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R updates#416842

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jbedo merged 15 commits intomasterfrom
r-updates
Jun 23, 2025
Merged

R updates#416842
jbedo merged 15 commits intomasterfrom
r-updates

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@jbedo jbedo commented Jun 15, 2025

Bump R and the package tree.

Things done

  • Built on platform(s)
    • x86_64-linux
    • aarch64-linux
    • x86_64-darwin
    • aarch64-darwin
  • For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
    • sandbox = relaxed
    • sandbox = true
  • Tested, as applicable:
  • Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
  • Tested basic functionality of all binary files (usually in ./result/bin/)
  • Nixpkgs 25.11 Release Notes (or backporting 24.11 and 25.05 Nixpkgs Release notes)
    • (Package updates) Added a release notes entry if the change is major or breaking
  • NixOS 25.11 Release Notes (or backporting 24.11 and 25.05 NixOS Release notes)
    • (Module updates) Added a release notes entry if the change is significant
    • (Module addition) Added a release notes entry if adding a new NixOS module
  • Fits CONTRIBUTING.md, pkgs/README.md, maintainers/README.md and other contributing documentation in corresponding paths.

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@github-actions github-actions bot added 10.rebuild-darwin: 11-100 This PR causes between 11 and 100 packages to rebuild on Darwin. 10.rebuild-linux: 11-100 This PR causes between 11 and 100 packages to rebuild on Linux. 11.by: package-maintainer This PR was created by a maintainer of all the package it changes. 6.topic: R R is a programming language for statistical computing and data visualization. labels Jun 15, 2025
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jbedo commented Jun 17, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 416842

x86_64-linux

⏩ 4 packages marked as broken and skipped:
  • python312Packages.orange3
  • python312Packages.orange3.dist
  • python313Packages.orange3
  • python313Packages.orange3.dist
❌ 9 packages failed to build:
  • python312Packages.cnvkit
  • python312Packages.cnvkit.dist
  • python313Packages.cnvkit
  • python313Packages.cnvkit.dist
  • quarto
  • rstudio
  • rstudio-server
  • rstudioServerWrapper
  • rstudioWrapper
✅ 50 packages built:
  • R
  • R.tex
  • cantor
  • diffoscope
  • diffoscope.dist
  • diffoscope.man
  • git-unroll
  • golden-cheetah-bin
  • jasp-desktop
  • jetbrains.dataspell
  • labplot
  • ocamlPackages.ocaml-r
  • postgresql13Packages.plr
  • postgresql14Packages.plr
  • postgresql15Packages.plr
  • postgresql16Packages.plr
  • postgresql17Packages.plr
  • python312Packages.flyingsquid
  • python312Packages.flyingsquid.dist
  • python312Packages.pgmpy
  • python312Packages.pgmpy.dist
  • python312Packages.rchitect
  • python312Packages.rchitect.dist
  • python312Packages.rpy2
  • python312Packages.rpy2.dist
  • python312Packages.xgboost
  • python312Packages.xgboost.dist
  • python313Packages.flyingsquid
  • python313Packages.flyingsquid.dist
  • python313Packages.pgmpy
  • python313Packages.pgmpy.dist
  • python313Packages.rchitect
  • python313Packages.rchitect.dist
  • python313Packages.rpy2
  • python313Packages.rpy2.dist
  • python313Packages.xgboost
  • python313Packages.xgboost.dist
  • rWrapper
  • radian
  • radian.dist
  • radianWrapper
  • resorter
  • sage
  • sageWithDoc
  • spark
  • spark_3_4
  • spip
  • vscode-extensions.reditorsupport.r
  • xgboost
  • xgboostWithCuda

@jbedo jbedo marked this pull request as ready for review June 17, 2025 02:07
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jbedo commented Jun 17, 2025

quarto & rstudio are broken due to deno

@jbedo jbedo requested review from 7c6f434c, b-rodrigues, bcdarwin, collares, omasanori and timokau and removed request for 7c6f434c, collares, omasanori and timokau June 17, 2025 02:09
This was referenced Jun 17, 2025
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@b-rodrigues b-rodrigues mentioned this pull request Jun 17, 2025
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@b-rodrigues b-rodrigues mentioned this pull request Jun 17, 2025
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@b-rodrigues b-rodrigues mentioned this pull request Jun 17, 2025
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b-rodrigues commented Jun 21, 2025 •
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With #416177 merged, quarto and Rstudio should be fixed now

Generated using nixpkgs-review.

