ValidateAzimuthReference does not recognize full namespace

[derrik-gratz]

I'm using AzimuthReference to generate a custom reference. Using debug, I can see that the line

Tool(object = object) <- ad

Creates a slot called Azimuth::AzimuthReference. But this is not recognized as valid when executing ValidateAzimuthReference at the end of AzimuthReference, as it is looking for AzimuthReference. If I execute the same check with the full namespace, e.g.:

inherits(Tool(object, slot = 'Azimuth::AzimuthReference'), what = 'AzimuthData')

The return is now true and the validation can proceed.

https://github.com/satijalab/azimuth/blob/fa45d4c153d2623b89792f8b57aab333e889cdab/R/azimuth.R#L800

[derrik-gratz]

This only seems to arise if you specify Azimuth::AzimuthReference() Which I did to have explicit calls in a wrapper function as part of a package

[Gesmira]

Hi, thanks for reporting this. I've included a fix on the development branch for the new version of Azimuth that is compatible with Seurat v5. To use this, you will have to install Seurat v5 and its dependencies which is described here: https://satijalab.org/seurat/articles/install.html

[z5ouyang]

Hi @Gesmira and @derrik-gratz, This seems happens again? I can successfully call "AzimuthReference" in the main script, but not in the function. success:

D1 <- readRDS("CCA.rds")
D_ref <- AzimuthReference(D1,refAssay=DefaultAssay(D1),
                            metadata=c("Celltype"))

Fail:

test <- function(){
  D1 <- readRDS("CCA.rds")
  D_ref <- AzimuthReference(D1,refAssay=DefaultAssay(D1),
                            metadata=c("Celltype"))
}
test()

[maud-p]

Hi @z5ouyang, @Gesmira , I am facing the same issue, I cannot source() a script that call AzimuthReference while I am able to run it in the main function. Do you have an idea how to solve it? would be a great help if AzimuthReference can be called inside a function! Thanks!