Seurat: future problem?

[jessie-wangjie]

Got this error only when I enabled the future parallel. I'm using the latest develop version

Error in norm.function(data = if (margin == 1) { :
unused arguments (custom_function = function(x) {
return(log1p(x = x/(exp(x = sum(log1p(x = x[x > 0]), na.rm = TRUE)/length(x = x)))))
}, margin = margin)
Calls: ... resolve.list -> signalConditionsASAP -> signalConditions

[andrewwbutler]

Hi,

Can you provide a reproducible example (or at very least the code you ran that generated the error)?

[Ryan-Zhu]

I see the same error when running NormalizeData() with future parallel turned on. Changing it back by plan("sequential") solves the problem. NormalizeData() is not parallelized anyway.

[cvillamar]

I had the same problem with NormalizeData() when using plan("multiprocess") in the development version of Seurat (Seurat_3.0.3.9029).
As @Ryan-Zhu pointed out, using plan("sequential") before NormalizeData() solved the issue.

[jessie-wangjie]

@andrewwbutler
I tried on the PBMC data, got the error as well.

library(Seurat)
plan("multiprocess",workers=15)
options(future.globals.maxSize=5000*1024^2)
pbmc.data <- Read10X(data.dir = "filtered_gene_bc_matrices/hg19/")
pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)
pbmc[["percent.mt"]] <- PercentageFeatureSet(pbmc, pattern = "^MT-")
pbmc <- subset(pbmc, subset = nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 5)
pbmc <- NormalizeData(pbmc, normalization.method = "LogNormalize", scale.factor = 10000)

Error in norm.function(data = if (margin == 1) { :
unused arguments (custom_function = function(x) {
return(log1p(x = x/(exp(x = sum(log1p(x = x[x > 0]), na.rm = TRUE)/length(x = x)))))
}, margin = margin)

[andrewwbutler]

Hi,

Thanks for reporting the bug. It should be fixed now in the latest development version if you try installing that.

[andrewwbutler]

Closing as I'm assuming this resolved this issue but feel free to reopen if not.