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10373 Commits

Author SHA1 Message Date
Ricardo Wurmus
6c02d882d2 gnu: r-bslib: Ensure that copied files are writable. 
* gnu/packages/cran.scm (r-bslib)[arguments]: Add phase 'fix-file-permissions.

Change-Id: Idccb1ef5a271f04f50e60b4a639c87bf2ac87b4e
 2025-11-13 11:16:43 +01:00
Ricardo Wurmus
fe07e80b00 gnu: r-sass: Ensure that copied files are writable. 
* gnu/packages/cran.scm (r-sass)[arguments]: Add phase 'fix-file-permissions.

Change-Id: If53ad242e5fcfa6951631ed7a1807a8930e92be3
 2025-11-13 11:16:43 +01:00
Ricardo Wurmus
a212e20f65 gnu: r-bslib: Enable tests. 
* gnu/packages/cran.scm (r-bslib)[arguments]: Enable most tests; add phase
'disable-bad-tests.
[native-inputs]: Add r-testthat and r-yaml.
[properties]: Record updater-extra-native-inputs.

Change-Id: I0221e3ee0dff309ba3f24e0d47b89efb59f7c9a1
 2025-11-13 11:16:43 +01:00
Jonas Freimuth
7cba63307b gnu: r-import: Update home-page 
* gnu/packages/cran.scm (r-import)[home-page]: rticulate.org is
  no longer under the control of the package author. The official
  home page is now hosted at github.io. See
  <https://github.com/rticulate/import/issues/102#issuecomment-3376610296>
  for mor information.

Change-Id: I1513fcfea1ba8ad14813ad8929d06d3fc1fa36b0
Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>
 2025-11-13 11:16:43 +01:00
Jonas Freimuth
76fcd954b5 gnu: r-import: Update to 1.3.4. 
* gnu/packages/cran.scm (r-import): Update to 1.3.4.

Change-Id: I61781fae0b164dc1ddd1a2f2a10c0d5b4dae7398
Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>
 2025-11-13 11:16:43 +01:00
Ricardo Wurmus
227c9d1553 gnu: r-rcppparallel: Update to 5.1.11-1. 
* gnu/packages/cran.scm (r-rcppparallel): Update to 5.1.11-1.

Change-Id: Idb02209dc955a531ede00527fe0216a9ce5caafd
 2025-11-13 11:16:42 +01:00
Ricardo Wurmus
bea42cbfdb gnu: r-colorout: Update to 1.3-3. 
* gnu/packages/cran.scm (r-colorout): Update to 1.3-3.

Change-Id: I4d6a6094061fab98fee8155c76ca760f3ef15cbe
 2025-11-13 11:16:42 +01:00
Ricardo Wurmus
ee46654370 gnu: Remove r-spatstat-core. 
In 2022 spatstat.core was replaced with spatstat.explore and spatstat.model.

See https://spatstat.org/2022/11/10/spatstat.core-split.html

* gnu/packages/cran.scm (r-spatstat-core): New variable.

Change-Id: I2193626f0c2346f3b2793026059c5fbc97d2c4d2
 2025-11-13 11:16:24 +01:00
Ricardo Wurmus
d877aca055 gnu: r-sdmtools: Replace removed constants. 
R 4.5.0 removed previously deprecated definitions.

* gnu/packages/cran.scm (r-sdmtools)[arguments]: Add phase 'patch-constants.

Change-Id: I06125aeff8b7b1f219f8458b6c9aeeb696e33f11
 2025-11-13 11:16:24 +01:00
Ricardo Wurmus
19b8400f8b gnu: r-xml: Use libxml2-with-zlib. 
* gnu/packages/cran.scm (r-xml)[inputs]: Replace libxml2 with libxml2-with-zlib.

Change-Id: I16de722bec362b87e0518e91de10e7a02afd8c71
 2025-11-13 11:16:24 +01:00
Sharlatan Hellseher
1bf145eee3 gnu: r-duckdb: Move to duckdb. 
* gnu/packages/cran.scm (r-duckdb): Move from here ...
* gnu/packages/duckdb.scm: ... to here.

Change-Id: Ic735854106fd0b0e693105183b7408d447de882c
 2025-11-11 20:18:00 +00:00
Ricardo Wurmus
59e8d1eb0c gnu: r-torch: Update to 0.16.3. 
* gnu/packages/cran.scm (r-torch): Update to 0.16.3.

Change-Id: I548e3c2e1b8c24fa4ee7e293966a0f27094e4c09
 2025-11-07 21:53:04 +01:00
Simon Tournier
76d78fb106 gnu: r-colorout: Adjust GCC@14. 
* gnu/packages/cran.scm (r-colorout)[arguments]: New phase that set GCC
compiler flag.

