BiocParallel

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Biocparallel batchtoolsparam rmd

1

@Bioconductor/sweave2rmd for review [Original](https://github.com/Bioconductor/BiocParallel/files/9507635/BiocParallel_BatchtoolsParam_3.pdf)

villafup

Add the load balancer for evenly distributing the tasks across workers

11

This pull request enables the load balancer in the apply function. There are three build-in balancers for `bplapply`, namely "sequential", "stepwise", and "random". the sequential balancer is the balancer used...

Jiefei-Wang

BiocParallel doesn't propagate warnings

3

This is not ideal imo, means that warnings silently disappear. Would be fine (ish) if at least a message showed up saying we encountered some warnings ```r library(BiocParallel) fun [[1]]...

alanocallaghan

Import of BigWig files with rtracklayer fails under MultiCoreParam

21

I'm seeing a weird bug in in my CAGEfightR package when trying to import BigWigFiles. Here's a reproducible example: ``` # Load the example data library(BiocParallel) library(rtracklayer) library(CAGEfightR) data('exampleDesign') #...

MalteThodberg

Related to Issue #111, I'd like to suggest that you add a layer that detects when a forked process dies, which results in no results for `parallel::mccollect()`, and give an...

HenrikBengtsson

Hello, I was trying to install BiocParallel with BiocManager::install("BiocParallel") but got the following errors. I've also tried alternative versions of Rs installed but the problem remains the same. Could you...

yjx1217

Not sure whether or not false positives are expected or not, but on a Torque/PBS cluster, `BiocParallel:::.batchtoolsClusterAvailable("sge")` returns TRUE (with BiocParallel 1.25.1): ```r > sapply(c("sge", "slurm", "lsf", "openlava", "torque"), BiocParallel:::.batchtoolsClusterAvailable)...

HenrikBengtsson

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.

mtmorgan

BiocParallel fail to start with MPI

2

Hello Everyone, We are having trouble running BiocParallel within our SLURM cluster environment. The foo.R script we are trying to run is ``` library("BiocParallel") library("Rmpi") param library("Rmpi") library("Rmpi") > param

raffaelepotami

Parallelization problems on Ubuntu

5

I'm not sure where the problem is and maybe you can help finding the root of it. When using OUTRIDER on a CentOS 7.7 machine `MulticoreParam` works perfectly. But on...

c-mertes