object 'Csparse_validate' not found

[Milad-Razavi]

Hello,

I'm getting the following error when running the default example.

infercnv_obj = infercnv::run(infercnv_obj,
                             cutoff=1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
                             out_dir=tempfile(), 
                             cluster_by_groups=TRUE, 
                             denoise=TRUE,
                             HMM=TRUE)

Computing SNN
Error in validityMethod(as(object, superClass)) : 
  object 'Csparse_validate' not found

> packageVersion("infercnv")
[1] ‘1.14.2’
> packageVersion("Matrix")
[1] ‘1.6.1.1’

R.version
               _                           
platform       x86_64-redhat-linux-gnu     
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
version.string R version 4.2.3 (2023-03-15)

I tried the solutions suggested here (https://github.com/satijalab/seurat/issues/6746) to no avail. I tried:

• install.packages("Matrix", repos="http://R-Forge.R-project.org"); # "Matrix version ‘1.6.2’ -> new error Error in validObject(.Object) : invalid class “Graph” object: superclass "mMatrix" not defined in the environment of the object's class
• Loading Matrix first
• I also tried uninstalling Matrix and re-installing it.

[tangsanpang2]

Hello, I also encountered the same problem, may I ask you to solve your problem

[GeorgescuC]

Hi @Milad-Razavi ,

The solution from that thread that seems to have worked for the most people is this one, https://github.com/satijalab/seurat/issues/6746#issuecomment-1688536884 , could you give it a try?

Otherwise, if the issue persists, you can try running infercnv using the Docker image trinityctat/infercnv:latest which should not produce that error.

Regards, Christophe.