Change-Id: I7616cbd7918e00faed307dcc41dd6fe9cbc02086
 2025-11-07 11:17:17 +01:00
Simon Tournier
10272557b7 gnu: r-blavaan: Adjust GCC@14. 
* gnu/packages/cran.scm (r-blavaan)[arguments]: Add phase that decreases
GCC@14 strictness.

Change-Id: Ic56b3d6ba1b92ee98b57ebfe0db4c1aa2a542b24
 2025-11-07 11:17:16 +01:00
Simon Tournier
fee483e713 gnu: r-densestbayes: Adjust GCC@14. 
* gnu/packages/cran.scm (r-densestbayes)[arguments]: Add phase that decreases
GCC@14 strictness.

Change-Id: I52c45b9f693d843f25f1d61ef440e5b1cf2808d2
 2025-11-07 11:17:16 +01:00
Simon Tournier
5797a07454 gnu: r-dtwclust: Adjust GCC@14. 
* gnu/packages/cran.scm (r-dtwclust)[arguments]: Add phase that decreases
GCC@14 strictness.

Change-Id: I4235fb9444e67112ee0906b479445b5b1c5ef7b0
 2025-11-07 11:17:15 +01:00
Ricardo Wurmus
93d892f333 gnu: r-rffc: Adjust to R@4.5.0. 
* gnu/packages/cran.scm (r-rffc)[arguments]: Replace Calloc and Free by
R_Calloc and R_Free.

Change-Id: I5102fff078f8ca2440dae250b9d439e5440fe394
Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>
 2025-11-07 11:17:10 +01:00
Ricardo Wurmus
3945e556c7 gnu: r-rcppparallel: Patch TBB task.h. 
Patching this file lets us compile downstream packages without errors.

* gnu/packages/cran.scm (r-rcppparallel)[arguments]: Add phase 'gcc-compatibility.

Change-Id: I966c09887f1536dcc623d322f6b141fad069e3dd
Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>
 2025-11-07 11:17:01 +01:00
Simon Tournier
80804e10c8 gnu: r-rstan: Adjust GCC@14. 
* gnu/packages/bioconductor.scm (r-rstan)[arguments]: Add phase that decreases
GCC@14 strictness.

Change-Id: I83920c1acfd944f36625385012f0dd28bbc3decc
 2025-11-07 09:55:48 +01:00
Simon Tournier
2fef4214ad gnu: Remove r-assertive-reflection. 
Package was removed from the CRAN repository and it depends on `'is.R()`
removed by R@4.5.0.

* gnu/packages/cran.scm (r-assertive-reflection): Delete variable.

Change-Id: I373b23e0a450c096799199d719d23dea11f5f9f3
 2025-11-07 09:55:47 +01:00
Simon Tournier
6c20f0eeb1 gnu: Remove r-assertive. 
Package was removed from the CRAN repository and its dependency
'r-assertive-reflection' relies on the R procedure 'is.R()' which had been
removed in R@4.5.0.

* gnu/packages/cran.scm (r-assertive): Delete variable.

Change-Id: I1a8126594162b0c0f4ef03a9177fb5b74c4754be
 2025-11-07 09:55:47 +01:00
Simon Tournier
c050da2303 gnu: r-paralleldist: Adjust GCC@14. 
* gnu/packages/cran.scm (r-paralleldist)[arguments]: Add phase that relax
GCC@14 strictness.

Change-Id: I7dd04d8547b35cb35fac0d1386185d37239d4a8e
 2025-11-07 09:55:46 +01:00
Simon Tournier
21065459b1 gnu: r-ifultools: Adjust R@4.5.0 and GCC@14. 
* gnu/packages/cran.scm (r-ifultools)[]arguments]: Add phase which adjust
C-level facilities Calloc, Free and Realloc.

Change-Id: I0414a805af1550be738b2ce0259318dbf3aecf15
 2025-11-07 09:55:45 +01:00
Simon Tournier
62bfec2a8d gnu: r-decon: Adjust to R@4.5.0 and GCC@14. 
* gnu/packages/cran.scm (r-decon)[arguments]: Add phase which replaces C-level
PI by M_PI.

Change-Id: I68a5f3ce808761880b6ff7780b2e1781d7164038
 2025-11-07 09:55:44 +01:00
Simon Tournier
4e1e433cdf gnu: r-rserve: Adjust R@4.5.0 and GCC@14. 
* gnu/packages/cran.scm (r-rserve)[arguments]: Adjust compiler flags.

