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2023-07-13gnu: hurd: Update libpciaccess to 0.17.Janneke Nieuwenhuizen
As suggested by youpi on IRC https://logs.guix.gnu.org/hurd/2023-05-17.log#132259 libpciaccess-0.16 is too old for the Hurd and would need Hurd-specific patches while libpciaccess-0.17 works out of the box. * gnu/packages/hurd.scm (hurd)[inputs]: Use libpciaccess-0.17. (netdde)[inputs]: Likewise. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-07-13gnu: Add libpciaccess-0.17.Janneke Nieuwenhuizen
* gnu/packages/xorg.scm (libpciaccess-0.17): New variable. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-07-13gnu: hurd: Update to v0.9.git20230216.Josselin Poiret
* gnu/packages/hurd.scm (hurd-headers): Update to v0.9.git20230216.
2023-07-13gnu: mig: Update to 1.8+git20230520.Josselin Poiret
* 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.
2023-07-13gnu: gnumach: Update to 1.8+git20221224.Josselin Poiret
* gnu/packages/hurd.scm (gnumach-headers): Update to 1.8+git20221224.
2023-07-13gnu: Add libc-for-target and glibc/hurd.Josselin Poiret
* 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>
2023-07-13gnu: hurd: Update supported systems.Josselin Poiret
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal, hurd-core-headers, gnumach): Update supported systems to %hurd-systems.
2023-07-13gnu: gnumach-headers: Cross-build without relying on x86.Josselin Poiret
* 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.
2023-07-13gnu: glibc/hurd-headers: Properly cross-build.Josselin Poiret
* 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.
2023-07-13gnu: arpack-ng: Update to 3.9.0.Ludovic Courtès
* 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.
2023-07-13gnu: sssd: Update to 2.9.1.Timotej Lazar
* 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>
2023-07-13shell: Really take system into account in the cache key.Ludovic Courtès
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'.
2023-07-13gnu: clang-runtime-15: Fix address sanitizer supportTobias Kortkamp
$ 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>
2023-07-13gnu: libleak: Update to 0.3.6.fanquake
* gnu/packages/debug.scm (libleak): Update to 0.3.6.
2023-07-12gnu: Add r-numbat.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-numbat): New variable.
2023-07-12gnu: Add r-bpcells.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bpcells): New variable.
2023-07-12gnu: nyxt: Update to 3.4.0.Andre A. Gomes
* gnu/packages/web-browsers.scm (nyxt): Update to 3.4.0. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-07-12gnu: strace: Update to 6.4.Michael Ford
* gnu/packages/linux.scm (strace): Update to 6.4. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-07-12transformations: Allow tuning go packages.Efraim Flashner
* 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.
2023-07-12gnu: go: Add CPU tuning targets.Efraim Flashner
* 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.
2023-07-12guix: cpu: Add gcc-architecture->micro-architecture-level mapping.Efraim Flashner
* guix/cpu.scm (gcc-architecture->micro-architecture-level): New variable.
2023-07-12guix: cpu: Refactor cpu->gcc-architecture.Efraim Flashner
* guix/cpu.scm (cpu->gcc-architecture): Refactor to wrap all the x86_64 options inside a common letrec-syntax.
2023-07-12guix: cpu: Rewrite fallback for x86_64 cpu->gcc-architecture.Efraim Flashner
* guix/cpu.scm (cpu->gcc-architecture): Adjust the fallback case to use cpu->micro-architecture-level.
2023-07-12guix: cpu: Add generalized CPU matching.Efraim Flashner
* guix/cpu.scm (cpu->micro-architecture-level): New variable.
2023-07-12gnu: %gcc-11-x86_64-micro-architectures: Add psabi entries.Efraim Flashner
* gnu/packages/gcc.scm (%gcc-11-x86_64-micro-architectures): Add entries for x86_64-v{1,2,3,4}.
2023-07-12gnu: r-tcgabiolinks: Update to 2.28.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.28.3.
2023-07-12gnu: r-bionero: Update to 1.8.5.Ricardo Wurmus
* 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.
2023-07-12gnu: r-biocthis: Update to 1.10.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.10.3.
2023-07-12gnu: r-basilisk: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.12.1.
2023-07-12gnu: r-delayedmatrixstats: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.22.1.
2023-07-12gnu: r-sparsematrixstats: Update to 1.12.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.12.2.
2023-07-12gnu: r-fishpond: Update to 2.6.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-fishpond): Update to 2.6.2.
2023-07-12gnu: r-bioccheck: Update to 1.36.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.36.1.
2023-07-12gnu: r-universalmotif: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.18.1.
2023-07-12gnu: r-variancepartition: Update to 1.30.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.30.2.
2023-07-12gnu: r-variantfiltering: Update to 1.36.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.36.1.
2023-07-12gnu: r-quasr: Update to 1.40.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-quasr): Update to 1.40.1.
2023-07-12gnu: r-motifbreakr: Update to 2.14.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.14.2.
2023-07-12gnu: r-lpsymphony: Update to 1.28.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.28.1. [native-inputs]: Add gfortran.
2023-07-12gnu: r-glmgampoi: Update to 1.12.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.12.2.
2023-07-12gnu: r-interactionset: Update to 1.28.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.28.1.
2023-07-12gnu: r-matrixgenerics: Update to 1.12.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.12.2.
2023-07-12gnu: r-systempiper: Update to 2.6.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.6.3.
2023-07-12gnu: r-summarizedexperiment: Update to 1.30.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.30.2.
2023-07-12gnu: r-maaslin2: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-maaslin2): Update to 1.14.1. [propagated-inputs]: Remove r-lpsymphony; add r-tibble.
2023-07-12gnu: r-limma: Update to 3.56.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-limma): Update to 3.56.2.
2023-07-12gnu: r-lfa: Update to 2.0.11.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-lfa): Update to 2.0.11. [propagated-inputs]: Add r-rspectra.
2023-07-12gnu: r-genomicfeatures: Update to 1.52.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.52.1.
2023-07-12gnu: r-deseq2: Update to 1.40.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.40.2.
2023-07-12gnu: r-biomart: Update to 2.56.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.56.1.
generated by cgit v1.2.3 (git 2.44.0) at 2024-06-02 09:15:14 +0000