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Author SHA1 Message Date
Josselin Poiret 999a6ac0cf
gnu: mig: Update to 1.8+git20230520. 
* gnu/packages/hurd.scm (mig)[source]: Update to 1.8+git20230520.
* gnu/packages/patches/gnumach-add-missing-const_mach_port_name_array_t-type.patch:
Drop patch.
* gnu/local.mk (dist_patch_DATA): Unregister it.
 2023-07-13 18:20:06 +02:00
Josselin Poiret 2edd67d34b
gnu: gnumach: Update to 1.8+git20221224. 
* gnu/packages/hurd.scm (gnumach-headers): Update to 1.8+git20221224.
 2023-07-13 18:20:06 +02:00
Josselin Poiret 0dd293b4d9
gnu: Add libc-for-target and glibc/hurd. 
* gnu/packages/patches/glibc-2.37-hurd-clock_t_centiseconds.patch
* gnu/packages/patches/glibc-2.37-hurd-local-clock_gettime_MONOTONIC.patch
* gnu/packages/patches/glibc-2.37-versioned-locpath.patch: New patches.
* gnu/local.mk (dist_patch_DATA): Register them.

* gnu/packages/base.scm (glibc/hurd, libc-for-target): New variables.
(glibc/hurd-headers): Use glibc/hurd.
* gnu/packages/commencement.scm (glibc-final-with-bootstrap-bash)[outputs,
source, arguments]
(glibc-final)[source]: Use libc-for-target instead of glibc.
* gnu/packages/cross-base.scm (cross-libc/deprecated, cross-libc*): Use
libc-for-target.