Change-Id: Ic3125adb771fda68a7a0e70c8a6c0c72ff14e3e2
 2025-11-07 09:55:44 +01:00
Simon Tournier
7c6e8e7d8d gnu: r-rbamtools: Adjust R@4.5.0 and GCC@14. 
* gnu/packages/cran.scm (r-rbamtools)[arguments]: Replace C-level procedures
Calloc and Free by R_Calloc and R_Free.

Change-Id: I8611f800ad291c764fa295da7b00083d2bb40e95
 2025-11-07 09:55:44 +01:00
Simon Tournier
50b254f2fe gnu: r-ibdreg: Adjust to R@4.5.0 and GCC@14. 
* gnu/packages/cran.scm (r-ibdreg)[arguments]: Replace Calloc and Free by
R_Calloc and R_Free.

Change-Id: I4022505ea4be164588c58f27561fc13d286545e8
 2025-11-07 09:55:43 +01:00
Simon Tournier
da9a52da9f gnu: r-freetypeharfbuzz: Adjust configure flags for meson-build-system. 
Follow up of 5a361d46ba.

* gnu/packages/cran.scm (r-freetypeharfbuzz): Remove 'static-package' package
procedure.
[arguments]<configure-flags>: Adapt flags for meson-build-system.

Change-Id: Ia24aac55378c697a4a0c34e989680457e8e22347
 2025-11-07 09:55:42 +01:00
Ludovic Courtès
9fcfb93944 gnu: Use ‘define-deprecated-package’ for deprecated packages. 
Use ‘define-deprecated-package’ instead of (define x (deprecated-package …))
throughout gnu/packages/*.scm.

Change-Id: I4e176da9ac660327489dab256ca4d12c4e78fe8d
 2025-10-23 19:35:06 +02:00
Andreas Enge
24896b9d44 gnu: r-rvest: Update to 1.0.5. 
* gnu/packages/cran.scm (r-rvest): Update to 1.0.5.

Fixes: guix/guix#3592
Change-Id: I5f56266b1d74ad56f64edcc16d71f14c7e4e7398
 2025-10-22 22:42:50 +02:00
John Kehayias
693dd808cc gnu: r-xml2: Update to 1.4.0. 
* gnu/packages/cran.scm (r-xml2): Update to 1.4.0.

Change-Id: I4ec43f8e2b660086c16bd3c4479d071ee0fbec9d
 2025-09-30 16:48:23 +09:00
Simon Tournier
00799525e7 gnu: Add r-tesseract. 
* gnu/packages/cran.scm (r-tesseract): New variable.

Change-Id: Ia4227bee7f02de4901c5a6542b6a3b8c2d880cd8
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-09-25 20:16:51 +02:00
Andreas Enge
b59ce2d245 gnu: Remove r-tfautograph. 
* gnu/packages/cran.scm (r-tfautograph): Delete variable.

Change-Id: I22c67207eee71c9337ef6c7528b4aeebf30987ce
 2025-09-14 18:22:09 +02:00
Andreas Enge
0b89b956c2 gnu: Remove r-tensorflow. 
* gnu/packages/cran.scm (r-tensorflow): Delete variable.

Change-Id: I33bd19c27d4ae0326305c2ab1948e66bbcf0992b
 2025-09-14 18:22:09 +02:00
Andreas Enge
37978a7897 gnu: Remove r-keras. 
* gnu/packages/cran.scm (r-keras): Delete variable.

Change-Id: I6d78b52605795cb285f893043b6f733dbf93a3fb
 2025-09-14 18:22:09 +02:00
Greg Hogan
3007edeee6 gnu: r-credentials: Switch to pinned input. 
* gnu/packages/cran.scm (r-credentials)[inputs]: Replace git-minimal
with git-minimal/pinned.

Change-Id: I888d779a49ac4ba18da55377c05deaa2be8f4061
 2025-08-21 18:40:04 +00:00
Greg Hogan
e2061ade54 gnu: r-gitcreds: Switch to pinned input. 
* gnu/packages/cran.scm (r-gitcreds)[inputs]: Replace git-minimal with
git-minimal/pinned.

Change-Id: Ifa2e3bed367cb4d70c6ef344aab0b8fd6aa8621f
 2025-08-21 18:39:54 +00:00
Spencer King
64ef6db09b gnu: Add r-circstats. 
* gnu/packages/cran.scm (r-circstats): New variable.

