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lshep merged 1 commit into from
Jul 7, 2026
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replace BiocParallel recommendation with CRAN Task View #177

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2 changes: 1 addition & 1 deletion index.Rmd
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Expand Up @@ -73,7 +73,6 @@ knitr::write_bib(c(
[bioc-common]: #reusebioc
[BiocContributions]: https://github.com/Bioconductor/BiocContributions/issues/new
[bioc-devel-mail]: https://stat.ethz.ch/mailman/listinfo/bioc-devel
[BiocParallel vignette]: https://bioconductor.org/packages/devel/bioc/vignettes/BiocParallel/inst/doc/Introduction_To_BiocParallel.pdf
[biocViews]: https://bioconductor.org/packages/devel/BiocViews.html
[BiocCredentials application]: https://git.bioconductor.org/BiocCredentials/
[build reports]: https://bioconductor.org/checkResults/
Expand Down Expand Up @@ -121,6 +120,7 @@ knitr::write_bib(c(
[New package workflow]: #new-package-workflow
[Open github issue]: https://help.github.com/articles/creating-an-issue/
[Packages Under Review]: https://github.com/Bioconductor/BiocContributions/issues
[Parallel Computing]: https://cran.r-project.org/web/views/HighPerformanceComputing.html
[resolve duplicate commits]: #resolve-duplicate-commits
[Pull upstream changes]: #pull-upstream-changes
[Pull Requests]: https://help.github.com/articles/creating-a-pull-request/
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33 changes: 12 additions & 21 deletions r-code.Rmd
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Expand Up @@ -523,24 +523,15 @@ negative.

### Parallel Recommendations

We recommend using `r BiocStyle::Biocpkg("BiocParallel")`. It provides a
consistent interface to the user and supports the major parallel computing
styles: forks and processes on a single computer, ad hoc clusters,
batch schedulers and cloud computing. By default, `BiocParallel`
chooses a parallel back-end appropriate for the OS and is supported
across Unix, Mac and Windows. Coding requirements for `BiocParallel`
are:

- Use `lapply()`-style iteration instead of explicit for loops.
- The `FUN` argument to `bplapply()` must be a self-contained
function; all symbols used in the function are from default R
packages, from packages `require()`'ed in the function, or passed in
as arguments.
- Allow the user to specify the BiocParallel back-end. Do this by
invoking `bplapply()` _without_ specifying `BPPARAM`; the user can
then override the default choice with `BiocParallel::register()`.

For more information see the [BiocParallel vignette][].

When implementing in package development, a minimal number of cores (1 or 2)
should be set as a default.
We recommend using more modern parallel computing packages such as
`r BiocStyle::CRANpkg("futurize")`, `r BiocStyle::CRANpkg("mirai")`,
`r BiocStyle::CRANpkg("furrr")` etc.

Developers should be mindful of supporting the major platforms (Linux, Windows,
and Mac) when providing parallel implementations.

For a more detailed summary of parallel recommendations, see the
High-Performance and [Parallel Computing][] CRAN Task View.

When using in package development, parallel operations should be set to use
either one or two cores by default.
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