Error in Running Findneighbors - Error in validityMethod(as(object, superClass)): Objekt 'Csparse_Validate' Not Found
I Am Using the Seurat Vignette in R to Analyse Transcriptomic Data I Suddenly Cannot Run My So Far Well-Working Script Due to This Error: Error in...
I am using the Seurat vignette in R to analyse transcriptomic data
I suddenly cannot run my so far well-working script due to this error:
Error in validityMethod(as(object, superClass)) : Object 'Csparse_validate' not found
Re-installing and/or updating many packages such as Seurat, Matrix, ... did not work, I also tried various versions of Matrix and also different datasets (that have worked beforehand) without any success
Is there anything else to solve this problem? Thanks in advance!
2 Answers
It's because of the Matrix version used in Seurat vs. installed. You can define Csparse_validate and rerun. The following line before FindNeighbors helps:
Csparse_validate = "CsparseMatrix_validate"
Removing ALL packages, then re-installing packages including Seurat and a BINARY version of Matrix (v 1.5-4.1) worked for me.
I don't know if it was THE cause, but in previous attempts in which I re-installed Matrix v1.6-1 (source version needing compilation) I kept getting this error every time I tried to run Seurat::FindNeighbors(object,dims=1:30). Another factor may be that you need to recreate the Seurat object (so don't load an existing Seurat object created with an older version of Seurat); not sure if this is actually causally involved, but this was among the things I did just before I got rid if this error.
Sarah Jenkins is a veteran tech journalist with over 12 years of experience covering artificial intelligence, mobile innovations, and digital ethics. Her insights have appeared in leading technology publications worldwide.