Change-Id: Ie953ac2f713c88b0f626f4e07e9dbfc6c12eb3dd
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-08-21 16:36:22 +02:00
Sharlatan Hellseher
4dbe551971 gnu: r-stringfish: Update to 0.17.0, fix build with gcc@14. 
* gnu/packages/cran.scm (r-stringfish): Update to 0.17.0.
  [arguments] <phases>: Add 'use-system-tbb, and
  'relax-gcc-14-strictness.
  [inputs]: Add tbb-2020.

Change-Id: Ibb7b7fface988727b185763b47cf7074119088f0
 2025-08-07 18:33:37 +01:00
Greg Hogan
97c45bbfc5 gnu: r-arrow: Update to 21.0.0. 
* gnu/packages/cran.scm (r-arrow): Update to 21.0.0.

Change-Id: I8394307862b54cbf879a990f0da11d4cb68458b8
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-08-06 09:43:47 +02:00
Andreas Enge
28dd761e5c gnu: r-proj4: Modernize input. 
* gnu/packages/cran.scm (r-proj4)[inputs]: Replace proj-7 by proj.
(properties)[updater-extra-inputs]: Change accordingly.

Change-Id: I165dc11f17388ce5dcd2e71a677235123e05891a
 2025-07-31 13:46:20 +02:00
Janneke Nieuwenhuizen
bb6309622c gnu: r-fast: Fix build with gcc-14. 
* gnu/packages/cran.scm (r-rfast)[arguments]: New field to relax gcc-14's
strictness.

Change-Id: I11fc6f40dbb6bc37831a0e7d647bc6dae10a6af0
 2025-07-18 20:17:24 +02:00
Janneke Nieuwenhuizen
20d0eb4c65 gnu: r-rcppparallel: Fix build with gcc-14. 
* gnu/packages/cran.scm (r-rcppparallel)[arguments]: Use G-Expressions.  Add
phase "relax-gcc-14-strictness".

Change-Id: I3d6c0d0986405dcc327bddb1eccaf95c298aec1d
 2025-07-18 20:17:23 +02:00
Jelle Licht
f139a6a4d4 gnu: r-waiter: Replace esbuild-node with node-esbuild. 
* gnu/packages/cran.scm (r-waiter):[native-inputs]: Replace esbuild-node with
node-esbuild.

Change-Id: Iaa6248345362f6e3adc3f4f84c8ee231f1de6ab9
 2025-06-23 16:08:22 +02:00
Ricardo Wurmus
3d7dfff1f9 gnu: r-ggh4x: Update to 0.3.1. 
* gnu/packages/cran.scm (r-ggh4x): Update to 0.3.1.
[propagated-inputs]: Add r-s7.

Change-Id: I8957f6b85404f92251e392a76fc63e66dca2a10b
 2025-05-31 23:46:22 +02:00
Ricardo Wurmus
dbc150a8ca gnu: r-paws-common: Update to 0.8.4. 
* gnu/packages/cran.scm (r-paws-common): Update to 0.8.4.

Change-Id: Ie3df6080a4f807ae16561bdc2c4813e6660cc274
 2025-05-31 23:46:22 +02:00
Ricardo Wurmus
c1c237868b gnu: r-mlr3learners: Update to 0.12.0. 
* gnu/packages/cran.scm (r-mlr3learners): Update to 0.12.0.

Change-Id: I656eb21bb9940cb8ce8d76009755112ccbc8ba43
 2025-05-31 23:46:21 +02:00
Ricardo Wurmus
b0545ed2f0 gnu: r-mlr3misc: Update to 0.18.0. 
* gnu/packages/cran.scm (r-mlr3misc): Update to 0.18.0.
[native-inputs]: Add r-mirai.

Change-Id: I41687ca18abaa117f671aaff5e9965bb6b96e990
 2025-05-31 23:46:21 +02:00
Ricardo Wurmus
cd31054c45 gnu: r-parsnip: Update to 1.3.2. 
* gnu/packages/cran.scm (r-parsnip): Update to 1.3.2.

Change-Id: Idcb3f0fd63cac4236d7b1a2bb9be71732880bbdc
 2025-05-31 23:46:21 +02:00
Ricardo Wurmus
e3162e1d5c gnu: r-workflowsets: Update to 1.1.1. 
* gnu/packages/cran.scm (r-workflowsets): Update to 1.1.1.
[propagated-inputs]: Remove r-glue.
[native-inputs]: Add r-dials, r-recipes, r-spelling, r-tidyclust, and r-yardstick.

Change-Id: I3ba532ae8d8f88cb7f2d5db8f14abe102108ece7
 2025-05-31 23:46:21 +02:00