Solution: object 'CRsparse_colSums' not found
raised after upgrading to Seurat
v5.0.1
#8202
Labels
bug
Something isn't working
After upgrading to
Seurat
/SeuratObject
v5.0.1 users who also haveAzimuth
and/orSignac
installed may encounter the following error:object 'CRsparse_colSums' not found
when trying to runcolSums
orrowSums
on anydgCMatrix
. This in turn breaks quite a bit ofSeurat
's basic functionality.To resolve the issue, re-install the TFBSTools package from source and then open a fresh R session:
If you're able to run the following snippet without raising errors, then the problem has been fixed:
The issue was not triggered by any changes to
Azimuth
orSeurat
directly — rather it is caused by upgrading theMatrix
package beyond v1.6-1.1 while theTFBSTools
package is already installed. SinceAzimuth
andSignac
both depend onTFBSTools
, andSeuratObject
v5.0.1 requiresMatrix
to be at least v1.6-3, upgrading toSeurat
/SeuratObject
v5.0.1 with either package installed triggers the issue.The underlying problem appears to be related to S4 method caching for the
TFBSTools
package. In the case that users installed the package before upgradingMatrix
to v1.6-3 the method lookup fordgCMatrix
gets resolved to includeCRsparse_colSums
somewhere along its call stack. Since R caches these lookups at compilation time, the method lookup cached forTFBSTools
does not change whenMatrix
is updated and ends up with a bad reference to a nonexistent function (CRsparse_colSums
). Re-installingTFBSTools
from source forces the package to recompile and the S4 method caches to update, resolving the issue.The text was updated successfully, but these errors were encountered: