Error in computeCommunProb - missing internal functions?

[daniannr]

Hi SpatialCellChat team,

I'm currently using SpatialCellChat 0.1.0 and having issues when running computeCommunProb. I ran the function and received this error:
SpatialCellChat <- computeCommunProb(SpatialCellChat, distance.use = TRUE, scale.distance = 1, contact.dependent = TRUE, interaction.range = 250, contact.range = 10)

Analyzing spatial transcriptomic data and preferring to infer interactions between individual cells...
Apply a predefined spatial distance threshold based on the interaction length(=250um)...
Contact range is set as 10um, to restrict the contact-dependent signaling.
Run CellChat on spatial transcriptomic data using distances as constraints <<< [2026-03-02 00:07:28.001226]
The input L-R pairs have both secreted signaling and contact-dependent signaling. Run CellChat in a contact-dependent manner for Cell-Cell Contact signaling, and in a diffusion manner based on the interaction.range for other L-R pairs.
Warning: Caught simpleError. Canceling all iterations ...
Error in geometricMean(data.use[RsubunitsV, , drop = F]) :
could not find function "geometricMean"

I tried troubleshooting by creating a new environment with the function:
`geometricMean <- function(x,na.rm=TRUE){
if (is.null(nrow(x))) {
exp(mean(log(x),na.rm=na.rm))
} else {
exp(apply(log(x),2L,mean,na.rm=na.rm))
}
}

new_computeExpr_complex <- SpatialCellChat:::computeExpr_complex
environment(new_computeExpr_complex) <- new.env(parent = asNamespace("SpatialCellChat"))
assign("geometricMean", geometricMean, envir = environment(new_computeExpr_complex))
assignInNamespace("computeExpr_complex", new_computeExpr_complex, ns = "SpatialCellChat")`

The error went away but another error popped up:
Warning: Caught simpleError. Canceling all iterations ... Error in HillFunctionFordataLR(dataLR = dataLR, Kh = Kh, n = n) : could not find function "HillFunctionFordataLR"

Please help! Thank you!

[Ethel-0]

@daniannr I am unable to reproduce this error. The two functions you mentioned are located in the file R/modeling.R. Perhaps you could try reinstalling SpatialCellChat.