gnu: glibc/hurd-headers: Properly cross-build.

* gnu/packages/base.scm (glibc/hurd-headers): Rely on cross-mig, and remove
hardcoded configure flag `--host=i586-pc-gnu`.
* gnu/packages/cross-base.scm (cross-kernel-headers*): Add `--host` and
`--build` configure flags.

gnu: arpack-ng: Update to 3.9.0.

* gnu/packages/maths.scm (arpack-ng): Update to 3.9.0.
[source]: Add 'patches'.
[build-system]: Switch to CMAKE-BUILD-SYSTEM.
[native-inputs]: Remove AUTOCONF, AUTOMAKE, and LIBTOOL.
(arpack-ng-openmpi)[inputs]: Use 'modify-inputs'.
[arguments]: Use gexps.
* gnu/packages/patches/arpack-ng-propagate-rng-state.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

gnu: sssd: Update to 2.9.1.

* gnu/packages/sssd.scm (sssd): Update to 2.9.1.
[native-inputs]: Add bc.
* gnu/packages/patches/sssd-system-directories.patch: Adjust for new version.

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

shell: Really take system into account in the cache key.

Fixes <https://issues.guix.gnu.org/63230>.

Previously, when running "guix shell -s X ...", OPTS would contain
something like '((system . "X") ... (system . "DEFAULT")).  Thus, since
'profile-cached-gc-root' would iterate over it in this order, "DEFAULT"
would be passed to 'profile-file-cache-key' and 'profile-spec-cache-key'
instead of "X".

* guix/scripts/shell.scm (profile-cached-gc-root): Reverse OPTS before
entering 'loop'.

gnu: clang-runtime-15: Fix address sanitizer support

$ guix shell clang-toolchain@15 -- clang -o test -fsanitize=address test.c
ld: cannot find /gnu/store/i429h17s15g48ir9vl1bzp3cv39l5pib-clang-runtime-15.0.7/lib/linux/libclang_rt.asan_static-x86_64.a: No such file or directory
ld: cannot find /gnu/store/i429h17s15g48ir9vl1bzp3cv39l5pib-clang-runtime-15.0.7/lib/linux/libclang_rt.asan-x86_64.a: No such file or directory
clang-15: error: linker command failed with exit code 1 (use -v to see invocation)

* gnu/packages/llvm.scm (clang-runtime-15): Fix address sanitizer
support by bringing back the static libraries.

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

gnu: libleak: Update to 0.3.6.

* gnu/packages/debug.scm (libleak): Update to 0.3.6.

gnu: Add r-numbat.

* gnu/packages/bioinformatics.scm (r-numbat): New variable.

gnu: Add r-bpcells.

* gnu/packages/bioinformatics.scm (r-bpcells): New variable.

gnu: nyxt: Update to 3.4.0.

* gnu/packages/web-browsers.scm (nyxt): Update to 3.4.0.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

gnu: strace: Update to 6.4.

* gnu/packages/linux.scm (strace): Update to 6.4.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

transformations: Allow tuning go packages.

* guix/transformations.scm (build-system-with-tuning-compiler): When
checking if a microarchitecture is supported by the compiler, also check
if it is a go compiler which supports that psabi.  Add a phase after
'setup-go-environment to set the go microarchitecture.

gnu: go: Add CPU tuning targets.

* gnu/packages/golang.scm (go-1.17)[properties]: New field.
(%go-1.17-arm-micro-architectures,
%go-1.17-powerpc64le-micro-architectures,
%go-1.18-x86_64-micro-architectures): New variables.
(go-1.18)[properties]: New field.

guix: cpu: Add gcc-architecture->micro-architecture-level mapping.

* guix/cpu.scm (gcc-architecture->micro-architecture-level): New
variable.

guix: cpu: Refactor cpu->gcc-architecture.

* guix/cpu.scm (cpu->gcc-architecture): Refactor to wrap all the x86_64
options inside a common letrec-syntax.

guix: cpu: Rewrite fallback for x86_64 cpu->gcc-architecture.

* guix/cpu.scm (cpu->gcc-architecture): Adjust the fallback case to use
cpu->micro-architecture-level.

guix: cpu: Add generalized CPU matching.

* guix/cpu.scm (cpu->micro-architecture-level): New variable.

gnu: %gcc-11-x86_64-micro-architectures: Add psabi entries.

* gnu/packages/gcc.scm (%gcc-11-x86_64-micro-architectures): Add entries
for x86_64-v{1,2,3,4}.

gnu: r-tcgabiolinks: Update to 2.28.3.

* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.28.3.

gnu: r-bionero: Update to 1.8.5.

* gnu/packages/bioconductor.scm (r-bionero): Update to 1.8.5.
[propagated-inputs]: Remove r-ggnewscale and r-networkd3; add r-ggdendro and r-rlang.

gnu: r-biocthis: Update to 1.10.3.

* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.10.3.