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Author SHA1 Message Date
Ricardo Wurmus 823def76d4
gnu: r-gofuncr: Update to 1.22.2. 
* gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.22.2.

Change-Id: Iba4be0c63d792caddcea69ee77aa94ce6869c1d2
 2024-02-11 16:55:14 +01:00
Ricardo Wurmus 666393ec34
gnu: r-glmgampoi: Update to 1.14.2. 
* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.14.2.

Change-Id: Id7265b49246e75d23086dc159da9b4f69a756a7d
 2024-02-11 16:55:14 +01:00
Ricardo Wurmus 579683f16f
gnu: r-trajectoryutils: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-trajectoryutils): Update to 1.10.1.

Change-Id: I18a94851cd139951c2987054c22f01809d2479b3
 2024-02-11 16:55:14 +01:00
Ricardo Wurmus 95785f4587
gnu: r-rcas: Update to 1.28.3. 
* gnu/packages/bioconductor.scm (r-rcas): Update to 1.28.3.
[propagated-inputs]: Remove r-ggseqlogo and pandoc; add r-seqlogo.

Change-Id: I8be7d8fc4278c8ec2db6932935f70292a4f47049
 2024-02-11 16:55:14 +01:00
Ricardo Wurmus d24ba5f374
gnu: r-genomeinfodb: Update to 1.38.6. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.38.6.

Change-Id: I57a53d4a73e9b4ce36d97092dab0789d6509484f
 2024-02-11 16:55:13 +01:00
Ricardo Wurmus 87110a22a9
gnu: r-dittoseq: Update to 1.14.2. 
* gnu/packages/bioconductor.scm (r-dittoseq): Update to 1.14.2.

Change-Id: I8930f72b47ff92b3b798d9a45fc0598bec1ba53e
 2024-02-11 16:55:13 +01:00
Ricardo Wurmus 64eb32a2d0
gnu: r-bsgenome: Update to 1.70.2. 
* gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.70.2.

Change-Id: I45ba28279e0b843bcd635c2e30fb696e85195ce7
 2024-02-11 16:55:13 +01:00
Ricardo Wurmus 6393305afa
gnu: r-animalcules: Update to 1.18.3. 
* gnu/packages/bioconductor.scm (r-animalcules): Update to 1.18.3.

Change-Id: I4f8d5897af796afbce269748c6a5676db72e4baf
 2024-02-11 16:55:13 +01:00
Ricardo Wurmus 39e92f8b66
gnu: r-curatedtcgadata: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.24.1.

Change-Id: I42ae64544b53d6ddd72b948af4093ef4dd31a9c6
 2024-02-11 16:55:13 +01:00
Ricardo Wurmus 2ac299e958
gnu: r-rhdf5lib: Update to 1.24.2. 
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.24.2.
[propagated-inputs]: Remove r-biocstyle and r-stringr.
[native-inputs]: Remove r-rmarkdown.

Change-Id: I76b1601397bc69651c0b788404c6b0c67d830830
 2024-02-11 16:55:13 +01:00
Andy Tai 240bbfee8d
gnu: parallel: Update to 20240122. 
* gnu/packages/parallel.scm (parallel): Update to 20240122.

Change-Id: I4e416cbad5b6f4267a9aab7996c9156a861e3ad1
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2024-02-11 12:20:53 +02:00
(unmatched-parenthesis 8f258b7c7a
gnu: parinfer-rust: Add phase to install editor plugins. 
* gnu/packages/text-editors.scm (rust-parinfer)[arguments]: Install the
bundled Vim and Kakoune plugins.

Change-Id: I881315481ec08c59576c4530ae72b877c399fc66
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2024-02-11 12:14:09 +02:00
David Pflug b6439fc5f8
gnu: Add python-gguf. 
* gnu/packages/machine-learning.scm (python-gguf): New variable.

