Error: (converted from warning) useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE.

[Ztxfrhhyy]

I would like to use slingshot for a seurat obj but run into an error. Here's my code and error message:

sds <- slingshot(Embeddings(data, "umap"), clusterLabels = data$seurat_clusters,

•              start.clus = 0, stretch = 0, useNames = FALSE)
  

Error: (converted from warning) useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE.

packageVersion("matrixStats")
[1] ‘1.1.0’
packageVersion("slingshot")
[1] ‘2.6.0’
packageVersion("SingleCellExperiment")
[1] ‘1.20.1’

It worked several weeks ago as:
sds <- slingshot(Embeddings(data, "umap"), clusterLabels = data$seurat_clusters,

•              start.clus = 0, stretch = 0)
  

But now even I add the useNames=TRUE/FALSE, it won't work. Could anybody help? Thanks!

[kstreet13]

Hi @Ztxfrhhyy,

This is a duplicate of this issue: #221
I would recommend updating to the latest R version and re-installing the relevant packages.
Also, useNames is not a valid argument for slingshot, so adding that won't change anything.

Best,
Kelly