gnu/packages/lisp-xyz.scm (cl-polymorphic-functions,
ecl-polymorphic-functions, sbcl-polymorphic-functions): New variables.

gnu: Add ctype.

* gnu/packages/lisp-xyz.scm (cl-ctype, ecl-ctype, sbcl-ctype): New variables.

gnu: Add compiler-macro-notes.

* gnu/packages/lisp-xyz.scm (cl-compiler-macro-notes,
ecl-compiler-macro-notes, sbcl-compiler-macro-notes): New variables.

gnu: Add fast-generic-functions.

* gnu/packages/lisp-xyz.scm (cl-fast-generic-functions,
ecl-fast-generic-functions, sbcl-fast-generic-functions): New variables.

gnu: Add sealable-metaobjects.

* gnu/packages/lisp-xyz.scm (cl-sealable-metaobjects,
ecl-sealable-metaobjects, sbcl-sealable-metaobjects): New variables.

gnu: Add dynamic-mixins.

* gnu/packages/lisp-xyz.scm (cl-dynamic-mixins, ecl-dynamic-mixins,
sbcl-dynamic-mixins): New variables.

gnu: Add defstar.

* gnu/packages/lisp-xyz.scm (cl-defstar, ecl-defstar, sbcl-defstar): New variables.

gnu: Add filtered-functions.

* gnu/packages/lisp-xyz.scm (cl-filtered-functions, ecl-filtered-functions,
sbcl-filtered-functions): New variables.

gnu: Add cl-definitions.

* gnu/packages/lisp-xyz.scm (cl-definitions, ecl-definitions,
sbcl-definitions): New variables.

gnu: sbcl-cl-reexport: Update to 20210219.

* gnu/packages/lisp-xyz.scm (sbcl-cl-reexport): Update to 20210219.
[native-inputs]: Add sbcl-prove.
[description]: Fix typo.

gnu: Add clache.

* gnu/packages/lisp-xyz.scm (cl-clache, ecl-clache, sbcl-clache): New variables.

gnu: Add screamer.

* gnu/packages/lisp-xyz.scm (cl-screamer, ecl-screamer, sbcl-screamer): New variables.

gnu: Add cl-algebraic-data-type.

* gnu/packages/lisp-xyz.scm (cl-algebraic-data-type,
ecl-cl-algebraic-data-type, sbcl-cl-algebraic-data-type): New variables.

gnu: Add cells.

* gnu/packages/lisp-xyz.scm (cl-cells, ecl-cells, sbcl-cells): New variables.

gnu: Add utils-kt.

* gnu/packages/lisp-xyz.scm (cl-utils-kt, ecl-utils-kt, sbcl-utils-kt): New variables.

gnu: x265: Enable assembly on for some arm build phases.

* gnu/packages/video.scm (x265)[arguments]: Enable assembly for
armhf-linux. Only disable assembly for aarch64-linux when building the
10-bit or 12-bit libraries.

gnu: x265: Honor make-flags.

* gnu/packages/video.scm (x265)[arguments]: Adjust custom 'build-12-bit,
'build-10-bit and 'install-more-libs phases to use standard 'make and
'install phases.

gnu: x265: Update to 3.5.

* gnu/packages/video.scm (x265): Update to 3.5.
[source]: Update to new upstream URI.
[arguments]: Adjust custom 'prepare-build phase due to changes in the
codebase. Remove trailing #t from phases and shorten find-files.

gnu: sbcl: Fix build on some architectures.

* gnu/packages/lisp.scm (sbcl)[arguments]: Update 'build-doc' phase to build
  the doc for SB-SIMD only on x86_64-linux.

gnu: Add ruby-braintree.

* gnu/packages/ruby.scm (ruby-braintree): New variable.

Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>

gnu: Add r-amaretto.

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

gnu: Add r-amountain.

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

gnu: r-partitions: Update to 1.10-4.

* gnu/packages/cran.scm (r-partitions): Update to 1.10-4.
[propagated-inputs]: Add r-mathjaxr.

gnu: r-metap: Update to 1.8.

* gnu/packages/bioconductor.scm (r-metap): Update to 1.8.
[propagated-inputs]: Add r-mathjaxr and r-qqconf.

gnu: Add r-qqconf.

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

gnu: r-metafor: Update to 3.4-0.

* gnu/packages/cran.scm (r-metafor): Update to 3.4-0.
[propagated-inputs]: Add r-mathjaxr, r-metadat, and r-pbapply.

gnu: Add r-metadat.

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

gnu: Add r-mathjaxr.

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

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

gnu: cl-zstd: Update to 2.0-1.134f058.

* gnu/packages/lisp-xyz.scm (sbcl-zstd): Update to 2.0-1.134f058.
  [inputs]: Remove labels.
  [arguments]: Use gexp.