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@gdurif gdurif commented Jul 17, 2025

rkeops was removed from CRAN because of bad cache directory management (CRAN policy violation).

Following CRAN resubmission raised some issues about function documentation (man pages) that are automatically generated from roxygen2 in-line documentation:

Please add \value to .Rd files regarding exported methods and explain the functions results in the documentation. Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, please document that too, e.g. \value{No return value, called for side effects} or similar)
Missing Rd-tags in up to 11 .Rd files, e.g.:
     complex.default.Rd: \value
     default.math.fun.Rd: \value
     install_rkeops.Rd: \value
     ...

You have examples for unexported functions. Please either omit these examples or export these functions.
Examples for unexported function
  arithmetic.multiply.LazyTensor() in:
     check_keopscore.Rd
  *.ComplexLazyTensor() in:
     check_pykeops.Rd
  check_pykeops() in:
     fix_variables.Rd
  check_rkeops() in:
     get_inner_dim.Rd
  Arg.default() in:
     identifier.Rd
  atan2() in:
     preprocess_reduction.Rd
  ifelse() in:
     set_pykeops_build_dir.Rd
  ifelse.LazyTensor() in:
     set_pykeops_verbosity.Rd
  Im.LazyTensor() in:
     setup_pykeops.Rd

\dontrun{} should only be used if the example really cannot be executed (e.g. because of missing additional software, missing API keys, ...) by the user. That's why wrapping examples in \dontrun{} adds the comment ("# Not run:") as a warning for the user. Does not seem necessary. Please replace \dontrun with \donttest.
Please unwrap the examples if they are executable in < 5 sec, or replace dontrun{} with \donttest{}.

Current PR corresponds to the release of rkeops v2.3.0, which is ready for CRAN submission.

  • Fix documentation issue
  • Modify Python setup and requirement management by reticulate (using the new py_require() function)
  • Better management of cache directory (already solved for rkeops v2.2.3 but now even better)
  • Many minor issues (c.f. commit list)

gdurif and others added 30 commits June 11, 2025 14:25
…g explicit functions when generating formulas for LazyTensor
… setup) + minor explanation about reticulate usage
…onttest with dontshow chunk setting up environment and cleaning afterward) + minor code refactoring
@gdurif gdurif added bug Something isn't working enhancement New feature or request R related to RKeOps labels Jul 17, 2025
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gdurif commented Jul 17, 2025

Note: only remaining TODO concerns re-enabling the CI check for rkeops (discussion in progress on the subject).

The package needs to be checked on MacOS before CRAN submission.

I can either try to re-enable the CI within this PR or we can merge this and I prepare another PR for re-enabling rkeops CI.

@gdurif gdurif requested a review from bcharlier July 17, 2025 10:56
@gdurif gdurif self-assigned this Jul 17, 2025
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3 participants