RunHarmony() Error on macOS: “Invalid number of ncores provided: 0. Maximum available cores: NA”

[Krystalkeke]

System Information

• OS: macOS (please specify your version, e.g., macOS 14.5 Sonoma)
• R version: 4.3.3 Patched (2024-04-09 r86847)
• Harmony version: 1.2.4
• Seurat version: 5.1.0

Reproducible Code

# Attempt to run Harmony on a Seurat object
sub <- sub %>% 
  RunHarmony(group.by.vars = "sample", plot_convergence = TRUE, ncores = 1)

Observed Error
Warning: HarmonyMatrix is deprecated and will be removed in the future from the API
Error in value[3L] : Invalid number of ncores provided: 0.
Maximum available cores: NA

[pati-ni]

Hi @Krystalkeke

Can you please provide the output of this command on you MacOS system?

RhpcBLASctl::omp_get_max_threads()

I am also confused why you the HarmonyMatrix warning because this function is deprecated...

Can you also confirm what type is the sub variable? A seurat object?

[pati-ni]

@Krystalkeke

also please share a sessionInfo() :)