Change-Id: Icf6138486cccc5b4c3141424baccf17c4edb3449
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2024-02-11 09:20:16 +01:00
Ludovic Courtès 9edbb2d7a4
services: Add ‘virtual-build-machine’ service. 
* gnu/services/virtualization.scm (<virtual-build-machine>): New record type.
(%build-vm-ssh-port, %build-vm-secrets-port, %x86-64-intel-cpu-models):
New variables.
(qemu-cpu-model-for-date, virtual-build-machine-ssh-port)
(virtual-build-machine-secrets-port): New procedures.
(%minimal-vm-syslog-config, %virtual-build-machine-operating-system):
New variables.
(virtual-build-machine-default-image):
(virtual-build-machine-account-name)
(virtual-build-machine-accounts)
(build-vm-shepherd-services)
(initialize-build-vm-substitutes)
(build-vm-activation)
(virtual-build-machine-offloading-ssh-key)
(virtual-build-machine-activation)
(virtual-build-machine-secret-root)
(check-vm-availability)
(build-vm-guix-extension): New procedures.
(initialize-hurd-vm-substitutes): Remove.
(hurd-vm-activation): Rewrite in terms of ‘build-vm-activation’.
* gnu/system/vm.scm (linux-image-startup-command): New procedure.
(operating-system-for-image): Export.
* gnu/tests/virtualization.scm (run-command-over-ssh): New procedure,
extracted from…
(run-childhurd-test): … here.
[test]: Adjust accordingly.
(%build-vm-os): New variable.
(run-build-vm-test): New procedure.
(%test-build-vm): New variable.
* doc/guix.texi (Virtualization Services)[Virtual Build Machines]: New
section.
(Build Environment Setup): Add cross-reference.

Change-Id: I0a47652a583062314020325aedb654f11cb2499c
 2024-02-10 23:21:07 +01:00
Ludovic Courtès 5f34796dc4
marionette: Add #:peek? to ‘wait-for-tcp-port?’. 
* gnu/build/marionette.scm (wait-for-tcp-port): Add #:peek? parameter
and honor it.

Change-Id: Ie7515a5223299390ab8af6fe5aa3cf63ba5c8078
 2024-02-10 22:59:56 +01:00
Ludovic Courtès b0a5c0742f
vm: Add ‘cpu-count’ field to <virtual-machine>. 
* gnu/system/vm.scm (<virtual-machine>)[cpu-count]: New field.
(virtual-machine-compiler): Honor it.

Change-Id: I907a89365f32ac7a9981c4ae5f59cf6eb199c3cc
 2024-02-10 22:59:52 +01:00
Ludovic Courtès 7a4f585ae1
vm: Export <virtual-machine> accessors. 
* gnu/system/vm.scm: Export.

Change-Id: If65d96f4052d070af5baee26f3dd9b233b8480f4
 2024-02-10 22:59:49 +01:00
Ludovic Courtès f7447b1a32
vm: Add ‘date’ field to <virtual-machine>. 
* gnu/system/vm.scm (<virtual-machine>)[date]: New field.
(virtual-machine-compiler): Honor it.

Change-Id: Idab1c152466d57cbc6784c031a99fdfd37080bcb
 2024-02-10 22:59:46 +01:00
Ludovic Courtès f331a667d3
services: secret-service: Make the endpoint configurable. 
Until now, the secret service had a hard-coded TCP endpoint on port
1004.  This change lets users specify arbitrary socket addresses.

* gnu/build/secret-service.scm (socket-address->string): New procedure,
taken from Shepherd.
(secret-service-send-secrets): Replace ‘port’ by ‘address’ and adjust
accordingly.
(secret-service-receive-secrets): Likewise.
* gnu/services/virtualization.scm (secret-service-shepherd-services):
Likewise.
(secret-service-operating-system): Add optional ‘address’ parameter and
honor it.  Adjust ‘start’ method accordingly.

Change-Id: I87a9514f1c170dca756ce76083d7182c6ebf6578
 2024-02-10 22:59:43 +01:00
Marco Rimoldi 11d5b505e5
gnu: openmolar-1: Update to release 1.1.6-g81838c8 and partial runtime fix. 
Fixes <https://issues.guix.gnu.org/29365>.

WebKit was removed from Qt5 in favor of WebEngine; upstream addressed
this in their last stable release, in 2018.  The package still fails at
runtime: this commit lays the ground for further fixes.

* gnu/packages/medical.scm (openmolar-1): Update to release 1.1.6-g81838c8.
[arguments]: Extend 'patch-/usr phase to source file localsettings.py.
[inputs]: Add python-pyqtwebengine.
[propagated-inputs]: Add qtwebengine-5.

Change-Id: Ia4e4c052397201c26834dec2358ca5c20beb581d
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-02-10 22:54:05 +01:00
TimotheeMathieu 9474e64b09
gnu: Add python-scikit-opt. 
* gnu/packages/python-science.scm (python-scikit-opt): New variable.

Change-Id: I47d6b35d9658a37a242b4db61d293fa7efd33802
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-02-10 22:51:59 +01:00
Mathieu Othacehe b64862e5cb
gnu: gnupg: Fix cross-compilation. 
* gnu/packages/gnupg.scm (gnupg)[arguments]: Pass libraries prefixes when
cross-crompiling.

Change-Id: I461ba02ddf5bb23277bd6685c2106e4ad37e2184
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-02-10 21:00:03 +01:00
Nguyễn Gia Phong e94e8eaedd
gnu: vim: Update to 9.1.0059. 
* gnu/packages/vim.scm (vim): Update to 9.1.0059.

Change-Id: Idf89d04a6c4e2297bcaad7a8b275de4a124001a9
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2024-02-10 18:48:39 +02:00
Sharlatan Hellseher e257de4365
gnu: emulators: Adjust copyright header. 
This is follow up commit 9ffdcb2492.

* gnu/packages/emulators.scm: Update copyright for "Felix Gruber
<felgru@posteo.net>".
* gnu/packages/simulation.scm: Remove "Copyright © 2024 Felix Gruber
<felgru@posteo.net>".

Change-Id: I3f39abb0fbe05e7c6af9715fb6cc41c20b6f0a45
 2024-02-10 15:58:51 +00:00
Sören Tempel 121bf9b296
gnu: fcft: Enable shaping support. 
While utf8proc is an optional dependency, it is required for shaping
support. Without utf8proc, fcft_rasterize_text_run_utf32() is a no-op.
This is a popular function used—among other things—by yambar, foot,
fuzzel and fnott. Therefore, many other Linux distributions (Arch,
Debian, Fedora, …) enable this feature and I think it would be nice
to have in Guix as well.

* gnu/packages/fontutils.scm (fcft): Depend on utf8proc.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I7489dbc7a42ffcca509d090df7d2a6250bf996ff
 2024-02-10 15:06:50 +00:00
Greg Hogan 354de73fa4
gnu: lldb: Update to 17.0.6. 
* gnu/packages/llvm.scm (lldb): Update to 17.0.6.
[inputs]: Change from LLVM-15 and CLANG-15 to LLVM-17 and CLANG-17.

Change-Id: Iad04ee722c81ecb223ea4d57d25ea57ca7df59a0
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-02-10 15:06:50 +00:00
Sharlatan Hellseher 6a59d3ad68
gnu: odamex: Remove package labels. 
* gnu/packages/games.scm (odamex) [inputs]: Remove labels.

Change-Id: Ie4b97a3dfaa3a0ce3a0e7c5c49ed52fe4e222480
 2024-02-10 15:06:50 +00:00
Sharlatan Hellseher 54592df80d
gnu: odamex: Unbundle some libraries. 
* gnu/packages/games.scm (odamex) [snippet]: Remove some bundled
libraries which may be replaced by inputs.
[arguments] <#:configure-flags>: Add options to build client, master and
server. Do not use internal libs explicitly.
[native-inputs]: Add pkg-config.

Change-Id: I1974febb2f5f37d963ecb5b663d17a330ba23129
 2024-02-10 15:06:50 +00:00
David Pflug 6aefab6c0c
gnu: odamex: Update to 10.4.0. 
* gnu/packages/games.scm (odamex): Update to 10.4.0.
[inputs]: Add fltk, jsoncpp, libpng, miniupnpc, portmidi and protobuf.

Change-Id: I371d18498640e15a7bfae527fea12d9432368f50
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-02-10 15:05:49 +00:00
Felix Gruber 9ffdcb2492
gnu: sameboy: Update to 0.16.2. 
* gnu/packages/emulators.scm (sameboy): Update to 0.16.2.

Change-Id: I86a31cfca9e69d63d3cb6a13d5db88a6b1abe2a8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-02-10 13:33:55 +00:00
Andy Tai d9efbd0f48
gnu: ocrad: Update to 0.29 
* gnu/packages/ocr.scm (ocrad): Update to 0.29

Change-Id: I9069a4b20016ed38961cd2606a841933b3151e1a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-02-10 13:31:51 +00:00
Timotej Lazar 069fb3fa7f
gnu: sssd: Update to 2.9.4. 
* gnu/packages/sssd.scm (sssd): Update to 2.9.4.

Change-Id: Ib5a4e03c4c732d362f8095aeb72509cfd6e7c4a1
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-02-10 13:29:37 +00:00
Ricardo Wurmus caa7a95157
gnu: r-desctools: Update to 0.99.54. 
* gnu/packages/statistics.scm (r-desctools): Update to 0.99.54.

Change-Id: Ic2f1a625021f11f83bacae0454c50e52551e01cf
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus aa7dd6fcca
gnu: r-tclust: Update to 1.5-6. 
* gnu/packages/statistics.scm (r-tclust): Update to 1.5-6.

