Function 'sexp_as_cholmod_sparse' not provided by package 'Matrix'

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1

Hello, I’m integrating datasets with scVI in R, and followed the tutorial (Integrating datasets with scVI in R — scvi-tools)
The format conversion and model training have been done, but when I runumap, with

combined_seurat ← RunUMAP(combined_seurat, dims = 1:10, reduction = “scvi”, n.components = 2)

I get the error Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters): function 'sexp_as_cholmod_sparse' not provided by package 'Matrix'.
My Matrix version is [1] ‘1.6.1.1’. Do you know which version of Matrix provides sexp_as_cholmod_sparse?

2

Hi. I assume you can also not compute RunUMAP on other dimensionality embeddings. In this case, please check this with Seurat or Matrix developers? We unfortunately can’t provide support beyond making sure that scVI trains correctly in R.

3

I remember this problem happening some time ago when Matrix package was updated and some dependent packages, like irlba, needed to be recompiled, as suggested in this thread. So, can you try running?

install.packages("irlba", type="source")
4

Thank you so much for replying. I’ve solved this problem.

5

Thank you so much! I’ve solved this problem by recompiling package irlba.