This is the code that I want to run:
Aldh1l1.neg_Atp1b2.pos_new <- FindNeighbors(Aldh1l1.neg_Atp1b2.pos_new, dims = 1:10) But it doesn't work due to this error:
Error in validityMethod(as(object, superClass)) : object 'CsparseMatrix_validate' not found I have already reinstalled the Seurat and Matrix packages several times. I have even reinstalled RStudio once.
The call stack looks like this:
> traceback() 15: validityMethod(as(object, superClass)) 14: isTRUE(x) 13: anyStrings(validityMethod(as(object, superClass))) 12: validObject(.Object) 11: .nextMethod(.Object = .Object, ... = ...) 10: callNextMethod() 9: initialize(value, ...) 8: initialize(value, ...) 7: new(Class = "Graph", i = c(0L, 62L, { ... TRUNCATED ... } 6: do.call(what = "new", args = object.list) 5: UpdateSlots(object = object) 4: `DefaultAssay<-.Graph`(object = `*tmp*`, value = assay) 3: `DefaultAssay<-`(object = `*tmp*`, value = assay) 2: FindNeighbors.Seurat(Aldh1l1.neg_Atp1b2.pos_new, dims = 1:10) 1: FindNeighbors(Aldh1l1.neg_Atp1b2.pos_new, dims = 1:10) 1 Answer
The underlying issues are discussed in this thread on the R-devel mailing list, from September 2022.
CsparseMatrix_validate was defined in Matrix 1.5-3 to replace the existing validity method for virtual class CsparseMatrix. The problem is that some packages built under Matrix 1.5-3 (or newer) cache the validity method in their namespace, but not the definition of CsparseMatrix_validate.
When the cached method is called, CsparseMatrix_validate must be found in whatever version of Matrix that you have installed. If that version is older than 1.5-3, then the symbol is not found, and the result is the error that you see.
To solve it for all users, the maintainer of the culprit package should put Matrix (>= 1.5-3) in their package's DESCRIPTION file under Imports or Depends.
Until that happens, it should suffice for individual users to install Matrix 1.5-3 (or newer):
> install.packages("Matrix", repos = "") > packageVersion("Matrix") [1] '1.5.3' If that doesn't work, then we'll need more details about your setup (library paths, etc.).
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