Command: nixpkgs-review pr 416842
Commit: de89502743c02119237c43bf6272b45ee97911b5

x86_64-linux

⏩ 1 package blacklisted:
  • tests.pkg-config.defaultPkgConfigPackages.tests-combined
❌ 15 packages failed to build:
  • jasp-desktop
  • python312Packages.cnvkit
  • python312Packages.cnvkit.dist
  • python312Packages.flyingsquid
  • python312Packages.flyingsquid.dist
  • python312Packages.pgmpy
  • python312Packages.pgmpy.dist
  • python313Packages.cnvkit
  • python313Packages.cnvkit.dist
  • python313Packages.flyingsquid
  • python313Packages.flyingsquid.dist
  • python313Packages.pgmpy
  • python313Packages.pgmpy.dist
  • sage
  • sageWithDoc
✅ 39 packages built:
  • R
  • R.tex
  • cantor (libsForQt5.cantor, plasma5Packages.cantor)
  • git-unroll
  • golden-cheetah-bin
  • jetbrains.dataspell
  • labplot
  • postgresql13Packages.plr
  • postgresql14Packages.plr
  • postgresql15Packages.plr
  • postgresql16Packages.plr
  • postgresqlPackages.plr (postgresql17Packages.plr)
  • python312Packages.rchitect
  • python312Packages.rchitect.dist
  • python312Packages.rpy2
  • python312Packages.rpy2.dist
  • python312Packages.xgboost
  • python312Packages.xgboost.dist
  • python313Packages.rchitect
  • python313Packages.rchitect.dist
  • python313Packages.rpy2
  • python313Packages.rpy2.dist
  • python313Packages.xgboost
  • python313Packages.xgboost.dist
  • quarto
  • radian
  • radian.dist
  • resorter
  • rstudio
  • rstudio-server
  • rstudioServerWrapper
  • rstudioWrapper
  • spark (spark3, spark_3_5)
  • spark_3_4
  • spip
  • tests.pkg-config.defaultPkgConfigPackages.libR
  • vscode-extensions.reditorsupport.r
  • xgboost
  • xgboostWithCuda
Error logs: `x86_64-linux`
python312Packages.pgmpy 
  /build/source/pgmpy/sampling/NUTS.py:187: RuntimeWarning: invalid value encountered in divide
    if np.random.rand() < candidate_set_size2 / (

pgmpy/tests/test_sampling/test_continuous_sampling.py::TestNUTSInference::test_sampling

/build/source/pgmpy/sampling/NUTS.py:589: RuntimeWarning: invalid value encountered in divide

if np.random.rand() < candidate_set_size2 / (


-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

=========================== short test summary info ============================

FAILED pgmpy/tests/test_estimators/test_MirrorDescentEstimator.py::TestMarginalEstimator::test_estimate_example_smoke_test - AssertionError:

Arrays are not equal


Mismatched elements: 3 / 4 (75%)

Max absolute difference among violations: 1.11022302e-16

Max relative difference among violations: 1.11022302e-16

ACTUAL: array([[1., 1.],

[1., 2.]])

DESIRED: array([[1., 1.],

[1., 2.]])

= 1 failed, 1157 passed, 22 skipped, 16 deselected, 532 warnings in 1382.37s (0:23:02) =

python313Packages.pgmpy 
  /build/source/pgmpy/sampling/NUTS.py:187: RuntimeWarning: invalid value encountered in divide
    if np.random.rand() < candidate_set_size2 / (

pgmpy/tests/test_sampling/test_continuous_sampling.py::TestNUTSInference::test_sampling

/build/source/pgmpy/sampling/NUTS.py:589: RuntimeWarning: invalid value encountered in divide

if np.random.rand() < candidate_set_size2 / (


-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

=========================== short test summary info ============================

FAILED pgmpy/tests/test_estimators/test_MirrorDescentEstimator.py::TestMarginalEstimator::test_estimate_example_smoke_test - AssertionError:

Arrays are not equal


Mismatched elements: 3 / 4 (75%)

Max absolute difference among violations: 1.11022302e-16

Max relative difference among violations: 1.11022302e-16

ACTUAL: array([[1., 1.],

[1., 2.]])

DESIRED: array([[1., 1.],

[1., 2.]])

= 1 failed, 1157 passed, 22 skipped, 16 deselected, 532 warnings in 550.08s (0:09:10) =

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b-rodrigues commented Jun 21, 2025

nixpkgs-review failed to build sage, but trying it now, it works. Flaky tests?

Kupac
Kupac approved these changes Jun 21, 2025
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I have tested TDbasedUFE, a package with many dependencies, and it seems to install fine. Also, examples I tried work well.

@github-actions github-actions bot added the 12.approvals: 1 This PR was reviewed and approved by one person. label Jun 21, 2025
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TomaSajt commented Jun 22, 2025

I successfully built jasp-desktop locally, not sure why it failed for you.

If it keeps failing for you, please send some logs.

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jbedo commented Jun 23, 2025

I also have no issues with jasp or sage, I think we're good to merge.

@jbedo jbedo mentioned this pull request Jun 23, 2025
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@jbedo jbedo merged commit 1a3f591 into master Jun 23, 2025
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@bcdarwin bcdarwin Awaiting requested review from bcdarwin

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6.topic: R R is a programming language for statistical computing and data visualization. 10.rebuild-darwin: 11-100 This PR causes between 11 and 100 packages to rebuild on Darwin. 10.rebuild-linux: 11-100 This PR causes between 11 and 100 packages to rebuild on Linux. 11.by: package-maintainer This PR was created by a maintainer of all the package it changes. 12.approvals: 1 This PR was reviewed and approved by one person.

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