Solution for `as_cholmod_sparse` and `CRsparse_rowSums` errors

[dcollins15]

After a recent update to the Matrix package, users have encountered issues running Seurat functions that depend on certain Matrix generics. Typically, this results in one of two errors:

Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'

OR

Error in .local(x, na.rm, dims, ...) :
  object 'CRsparse_colSums' not found

Solution

To resolve the first error, re-install the irlba package from source:

install.packages("irlba", type="source", force = TRUE)

To resolve the second error, re-install the TFBSTools package from source:

BiocManager::install("TFBSTools", type = "source", force = TRUE)

Details

The errors are encountered if either irlba or TFBSTools was installed with Matrix <=1.6-1 and then run with Matrix >=1.6-2. When a package is installed, the definitions for all its S4 classes/methods are cached, including methods from its dependencies (unless they're explicitly included in the package's NAMESPACE using an importClassesFrom directive). In this case, S4 references from Matrix <= 1.6-1 that were cached by irlba and TFBSTools and then dropped in Matrix >= 1.6-2, cannot be properly resolved. For a more detailed discussion on S4 caching and the Matrix package, please checkout this thread.

Re-installing the affected packages from source resolves the issue by refreshing their S4 method caches.

[sjm0240111]

Thanks! @dcollins15 . This works for me!

[Dragonmasterx87]

This solution worked for me allowing Pando to be compatible with my current seurat/signac environments. Thanks @dcollins15 !

[Cimorgh-IT]

Thanks, it worked for me.

[GerardoZA]

Thank you!
This also worked for me.

[emidalla]

Thanks @dcollins15 , that worked for me as well!