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FertigLab / CoGAPS

Bayesian MCMC matrix factorization algorithm
https://www.bioconductor.org/packages/release/bioc/html/CoGAPS.html
BSD 3-Clause "New" or "Revised" License
61 stars 17 forks source link

limit number of cores for tests #83

Closed dimalvovs closed 7 months ago

dimalvovs commented 7 months ago

The automated build-check process yields test failures during check. This happens because although usually unset, the base _R_CHECK_LIMIT_CORES_ is set to 2 during CRAN checks and is ignored in the package's parallel implementation.

Error: Error:   _R_CHECK_LIMIT_CORES_' environment variable detected, BiocParallel
  workers must be <= 2 was (4)

Here is the description from RShowDoc("R-ints")

_R_CHECK_LIMIT_CORES_
If set, check the usage of too many cores in package parallel. If set to ‘warn’ gives a warning, to ‘false’ or ‘FALSE’ the check is skipped, and any other non-empty value gives an error when more than 2 children are spawned. Default: unset (but ‘TRUE’ for CRAN submission checks).

We should add support for _R_CHECK_LIMIT_CORES_ variable.

dimalvovs commented 7 months ago

reproduce locally with R CMD check CoGAPS_X.XX.X.tar.gz --no-manual --as-cran