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Author SHA1 Message Date
Ricardo Wurmus
a065e12f82
gnu: r-pando: Relax requirements. 
* gnu/packages/bioinformatics.scm (r-pando)[arguments]: Patch DESCRIPTION
file.
 2023-07-15 11:11:02 +02:00
Artyom Bologov
b5a5e4d712
gnu: cl-nhooks: Update to 1.2.1. 
* gnu/packages/lisp-xyz.scm (sbcl-nhooks): Update to 1.2.1.
  [native-inputs]: Remove sbcl-fiveam, add sbcl-lisp-unit2.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-07-15 10:56:46 +02:00
Ricardo Wurmus
5dc2a88f99
gnu: node-lts: Install files irrespective of number of hardlinks. 
* gnu/packages/node.scm (node-lts)[arguments]: Add build phase
'ignore-number-of-hardlinks.
 2023-07-15 10:01:58 +02:00
Ricardo Wurmus
529d91de1e
gnu: node-lts: Simplify snippet. 
* gnu/packages/node.scm (node-lts)[source]: Remove quasiquote, trailing #T,
and IF with explicit booleans.
 2023-07-15 10:01:58 +02:00
Tobias Geerinckx-Rice
00ed2901f5
gnu: cabal-install, ghc-cabal-syntax: Use HTTPS home page. 
* gnu/packages/haskell-apps.scm (cabal-install)[home-page]: Use HTTPS.
* gnu/packages/haskell-xyz.scm (ghc-cabal-syntax)[home-page]: Likewise.
 2023-07-09 02:00:17 +02:00
Tobias Geerinckx-Rice
2195645725
gnu: bwa-pssm: Update home page. 
* gnu/packages/bioinformatics.scm (bwa-pssm)[home-page]: Update.
 2023-07-09 02:00:17 +02:00
Tobias Geerinckx-Rice
de088be221
gnu: brdf-explorer: Mark up description. 
* gnu/packages/graphics.scm (brdf-explorer)[synopsis, description]:
 Use @acronym{}.
 2023-07-09 02:00:10 +02:00
Tobias Geerinckx-Rice
c848cd643c
gnu: brdf-explorer: Use Web Archived home page. 
* gnu/packages/graphics.scm (brdf-explorer)[home-page]:
 Refer to Web Archive.
 2023-07-09 02:00:10 +02:00
Tobias Geerinckx-Rice
6f80e25f35
gnu: blasr-libcpp, blasr: Use Web Archived home pages. 
* gnu/packages/bioinformatics.scm (blasr-libcpp, blasr)[home-page]:
 Refer to Web Archive.
 2023-07-09 02:00:10 +02:00
Tobias Geerinckx-Rice
a1ae54b10b
gnu: yadifa: Update to 2.6.4. 
* gnu/packages/dns.scm (yadifa): Update to 2.6.4.
[arguments]: Add a new 'unhard-code phase.
 2023-07-09 02:00:10 +02:00
Tobias Geerinckx-Rice
1c347cd56a
gnu: knot: Use G-expressions. 
* gnu/packages/dns.scm (knot)[arguments]:
Rewrite as G-expressions.
 2023-07-09 02:00:10 +02:00
Tobias Geerinckx-Rice
60bb22a9da
gnu: knot: Update to 3.2.8. 
* gnu/packages/dns.scm (knot): Update to 3.2.8.
 2023-07-09 02:00:09 +02:00
Tobias Geerinckx-Rice
eaac211730
gnu: nsd: Use G-expressions. 
* gnu/packages/dns.scm (nsd)[arguments]:
Rewrite as G-expressions.
 2023-07-09 02:00:09 +02:00
Tobias Geerinckx-Rice
626c0b7cd6
gnu: nsd: Update to 4.7.0. 
* gnu/packages/dns.scm (nsd): Update to 4.7.0.
 2023-07-09 02:00:09 +02:00
Tobias Geerinckx-Rice
69c3a06a1c
gnu: btor2tools: Use HTTPS home page. 
* gnu/packages/maths.scm (btor2tools)[home-page]: Use HTTPS.
 2023-07-09 02:00:09 +02:00
Tobias Geerinckx-Rice
86e95b2205
gnu: boolector: Use HTTPS home page. 
* gnu/packages/maths.scm (boolector)[home-page]: Use HTTPS.
 2023-07-09 02:00:01 +02:00
John Kehayias
917a299831
gnu: python-yubikey-manager: Update to 5.1.1. 
* gnu/packages/security-tokens.scm (python-yubikey-manager): Update to
5.1.1.
[source]: Update url.
[build-system]: Switch to pyproject-build-system.
[arguments]: Delete.
[propagated-inputs]: Remove python-six.  Add python-keyring.  Reorder alphabetically.
[native-inputs]: Remove python-mock.  Add python-makefun, python-poetry-code and
python-pytest.  Reorder alphabetically.

Co-authored-by: John Kehayias <john.kehayias@protonmail.com>
 2023-07-14 12:16:39 -04:00
John Kehayias
51de28452a
gnu: Add python-makefun. 
* gnu/packages/python-xyz.scm (python-makefun): New variable.

Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
 2023-07-14 12:16:37 -04:00
John Kehayias
66f0304e1d
gnu: python-fido2: Update to 1.1.1. 
* gnu/packages/security-tokens.scm (python-fido2): Update to 1.1.1.
[build-system]: Switch to pyproject-build-system.
[arguments]: Enable tests.  Use gexps in phases.
[propagated-inputs]: Remove python-six.  Add python-pyscard.
[native-inputs]: Remove python-mock and python-pyfakefs.  Add
python-poetry-core and python-pytest.

Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
 2023-07-14 12:16:31 -04:00
John Kehayias
221806905b
gnu: python-pyscard: Update to 2.0.7. 
* gnu/packages/security-token.scm (python-pyscard): Update to 2.0.7.
[arguments]{phases}: Use search-input-directory.  Remove trailing #t.

Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
 2023-07-14 12:13:34 -04:00
John Kehayias
09e73683a2
gnu: godot: Update to 4.1. Rename godot@3 to godot-lts. 
* gnu/packages/game-development.scm (godot): Update to 4.1.
[source]: Update snippet: remove embree and enet; add amd-fsr, astcenc,
basis_universal, brotli, linuxbsd_headers, etcpak, meshoptimizer, msdfgen,
noise, openxr, rvo2, spirv-reflect, thorvg, volk, vulkan.
[arguments]: Remove #:scons.  Update #:scons-flags to unbundle more
libraries.
[phases]: Remove 'build-headless phase (headless is no longer has a separate
build).  Add 'fix-dl-open-paths and 'unbundle-xkbcommon phases.  In 'install
phase, remove headless output.  Update 'wrap phase to remove eudev.
[outputs]: Remove headless.
[inputs]: Add dbus, embree, enet, fontconfig, glslang, libpng, harfbuzz,
icu4c, libxkbcommon, openxr, speech-dispatcher, vulkan-loader, zlib.  Remove
bullet.  Rename freetype to freetype-with-brotli.
(godot-lts): New variable.  godot@3 is the LTS release.
* gnu/packages/games.scm (superstarfighter)[native-inputs]: Use it.
[inputs]: Use it.
 2023-07-14 11:08:31 -04:00
John Kehayias
49b0a5ee5f
gnu: Add freetype-with-brotli. 
* gnu/packages/fontutils.scm (freetype-with-brotli): New variable.
 2023-07-14 10:53:19 -04:00
Philip McGrath
ff4f5a725e
gnu: racket: Update to 8.9. 
* gnu/packages/chez.scm (chez-scheme-for-racket): Update to
9.9.9-pre-release.16.
* gnu/packages/racket.scm (%racket-version): Update to 8.9.
(racket)[inputs]<deinprogramm, draw, drracket, future-visualizer, gui>
<htdp, macro-debugger, math, pict, plot, rackunit, redex, scribble>
<slideshow, snip, typed-racket, srfi, swindle, syntax-color>
<web-server>: Update checksums.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-07-14 16:16:25 +02:00
Tobias Geerinckx-Rice
bdd359526e
gnu: avfs: Use HTTPS home page. 
* gnu/packages/file-systems.scm (avfs)[home-page]: Use HTTPS.
 2023-07-09 02:00:11 +02:00
Tobias Geerinckx-Rice
2be1a6795f
gnu: 4ti2: Update home page. 
* gnu/packages/maths.scm (4ti2)[home-page]: Update.
 2023-07-09 02:00:11 +02:00
Tobias Geerinckx-Rice
8a9a7ae36e
gnu: aumix: Use Web Archive URLs. 
* gnu/packages/linux.scm (aumix)[source, home-page]:
Use copies archived by the Wayback Machine.
 2023-07-09 02:00:10 +02:00
Tobias Geerinckx-Rice
0f766e8439
gnu: armadillo: Update to 12.4.1. 
* gnu/packages/maths.scm (armadillo): Update to 12.4.1.
 2023-07-09 02:00:10 +02:00
Tobias Geerinckx-Rice
24d2c2bcda
gnu: aspell-dict-nb: Correct to 0.50-2. 
* gnu/packages/aspell.scm (aspell-dict-nb): Fix version number.
No hash change.
 2023-07-09 02:00:10 +02:00
Tobias Geerinckx-Rice
6d552a1426
gnu: Use aquamaniac.de/ as home page for its projects. 
* gnu/packages/gnucash.scm (gwenhywfar, aqbanking)[home-page]:
Use top-level directory as done upstream.
 2023-07-09 02:00:09 +02:00
Tobias Geerinckx-Rice
67fb8efdf7
gnu: ghostscript: Fix CVE-2023-36664. 
* gnu/packages/ghostscript.scm (ghostscript/fixed): New variable.
(ghostscript)[replacement]: Assign it to new field.
* gnu/packages/patches/ghostscript-CVE-2023-36664.patch,
gnu/packages/patches/ghostscript-CVE-2023-36664-fixup.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
 2023-07-09 02:00:04 +02:00
Tobias Geerinckx-Rice
b29bd4d35e
gnu: antiword: Use Web Archive URLs. 
* gnu/packages/textutils.scm (antiword)[source, home-page]:
Use copies archived by the Wayback Machine.
 2023-07-09 02:00:03 +02:00
Tobias Geerinckx-Rice
5cbb60562d
gnu: anthy: Mark up description. 
* gnu/packages/anthy.scm (anthy)[description]: Use @file{}.
 2023-07-09 02:00:03 +02:00
Tobias Geerinckx-Rice
b0e5576702
gnu: anthy: Add source mirror URL. 
* gnu/packages/anthy.scm (anthy)[source]: Add a Japanese Gentoo
distfiles mirror.
 2023-07-09 02:00:03 +02:00
Tobias Geerinckx-Rice
5799552739
gnu: altermime: Cross-compile. 
* gnu/packages/mail.scm (altermime)[arguments]: Use CC-FOR-TARGET.
Add a new 'do-not-strip phase.
 2023-07-09 02:00:03 +02:00
Tobias Geerinckx-Rice
bce8c88f42
gnu: altermime: Use G-expressions. 
* gnu/packages/mail.scm (altermime)[arguments]:
Rewrite as G-expressions.  Don't explicitly return #t from phases.
 2023-07-09 02:00:02 +02:00
Tobias Geerinckx-Rice
1d7e1fbc38
gnu: altermime: Download over HTTPS. 
* gnu/packages/mail.scm (altermime)[source]: Use HTTPS.
 2023-07-09 02:00:02 +02:00
Tobias Geerinckx-Rice
11ae5491f9
gnu: alpine: Download over HTTPS. 
* gnu/packages/mail.scm (alpine)[source]: Use HTTPS.
 2023-07-09 02:00:02 +02:00
Tobias Geerinckx-Rice
d3fa3e7313
gnu: aiger: Use HTTPS source & home page. 
* gnu/packages/maths.scm (aiger)[source, home-page]: Use HTTPS.
 2023-07-09 02:00:01 +02:00
Tobias Geerinckx-Rice
24e5db1bc2
gnu: borg: Update to 1.2.4. 
* gnu/packages/backup.scm (borg): Update to 1.2.4.
 2023-07-09 02:00:01 +02:00
Christopher Baines
5f7c714c63
gnu: rumpkernel: Don't error for non x86 systems. 
As the lack of handling other systems, say aarch64-linux here seemed to cause
problems with guix pull on these systems.  This should work around #64609.

* gnu/packages/hurd.scm (rumpkernel)[arguments]: Don't error for any system.
 2023-07-14 11:54:02 +01:00
Christopher Baines
a041bbb4bf
Revert "gnu: mig: Update to 1.8+git20230520." 
As noted in the comment, I think using git-fetch caused problems computing
derivaations for i586-linux (Guix would just use more and more memory).

This reverts commit 999a6ac0cf.
 2023-07-14 11:53:12 +01:00
Efraim Flashner
ddbfef2e95
gnu: zig-0.9: Fix building on riscv64-linux. 
* gnu/packages/zig.scm (zig-0.9)[source]: Add patch.
[arguments]: Skip tests when building for riscv64-linux. When building
for riscv64-linux add a phase to adjust the tests.
* gnu/packages/patches/zig-0.9-riscv-support.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2023-07-14 09:20:01 +03:00
Leo Famulari
92d18dc568
gnu: linux-libre: Update to 6.3.13. 
* gnu/packages/linux.scm (linux-libre-6.3-version): Update to 6.3.13.
(linux-libre-6.3-pristine-source): Update hash.