This part fixes

    https://issues.guix.gnu.org/63641#25

* gnu/packages/commencement.scm (%final-inputs): Change to memoized lambda
taking "system".
* gnu/packages/commencement.scm (canonical-package): Likewise, and update
user, passing (%current-system).
(make-gcc-toolchain): Update user, passing (%current-system).
* gnu/packages/base.scm (%final-inputs): Likewise.
* guix/scripts/refresh.scm (options->update-specs): Likewise.
* guix/build-system/gnu.scm (standard-packages): Add optional "system"
parameter.
(lower): Update caller.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
Co-authored-by: Janneke Nieuwenhuizen <janneke@gnu.org>
 2023-07-13 18:20:05 +02:00
Josselin Poiret 0613df90dd
gnu: hurd: Update supported systems. 
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal,
hurd-core-headers, gnumach): Update supported systems to %hurd-systems.
 2023-07-13 18:20:04 +02:00
Josselin Poiret c2bb342b5f
gnu: gnumach-headers: Cross-build without relying on x86. 
* gnu/packages/hurd.scm (gnumach-headers): Remove configure flags where we
say the builder is running x86.
* gnu/packages/cross-base.scm (cross-gnumach-headers): Work around limitation
of build system, by manually changing the target host_cpu without relying on
--host, because we don't have a working cross-compiler yet.
 2023-07-13 18:20:04 +02:00
Josselin Poiret 85ebfcf4ff
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.
 2023-07-13 18:20:01 +02:00
Ludovic Courtès ff208b4b62
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.
 2023-07-13 17:59:57 +02:00
Timotej Lazar 5594f4c999
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>
 2023-07-13 17:58:38 +02:00
Ludovic Courtès 9c51330315
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'.
 2023-07-13 17:20:02 +02:00
Tobias Kortkamp ae92d98b93
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>
 2023-07-13 17:20:02 +02:00
fanquake dd4c199210
gnu: libleak: Update to 0.3.6. 
* gnu/packages/debug.scm (libleak): Update to 0.3.6.
 2023-07-13 10:47:33 +02:00
Ricardo Wurmus 2794caed7c
gnu: Add r-numbat. 
* gnu/packages/bioinformatics.scm (r-numbat): New variable.
 2023-07-12 21:34:07 +02:00
Ricardo Wurmus 3b524cde71
gnu: Add r-bpcells. 
* gnu/packages/bioinformatics.scm (r-bpcells): New variable.
 2023-07-12 16:45:42 +02:00
Andre A. Gomes 713d3952e4
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>
 2023-07-12 16:11:40 +02:00
Michael Ford e94abf55b7
gnu: strace: Update to 6.4. 
* gnu/packages/linux.scm (strace): Update to 6.4.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-07-12 15:57:54 +02:00
Efraim Flashner 691b97aed9
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.
 2023-07-12 16:48:28 +03:00
Efraim Flashner b90310cf85
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.
 2023-07-12 16:48:28 +03:00
Efraim Flashner 1701b1244d
guix: cpu: Add gcc-architecture->micro-architecture-level mapping. 
* guix/cpu.scm (gcc-architecture->micro-architecture-level): New
variable.
 2023-07-12 16:48:28 +03:00
Efraim Flashner 4dd5fa9e76
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.
 2023-07-12 16:48:28 +03:00
Efraim Flashner b93057256f
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.
 2023-07-12 16:48:28 +03:00
Efraim Flashner cb0cab2db0
guix: cpu: Add generalized CPU matching. 
* guix/cpu.scm (cpu->micro-architecture-level): New variable.
 2023-07-12 16:48:27 +03:00
Efraim Flashner db6503a6ff
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}.
 2023-07-12 16:48:24 +03:00
Ricardo Wurmus f2f27c4952
gnu: r-tcgabiolinks: Update to 2.28.3. 
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.28.3.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 2ef18c24a4
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.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus cbdaf26d0c
gnu: r-biocthis: Update to 1.10.3. 
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.10.3.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 165a4755a4
gnu: r-basilisk: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.12.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus bdd11e0229
gnu: r-delayedmatrixstats: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.22.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 5a61307327
gnu: r-sparsematrixstats: Update to 1.12.2. 
* gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.12.2.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 72c0125649
gnu: r-fishpond: Update to 2.6.2. 
* gnu/packages/bioconductor.scm (r-fishpond): Update to 2.6.2.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 3bfbd6ddd8
gnu: r-bioccheck: Update to 1.36.1. 
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.36.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus aada7f3a53
gnu: r-universalmotif: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.18.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus e728562cd3
gnu: r-variancepartition: Update to 1.30.2. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.30.2.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus c4ea43f75c
gnu: r-variantfiltering: Update to 1.36.1. 
* gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.36.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 8637eba2a5
gnu: r-quasr: Update to 1.40.1. 
* gnu/packages/bioconductor.scm (r-quasr): Update to 1.40.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 1d53aa680e
gnu: r-motifbreakr: Update to 2.14.2. 
* gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.14.2.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus a98f8bdcf3
gnu: r-lpsymphony: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.28.1.
[native-inputs]: Add gfortran.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 0514c45d4a
gnu: r-glmgampoi: Update to 1.12.2. 
* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.12.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 75a5504e49
gnu: r-interactionset: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.28.1.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 6652f72e13
gnu: r-matrixgenerics: Update to 1.12.2. 
* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.12.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 1b83659902
gnu: r-systempiper: Update to 2.6.3. 
* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.6.3.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 0a0304ef3a
gnu: r-summarizedexperiment: Update to 1.30.2. 
* gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.30.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 464ad1fd79
gnu: r-maaslin2: Update to 1.14.1. 
* gnu/packages/bioconductor.scm (r-maaslin2): Update to 1.14.1.
[propagated-inputs]: Remove r-lpsymphony; add r-tibble.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 5588562fb9
gnu: r-limma: Update to 3.56.2. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.56.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 5db8d3e600
gnu: r-lfa: Update to 2.0.11. 
* gnu/packages/bioconductor.scm (r-lfa): Update to 2.0.11.
[propagated-inputs]: Add r-rspectra.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 3193a2a04d
gnu: r-genomicfeatures: Update to 1.52.1. 
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.52.1.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 2b62bc3f67
gnu: r-deseq2: Update to 1.40.2. 
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.40.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 6604189891
gnu: r-biomart: Update to 2.56.1. 
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.56.1.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 1f0633db11
gnu: r-annotationforge: Update to 1.42.2. 
* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.42.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus c397d6a5e1
gnu: r-genomeinfodb: Update to 1.36.1. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.36.1.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 3c201e1aab
gnu: r-annotationdbi: Update to 1.62.2. 
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.62.2.
 2023-07-12 14:29:10 +02:00