Martin Morgan

multicore collects children inappropriately

6

This script ``` library(batchtools) res

explicitly undo side effects of makeCluster

2

Some `makeCluster*` operations have side effects, e.g., opening connections ``` > nrow(showConnections()) [1] 0 > cl = makeClusterFunctionsSocket(2) > nrow(showConnections()) [1] 2 ``` There is no way to 'undo' (e.g.,...

opts_chunk$get("output.dir") contains a mangled file path?

6

This repo https://github.com/mtmorgan/outputdir has an Rnw vignette. The vignette has a main document and a child document. The code chunk to include the child document includes fig.path that references `opts_chunk$get("output.dir")`....

`Accept` headers can contain multiple types, e.g., `"application/json, text/plain"`, but `accept()` previously produced a warning (because `if (substr(type, 1, 1) == ".")` is non-scalar) on vector arguments with length >...

Revise default param registration

5

MulticoreParam() is appealing for interactive use, but problematic in package use, as discussed eg https://github.com/drisso/zinbwave/issues/38#issuecomment-655587766. Update default strategy to use SnowParam() as the default.

Use of DoparParam

1

(from @vjcitn) The BiocParallel vignette mentions foreach support and DoParParam ... but for package authors the steps of makeCluster, registerDo* and stopCluster the vignette should indicate what a *package author*...

``` library(BiocParallel) fun

Loading an (arbitrary) package slows down bplapply()

1

2.5x longer when mgcv is loaded. ``` > library(BiocParallel) > system.time(bplapply(1:1e2 , function(...) {}, BPPARAM = MulticoreParam(workers = 2, tasks=1e2))) user system elapsed 0.089 0.008 5.832 > library(mgcv) Loading required...

Automatically check that user code references exported, local, or attached package variables

2

Systematically integrate function to check on non-local use into bplapply and friends

Add bpexport functionality

9

`bpexport` to make local variables available to remote computation. From the [mailing list](https://stat.ethz.ch/pipermail/bioc-devel/2013-November/004868.html)