Error encontered with addDoubletScores() function

[sylestiel]

Hi,

I upgraded to R version 4.1.1 and encountered an error at the addDoubletScores(proj) step.

ArchR-addDoubletScores-4e4866ee3f3d-Date-2021-09-22_Time-16-46-41.log

This has not been an issue with earlier R version.

Can you help throw some light on this problem.

Thanks!

[rcorces]

#904 (comment)
Some sort of compatibility error. We dont have bandwidth to address this right now so just avoid R 4.1.1

[sylestiel]

I installed and read in the following to be able to run ArchR using R 4.1.1
library(parallel)
library(magick)

Appears to be running now.

[jenellewallace]

Just to let you know, I'm using R version 4.1.0 (2021-05-18) on Ubuntu 20.04.3 LTS and I also found it necessary to run "library(parallel") to get multiple threads to work.

[rcorces]

Re: parallel in newer versions of R

This had been bothering me for a while so I finally tracked it down. Description below.

In a recent update in Bioconductor, the BiocGenerics function stopped depending on and importing parallel. So in newer versions of Bioconductor, parallel no longer gets loaded alongside BiocGenerics and thus needed to be loaded separately. I've fixed this by adding a require statement when mclapply runs: 0630ae0

This has been fixed on release_1.0.2

see https://bioconductor.org/packages/release/bioc/html/BiocGenerics.html
vs
https://bioconductor.org/packages/3.1/bioc/html/BiocGenerics.html