ERROR: RunSVD - Problems with Matrix/irlba

[kdzimm]

When I run the "RunSVD" in the latest version of Signac I get the following error:

Running SVD
Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) :
function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: RunSVD ... RunSVD -> RunSVD.Assay -> RunSVD -> RunSVD.default -> irlba
Execution halted

Has anyone else seen this error recently? I have poked around a lot and it looks like the latest version of Matrix caused some issues with Seurat, but I am not having problems with Seurat. It is the RunSVD command where I run into issues. I have tried downgrading Matrix, but that causes other issues

[timoast]

Try reinstalling some packages: irlba, Matrix, SeuratObject. There have been several issues opened in the Signac and Seurat repos that you can take a look at for more suggestions, you can search your error message to find them

[kayarimagenomics]

I am having this issue and I reinstalled all of these dependencies. Tried Seurat 4 vs 5, tried matrix 1.6-,2,3,4,&5. I have not been able to fix this issue.

[kayarimagenomics]

It was irlba - updated to the latest version and it worked

[realmungmung]

how did you update it to the latest version? I installed irlba but still got the same error

[timoast]

Please see #1596