Change-Id: Ic456aba29495c670f9a9be8ae9257017730cf1f2
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus 3b591901b9
gnu: r-robust: Update to 0.7-4. 
* gnu/packages/statistics.scm (r-robust): Update to 0.7-4.

Change-Id: I038772a5d83c9a0e40a4aa24a8bd8cabc3ff623a
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus e5de0b6ad1
gnu: r-ggthemes: Update to 5.1.0. 
* gnu/packages/statistics.scm (r-ggthemes): Update to 5.1.0.

Change-Id: I8eb945aea1aeba6d61d9d03497ba1e3095caa9dd
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus f4d5bc057a
gnu: r-gplots: Update to 3.1.3.1. 
* gnu/packages/statistics.scm (r-gplots): Update to 3.1.3.1.

Change-Id: Ie8a457837a9f59a98507921c559ff981e876f64a
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus b39fef6d2b
gnu: r-rcpparmadillo: Update to 0.12.8.0.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.12.8.0.0.

Change-Id: I42e39e8c8c25d068378f2a8e8743b4b77c61cdc4
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus 4e61ed04aa
gnu: r-seqminer: Update to 9.4. 
* gnu/packages/cran.scm (r-seqminer): Update to 9.4.

Change-Id: I38a72f26363440e79aff6c4262c5d856d7ed96c9
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus e9734b5e0f
gnu: r-spatstat-linnet: Update to 3.1-4. 
* gnu/packages/cran.scm (r-spatstat-linnet): Update to 3.1-4.

Change-Id: I60eff13181a3f7b65c3904f185f22820b33fec4d
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus e95d7a731f
gnu: r-spatstat-model: Update to 3.2-10. 
* gnu/packages/cran.scm (r-spatstat-model): Update to 3.2-10.

Change-Id: I38663d7ae11711d91d503892b4443086be812ca3
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus 99b21bc91b
gnu: r-hardhat: Update to 1.3.1. 
* gnu/packages/cran.scm (r-hardhat): Update to 1.3.1.

Change-Id: I2e2ee02f48e6b0531caeabb85e1c34535092c3cb
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus 5d0f4fc6e2
gnu: r-distributional: Update to 0.4.0. 
* gnu/packages/cran.scm (r-distributional): Update to 0.4.0.
[propagated-inputs]: Remove r-digest, r-farver, r-ggplot2, and r-scales.

Change-Id: Ic83e5ba2972dd32b1bbc69aad1e241739ce12480
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus 681dc57842
gnu: r-aws: Update to 2.5-5. 
* gnu/packages/cran.scm (r-aws): Update to 2.5-5.

Change-Id: I39f0394bfed327c04c275e1c42d2d47b2cef27fe
 2024-02-10 13:52:35 +01:00
Ricardo Wurmus c59571a48a
gnu: r-lisreltor: Update to 0.3. 
* gnu/packages/cran.scm (r-lisreltor): Update to 0.3.

Change-Id: I423e7116d80f236c39a3f30d4f9e3717658433a9
 2024-02-10 13:52:34 +01:00
Ricardo Wurmus 32ebcb194f
gnu: r-lim: Update to 1.4.7.1. 
* gnu/packages/cran.scm (r-lim): Update to 1.4.7.1.

Change-Id: Ibe9c04b0f0e7109f9e01f4902f034175da933fb6
 2024-02-10 13:52:34 +01:00
Ricardo Wurmus b65761c620
gnu: r-idpmisc: Update to 1.1.21. 
* gnu/packages/cran.scm (r-idpmisc): Update to 1.1.21.

Change-Id: I5acf372d08a8a7829bd3d2f6e17897234bf0856a
 2024-02-10 13:52:34 +01:00
Ricardo Wurmus 808741693a
gnu: r-smpracticals: Update to 1.4-3.1. 
* gnu/packages/cran.scm (r-smpracticals): Update to 1.4-3.1.

Change-Id: I200db8be3842c8716a3e5583a43b975294e5e03e
 2024-02-10 13:52:34 +01:00
Ricardo Wurmus 5a9ed60d26
gnu: r-parameters: Update to 0.21.5. 
* gnu/packages/cran.scm (r-parameters): Update to 0.21.5.

Change-Id: If0de907fd0f0004468f3dcb4f4f5ca438a380c56
 2024-02-10 13:52:34 +01:00
Ricardo Wurmus a2b4ae0a67
gnu: r-plot3d: Update to 1.4.1. 
* gnu/packages/cran.scm (r-plot3d): Update to 1.4.1.

Change-Id: I5734b726f80b5ac06b217d0bcee90f1584823bfc
 2024-02-10 13:52:34 +01:00