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117250 commits

Author SHA1 Message Date
Janneke Nieuwenhuizen
bbfb41ed9d
gnu: gnumach: Support "noide" argument.
* gnu/packages/patches/gnumach-support-noide.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/hurd.scm (gnumach-headers): Use it.
* doc/guix.texi (Bootloader Configuration): Document it.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-07-13 18:59:17 +02:00
Janneke Nieuwenhuizen
c22c29b0c4
bootloader: grub: Use rumpdisk-style root when booting with "noide".
* gnu/bootloader/grub.scm (make-grub-configuration): When "noide" is in
arguments, use device name "wd0" rather than "hd0".

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-07-13 18:59:13 +02:00
Janneke Nieuwenhuizen
7f86dad611
system: hurd: Boot with pci.arbiter and rumpdisk.
* gnu/system.scm (hurd-multiboot-modules): Add commands for pci.arbiter and
rumpdisk.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-07-13 18:59:06 +02:00
Janneke Nieuwenhuizen
09657f3ee7
services: childhurd: Bump default qemu memory to 2048MB.
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>
2023-07-13 18:59:02 +02:00
Janneke Nieuwenhuizen
fe873fb417
hurd-boot: Setup pci-arbiter and rumpdisk translators.
* 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>
2023-07-13 18:58:58 +02:00
Janneke Nieuwenhuizen
5981e99f0a
gnu: hurd: Add rumpkernel.
* 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>
2023-07-13 18:58:53 +02:00
Janneke Nieuwenhuizen
451b2db3df
gnu: parted: Support building for the Hurd.
* 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>
2023-07-13 18:58:47 +02:00
Janneke Nieuwenhuizen
c8799fafa4
gnu: hurd-minimal: Include libshouldbeinlibc and libstore.
* 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>
2023-07-13 18:58:43 +02:00
Janneke Nieuwenhuizen
f86de02dde
gnu: Add rumpkernel.
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>
2023-07-13 18:58:39 +02:00
Janneke Nieuwenhuizen
18757f1a25
gnu: hurd: Update libpciaccess to 0.17.
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>
2023-07-13 18:58:34 +02:00
Janneke Nieuwenhuizen
5ffdcb3aa1
gnu: Add libpciaccess-0.17.
* gnu/packages/xorg.scm (libpciaccess-0.17): New variable.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
2023-07-13 18:58:06 +02:00
Josselin Poiret
1f19387ca7
gnu: hurd: Update to v0.9.git20230216.
* gnu/packages/hurd.scm (hurd-headers): Update to v0.9.git20230216.
2023-07-13 18:20:07 +02:00
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