This Git repository uses the Git Flow branching model (the git flow extension is useful for this). The develop branch contains the latest contributions and other code that will appear in the next release, and the master branch contains the code of the latest release.
Contributing to this package is easy. Just send a pull request. When you send your PR, make sure develop is the destination branch on the BiocParallel.FutureParam repository. Your PR should pass R CMD check --as-cran, which will also be checked by GitHub Actions and AppVeyor CI when the PR is submitted.
We abide to the Code of Conduct of Contributor Covenant.
+This Git repository uses the Git Flow branching model (the git flow extension is useful for this). The develop branch contains the latest contributions and other code that will appear in the next release, and the master branch contains the code of the latest release.
Contributing to this package is easy. Just send a pull request. When you send your PR, make sure develop is the destination branch on the BiocParallel.FutureParam repository. Your PR should pass R CMD check --as-cran, which will also be checked by GitHub Actions and AppVeyor CI when the PR is submitted.
We abide to the Code of Conduct of Contributor Covenant.
<%
-md <- R.rsp::rstring(file=“vignettes/FutureParam.md.rsp”, postprocess=FALSE)
+WARNING: This package is experimental and a proof of concept what could be done with BiocParallel and the future framework.
+<% ## Reuse the future vignette md <- R.rsp::rstring(file=“vignettes/FutureParam.md.rsp”, postprocess=FALSE)
+md <- unlist(strsplit(md, split=“”, fixed=TRUE)) md <- md[-seq_len(grep(“^##”, md)[1]-1)]
vignettes/FutureParam.md.rsp
+ Source: vignettes/FutureParam.md.rsp
FutureParam.md.rspThe future package provides a generic API for using futures in R. A future is a simple yet powerful mechanism to evaluate an R expression and retrieve its value at some point in time. Futures can be resolved in many different ways depending on which strategy is used. There are various types of synchronous and asynchronous futures to choose from in the future package. Additional futures are implemented in other packages. For instance, the future.batchtools package provides futures for any type of backend that the batchtools package supports. For an introduction to futures in R, please consult the vignettes of the future package.
-The BiocParallel.FutureParam package provides FutureParam, a BiocParallelParam class, for the BiocParallel package that works with any type of future. The BiocParallel.FutureParam package is cross platform just as the future package.
-Below is an example showing how to use FutureParam with multicore futures. A multicore future will be evaluated in parallel using forked workers, which is not supported on MS Windows when it will fall back to sequential processing.
-
-library("BiocParallel.FutureParam")
-register(FutureParam())
-plan(multicore)
-
-mu <- 1.0
-sigma <- 2.0
-x <- bplapply(1:3, mu = mu, sigma = sigma, function(i, mu, sigma) {
- rnorm(i, mean = mu, sd = sigma)
-})The future +package provides a generic API for using futures in R. A future is a +simple yet powerful mechanism to evaluate an R expression and retrieve +its value at some point in time. Futures can be resolved in many +different ways depending on which strategy is used. There are various +types of synchronous and asynchronous futures to choose from in the future package. +Additional futures are implemented in other packages. For instance, the +future.batchtools +package provides futures for any type of backend that the batchtools +package supports. For an introduction to futures in R, please consult +the vignettes of the future package.
+The BiocParallel.FutureParam +package provides FutureParam, a BiocParallelParam class, for the BiocParallel +package that works with any type of future. The +BiocParallel.FutureParam package is cross platform just as the future +package.
+Below is an example showing how to use FutureParam with +multicore futures. A multicore future will be evaluated in +parallel using forked workers, which is not supported on MS Windows when +it will fall back to sequential processing.
+
+library("BiocParallel.FutureParam")
+register(FutureParam())
+plan(multicore)
+
+mu <- 1.0
+sigma <- 2.0
+x <- bplapply(1:3, mu = mu, sigma = sigma, function(i, mu, sigma) {
+ rnorm(i, mean = mu, sd = sigma)
+})Due to the generic nature of futures, the FutureParam class provides the same functionality as many of the existing BiocParallelParam classes, e.g. SerialParam, SnowParam, MulticoreParam, BatchtoolsParam and DoparParam. In addition, it provides supports for additional backends that are not yet implemented in BiocParallel, e.g. callr and batchtools.
-