 2023-07-13 22:17:27 -04:00
Ricardo Wurmus
ea81a0417a
gnu: Add python-plotnine. 
* gnu/packages/python-science.scm (python-plotnine): New variable.
 2023-07-13 22:29:24 +02:00
Ricardo Wurmus
f7c6d31e33
gnu: python-mizani: Fix embedded version string. 
* gnu/packages/python-xyz.scm (python-mizani)[native-inputs]: Add
python-setuptools-scm to correct embedded version form 0.0.0 to 0.9.2.
 2023-07-13 22:29:24 +02:00
Janneke Nieuwenhuizen
b4fe82bd8a
gnu: gnumach: Disable builtin networking. 
See also

    https://logs.guix.gnu.org/hurd/2023-05-25.log#163610

* gnu/packages/hurd.scm (gnumach)[arguments]: Add --disable-net-group,
--disable-pcmcia-group, and --disable-wireless-group.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-07-13 19:00:09 +02:00
Janneke Nieuwenhuizen
37256c02a2
gnu: netdde: Resurrect and update to 2.6.32.65-2-e67c284ac1. 
* gnu/packages/patches/netdde-build-fix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/hurd.scm (netdde)[source]: Update to
e67c284ac113d939b10b4578334f27dab29d5b08 and use it.
[inputs]: Add zlib:static.
[arguments]: Remove #true from build phases.  In 'build' phase, remove
obsolete CFLAGS, and also build static version.  In 'install' phase,
install them in <out>/hurd.  There is no check target, so set #:tests?
to #false.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-07-13 18:59:22 +02:00
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
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
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
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
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
Ricardo Wurmus
565d84170a
gnu: r-affy: Update to 1.78.1. 
* gnu/packages/bioconductor.scm (r-affy): Update to 1.78.1.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus
a9d140996c
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.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
b864a5956f
gnu: r-iranges: Update to 2.34.1. 
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.34.1.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
5eaf9f6b83
gnu: r-delayedarray: Update to 0.26.6. 
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.6.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
6e83dee12a
gnu: r-bambu: Update to 3.2.5. 
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.5.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
f0c82ddced
gnu: r-alevinqc: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.16.1.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
4db85c197b
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.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
558637533f
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.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
b4cafa71ae
gnu: Add r-saturn. 
* gnu/packages/bioconductor.scm (r-saturn): New variable.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
990bac0ea5
gnu: Add r-pfamanalyzer. 
* gnu/packages/bioconductor.scm (r-pfamanalyzer): New variable.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
b10bff65be
gnu: r-mzr: Update to 2.34.1. 
* gnu/packages/bioconductor.scm (r-mzr): Update to 2.34.1.
[properties]: Tell updater to not remove the "boost" input.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
ee50cae529
gnu: r-norm: Update to 1.0-11.1. 
* gnu/packages/statistics.scm (r-norm): Update to 1.0-11.1.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
c141725c65
gnu: r-logspline: Update to 2.1.20. 
* gnu/packages/statistics.scm (r-logspline): Update to 2.1.20.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
5a1c16fa18
gnu: r-pbapply: Update to 1.7-2. 
* gnu/packages/statistics.scm (r-pbapply): Update to 1.7-2.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
42c29d9d22
gnu: r-robust: Update to 0.7-2. 
* gnu/packages/statistics.scm (r-robust): Update to 0.7-2.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
2108aa1975
gnu: r-rrcov: Update to 1.7-4. 
* gnu/packages/statistics.scm (r-rrcov): Update to 1.7-4.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
387c1fafce
gnu: r-robustbase: Update to 0.99-0. 
* gnu/packages/statistics.scm (r-robustbase): Update to 0.99-0.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
86c7032abf
gnu: r-deoptimr: Update to 1.0-14. 
* gnu/packages/statistics.scm (r-deoptimr): Update to 1.0-14.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
f9dc378cb4
gnu: r-mvtnorm: Update to 1.2-2. 
* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.2-2.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
e8ef13993e
gnu: r-rmarkdown: Update to 2.23. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.23.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
7cb71cb2fb
gnu: r-rcpparmadillo: Update to 0.12.4.1.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.12.4.1.0.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
b8112b4600
gnu: r-rstudioapi: Update to 0.15.0. 
* gnu/packages/statistics.scm (r-rstudioapi): Update to 0.15.0.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
c5c0f85b77
gnu: r-xml2: Update to 1.3.5. 
* gnu/packages/statistics.scm (r-xml2): Update to 1.3.5.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
4ec94fe0a9
gnu: r-locfit: Update to 1.5-9.8. 
