| Age | Commit message (Expand) | Author |
|---|
| 2023-07-13 | 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>
| Josselin Poiret |
| 2023-07-13 | 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.
| Josselin Poiret |
| 2023-07-13 | 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.
| Josselin Poiret |
| 2023-07-13 | 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.
| Josselin Poiret |
| 2023-07-13 | 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.
| Ludovic Courtès |
| 2023-07-13 | 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>
| Timotej Lazar |
| 2023-07-13 | 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>
| Tobias Kortkamp |
| 2023-07-13 | gnu: libleak: Update to 0.3.6....* gnu/packages/debug.scm (libleak): Update to 0.3.6.
| fanquake |
| 2023-07-12 | gnu: Add r-numbat....* gnu/packages/bioinformatics.scm (r-numbat): New variable.
| Ricardo Wurmus |
| 2023-07-12 | gnu: Add r-bpcells....* gnu/packages/bioinformatics.scm (r-bpcells): New variable.
| Ricardo Wurmus |
| 2023-07-12 | 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>
| Andre A. Gomes |
| 2023-07-12 | gnu: strace: Update to 6.4....* gnu/packages/linux.scm (strace): Update to 6.4.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
| Michael Ford |
| 2023-07-12 | 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.
| Efraim Flashner |
| 2023-07-12 | 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}.
| Efraim Flashner |
| 2023-07-12 | gnu: r-tcgabiolinks: Update to 2.28.3....* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.28.3.
| Ricardo Wurmus |
| 2023-07-12 | 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.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-biocthis: Update to 1.10.3....* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.10.3.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-basilisk: Update to 1.12.1....* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.12.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-delayedmatrixstats: Update to 1.22.1....* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.22.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-sparsematrixstats: Update to 1.12.2....* gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.12.2.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-fishpond: Update to 2.6.2....* gnu/packages/bioconductor.scm (r-fishpond): Update to 2.6.2.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-bioccheck: Update to 1.36.1....* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.36.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-universalmotif: Update to 1.18.1....* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.18.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-variancepartition: Update to 1.30.2....* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.30.2.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-variantfiltering: Update to 1.36.1....* gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.36.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-quasr: Update to 1.40.1....* gnu/packages/bioconductor.scm (r-quasr): Update to 1.40.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-motifbreakr: Update to 2.14.2....* gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.14.2.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-lpsymphony: Update to 1.28.1....* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.28.1.
[native-inputs]: Add gfortran.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-glmgampoi: Update to 1.12.2....* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.12.2.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-interactionset: Update to 1.28.1....* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.28.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-matrixgenerics: Update to 1.12.2....* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.12.2.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-systempiper: Update to 2.6.3....* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.6.3.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-summarizedexperiment: Update to 1.30.2....* gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.30.2.
| Ricardo Wurmus |
| 2023-07-12 | 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.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-limma: Update to 3.56.2....* gnu/packages/bioconductor.scm (r-limma): Update to 3.56.2.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-lfa: Update to 2.0.11....* gnu/packages/bioconductor.scm (r-lfa): Update to 2.0.11.
[propagated-inputs]: Add r-rspectra.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-genomicfeatures: Update to 1.52.1....* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.52.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-deseq2: Update to 1.40.2....* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.40.2.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-biomart: Update to 2.56.1....* gnu/packages/bioconductor.scm (r-biomart): Update to 2.56.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-annotationforge: Update to 1.42.2....* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.42.2.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-genomeinfodb: Update to 1.36.1....* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.36.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-annotationdbi: Update to 1.62.2....* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.62.2.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-affy: Update to 1.78.1....* gnu/packages/bioconductor.scm (r-affy): Update to 1.78.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-isoformswitchanalyzer: Update to 2.0.1....* gnu/packages/bioconductor.scm (r-isoformswitchanalyzer): Update to 2.0.1.
[propagated-inputs]: Remove r-drimseq; add r-biocparallel, r-pfamanalyzer, r-s4vectors,
r-saturn, r-summarizedexperiment, r-sva, and r-tidyr.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-iranges: Update to 2.34.1....* gnu/packages/bioconductor.scm (r-iranges): Update to 2.34.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-delayedarray: Update to 0.26.6....* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.6.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-bambu: Update to 3.2.5....* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.5.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-alevinqc: Update to 1.16.1....* gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.16.1.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-ancombc: Update to 2.2.1....* gnu/packages/bioconductor.scm (r-ancombc): Update to 2.2.1.
[propagated-inputs]: Remove r-dplyr, r-emmeans, r-magrittr, r-rlang, r-rngtools,
r-tibble, and r-tidyr; add r-gtools, r-matrix, and r-multcomp.
| Ricardo Wurmus |
| 2023-07-12 | gnu: r-gdsfmt: Update to 1.36.1....* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.36.1.
[properties]: Tell updater to leave the extra inputs be.
| Ricardo Wurmus |
