From c5851c79c120628863a5541ad26dd2e1d3ebcc34 Mon Sep 17 00:00:00 2001 From: LiNk-NY Date: Mon, 6 Jul 2026 15:21:53 -0400 Subject: [PATCH] replace BiocParallel recommendation with CRAN Task View --- index.Rmd | 2 +- r-code.Rmd | 33 ++++++++++++--------------------- 2 files changed, 13 insertions(+), 22 deletions(-) diff --git a/index.Rmd b/index.Rmd index 5127e03..aa2a214 100644 --- a/index.Rmd +++ b/index.Rmd @@ -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/ @@ -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/ diff --git a/r-code.Rmd b/r-code.Rmd index 617867e..ff6f180 100644 --- a/r-code.Rmd +++ b/r-code.Rmd @@ -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.