* gnu/packages/statistics.scm (r-locfit): Update to 1.5-9.8.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
1493844a1e
gnu: r-dbplyr: Update to 2.3.3. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 2.3.3.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
6276fbb64a
gnu: r-testthat: Update to 3.1.10. 
* gnu/packages/statistics.scm (r-testthat): Update to 3.1.10.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
b372435930
gnu: r-matrix: Update to 1.6-0. 
* gnu/packages/statistics.scm (r-matrix): Update to 1.6-0.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
f072cd9486
gnu: r-kernsmooth: Update to 2.23-22. 
* gnu/packages/statistics.scm (r-kernsmooth): Update to 2.23-22.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
42b5758b82
gnu: r-paws: Update to 0.3.0. 
* gnu/packages/cran.scm (r-paws): Update to 0.3.0.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
5933aadf2f
gnu: r-paws-compute: Update to 0.3.1. 
* gnu/packages/cran.scm (r-paws-compute): Update to 0.3.1.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
c7d49778e2
gnu: r-paws-storage: Update to 0.3.0. 
* gnu/packages/cran.scm (r-paws-storage): Update to 0.3.0.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
39302d72b8
gnu: r-paws-database: Update to 0.3.0. 
* gnu/packages/cran.scm (r-paws-database): Update to 0.3.0.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
6df06f6712
gnu: r-paws-networking: Update to 0.3.0. 
* gnu/packages/cran.scm (r-paws-networking): Update to 0.3.0.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
5e436baab7
gnu: r-paws-management: Update to 0.3.1. 
* gnu/packages/cran.scm (r-paws-management): Update to 0.3.1.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
969d35e169
gnu: r-paws-machine-learning: Update to 0.3.0. 
* gnu/packages/cran.scm (r-paws-machine-learning): Update to 0.3.0.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
9ac7524dd4
gnu: r-paws-analytics: Update to 0.3.0. 
* gnu/packages/cran.scm (r-paws-analytics): Update to 0.3.0.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
885c7b0b3c
gnu: r-paws-security-identity: Update to 0.3.1. 
* gnu/packages/cran.scm (r-paws-security-identity): Update to 0.3.1.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
f85b362b81
gnu: r-paws-application-integration: Update to 0.3.1. 
* gnu/packages/cran.scm (r-paws-application-integration): Update to 0.3.1.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
688e22f4b7
gnu: r-paws-end-user-computing: Update to 0.3.0. 
* gnu/packages/cran.scm (r-paws-end-user-computing): Update to 0.3.0.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
52312a4551
gnu: r-paws-developer-tools: Update to 0.3.1. 
* gnu/packages/cran.scm (r-paws-developer-tools): Update to 0.3.1.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
17148282b6
gnu: r-paws-cost-management: Update to 0.3.1. 
* gnu/packages/cran.scm (r-paws-cost-management): Update to 0.3.1.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
a656a07e37
gnu: r-paws-customer-engagement: Update to 0.3.0. 
* gnu/packages/cran.scm (r-paws-customer-engagement): Update to 0.3.0.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
8302b17bff
gnu: r-paws-common: Update to 0.5.8. 
* gnu/packages/cran.scm (r-paws-common): Update to 0.5.8.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
432ffdb433
gnu: r-delaporte: Update to 8.1.1. 
* gnu/packages/cran.scm (r-delaporte): Update to 8.1.1.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
6945b8502a
gnu: r-intervals: Update to 0.15.4. 
* gnu/packages/cran.scm (r-intervals): Update to 0.15.4.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
24177b718f
gnu: r-readtext: Update to 0.90. 
* gnu/packages/cran.scm (r-readtext): Update to 0.90.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
7ecefb14dd
gnu: r-downlit: Update to 0.4.3. 
* gnu/packages/cran.scm (r-downlit): Update to 0.4.3.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
362b352c92
gnu: r-mlr3tuning: Update to 0.19.0. 
* gnu/packages/cran.scm (r-mlr3tuning): Update to 0.19.0.
[native-inputs]: Add r-knitr.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
11fe7a5bdc
gnu: r-seurat: Update to 4.3.0.1. 
* gnu/packages/cran.scm (r-seurat): Update to 4.3.0.1.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
e744151010
gnu: r-scattermore: Update to 1.2. 
* gnu/packages/cran.scm (r-scattermore): Update to 1.2.
 2023-07-12 14:29:07 +02:00
Ricardo Wurmus
869a579c83
gnu: r-confintr: Update to 1.0.2. 
* gnu/packages/cran.scm (r-confintr): Update to 1.0.2.
 2023-07-12 14:29:07 +02:00