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2023-07-13services: childhurd: Bump default qemu memory to 2048MB.Janneke Nieuwenhuizen
When booting with pci-arbiter and rumpdisk and using 1024MB of memory for qemu, booting hangs, or seems to hang, at the end of the rumpdisk boot messages. At least 1200MB is required, currently. * gnu/services/virtualization.scm (<hurd-vm-configuration>)[memory-size]: Bump to 2048. * gnu/system/examples/bare-hurd.tmpl: Suggest using 2048 here too. Update example `guix system image' and "qemu" command lines too. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-07-13hurd-boot: Setup pci-arbiter and rumpdisk translators.Janneke Nieuwenhuizen
* gnu/build/hurd-boot.scm (make-hurd-device-nodes): Create "servers/bus/pci. (set-hurd-device-translators): Create transators for pci-arbiter, rumpdisk, and /dev/wd0..3s1..4. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-07-13gnu: hurd: Add rumpkernel.Janneke Nieuwenhuizen
* gnu/packages/patches/hurd-fix-rumpdisk-build.patch, gnu/packages/patches/hurd-rumpdisk-no-hd.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/hurd.scm (hurd): Use them. (hurd)[inputs]: Replace util-linux with util-linux:static, add parted, rumpkernel. [arguments]: Rename `prepare-dde' phase to 'prepare-addons'. Add "rumpdisk" directory. Add --enable-static-progs=... option to #:configure-flags, and remove --without-parted. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-07-13gnu: parted: Support building for the Hurd.Janneke Nieuwenhuizen
* gnu/packages/disk.scm (parted)[inputs]: Remove lvm2, add hurd-minimal when building for the Hurd. [arguments]: Add configure-flag '--disable-device-mapper' when building for the Hurd. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-07-13gnu: hurd-minimal: Include libshouldbeinlibc and libstore.Janneke Nieuwenhuizen
* gnu/packages/hurd.scm (hurd-minimal)[inputs]: Add gnumach-headers. [arguments]: Rewrite to include libshouldbeinlibc and libstore. * gnu/packages/cross-base.scm (cross-kernel-headers*): Update xhurd-minimal accordingly: Add xgnumach-headers, add them to cpath, use gexps for modify-phases, add delete-shared-target phase. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-07-13gnu: Add rumpkernel.Janneke Nieuwenhuizen
This uses the Debian Salsa rumpkernel package git as upstream as that is where delopment happens. Once things have stabalized upstream may change to the NetBSD git from where Debian takes their snapshots. * gnu/packages/hurd.scm (rumpkernel): New variable. (hurd-headers)[native-inputs]: Use cross-mig directly. (gnumach)[native-inputs]: Likewise. (hurd)[native-inputs]: Likewise. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
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.
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