Matrix issue

[kayarimagenomics]

I am having an issue with the RunSVD() function
zhang <- RunSVD(zhang)

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'

When I had this issue in seurat it is because the Matrix package needs to be the version 1.6-1
When I then change matrix to 1.6.1

remotes::install_version("Matrix", version = "1.6-1")
packageVersion("Matrix")
library(Matrix)
library(Signac) 

> Error: package or namespace load failed for 'Signac' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
>  namespace 'Matrix' 1.6-1 is already loaded, but >= 1.6.3 is required

[timoast]

You don't need to downgrade the Matrix version, it should be fixed by reinstalling some packages that depend on Matrix. The key point is that you need to reinstall from source, not using the package binaries.

You can try:

install.packages("Matrix")  # to update Matrix
install.packages(c("SeuratObject", "irlba"), type = "source")

Restart your R session after installing the packages.

See also #1559 and satijalab/seurat#8100

[realmungmung]

I tried this method and still got the same error :..(
Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) :
function 'as_cholmod_sparse' not provided by package 'Matrix'

[jpcartailler]

Same RunVSD issue, added some details on this other thread since that's where I first found ideas around how to fix the issue, albeit it isn't fixed on my end yet.
satijalab/seurat#8100 (comment)

[timoast]

@jpcartailler from your other post:

Seurat 4.3.0
SeuratObject 5.0.1

you have incompatible versions of Seurat and SeuratObject installed. You would need to update Seurat to v5

[timoast]

Main issue thread can be found here: #1596