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

[darkcircle]

Recently, 'Matrix' package seem to be hugely changed,

> KTM_seu_sub <- FindNeighbors(KTM_seu_sub, reduction = "pca", dims = 1:40) 
Computing nearest neighbor graph
Computing SNN
Error in validityMethod(as(object, superClass)) :
    object 'Csparse_validate' not found

so many functions have the similar issue like above thing.
Is there something workaround to avoid that message?

[samuel-marsh]

Hi,

Could you provide the output of sessionInfo?

Best,
Sam

[JungiJeong-BI]

Hi, i had the same problem today.
In my case, "Matrix_1.6-1" caused these results.

seurat <- FindClusters(seurat, verbose = FALSE, resolution = 0.4)
Error in validityMethod(as(object, superClass)) :
  object 'Csparse_validate' not found

My solution is re-install Matrix library to the previous version

remove.packages("Matrix")
install.packages("https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.5-1.tar.gz")

i hope this could be helped

[darkcircle]

Hi, i had the same problem today. In my case, "Matrix_1.6-1" caused these results.

seurat <- FindClusters(seurat, verbose = FALSE, resolution = 0.4)
Error in validityMethod(as(object, superClass)) :
  object 'Csparse_validate' not found

My solution is re-install Matrix library to the previous version

remove.packages("Matrix")
install.packages("https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.5-1.tar.gz")

i hope this could be helped

Cool !!! My problem is the same with this.
I should do that until this problem is permanently fixed.

@samuel-marsh could you check (test) for the issue mentioned by @JungiJeong-BI 's comment?

[CaitlinGHowe]

Hi, i had the same problem today. In my case, "Matrix_1.6-1" caused these results.

seurat <- FindClusters(seurat, verbose = FALSE, resolution = 0.4)
Error in validityMethod(as(object, superClass)) :
  object 'Csparse_validate' not found

My solution is re-install Matrix library to the previous version

remove.packages("Matrix")
install.packages("https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.5-1.tar.gz")

i hope this could be helped

Cool !!! My problem is the same with this. I should do that until this problem is permanently fixed.

@samuel-marsh could you check (test) for the issue mentioned by @JungiJeong-BI 's comment?

I'm receiving the same error message when running FindNeighbors(), but the issue persists even when I re-install Matrix (either Matrix_1.5-1 or Matrix_1.6-1): Error in validityMethod(as(object, superClass)) :
object 'Csparse_validate' not found

[mhkowalski]

Hi, I'm not able to reproduce this (even with Matrix_1.6-1 installed). You may want to see the discussion here (#6746), in which it is recommended to remove the Matrix package by manually removing the folder or try loading Matrix BEFORE loading any other packages.

Hope this helps, and please feel free to comment if you continue having issues.

[Harmony714]

I encountered the same issue as well. I tried to uninstall and reinstall the 'Matrix' package, but the error still persists. My R version is 4.3.1.

[Harmony714]

Hi, I'm not able to reproduce this (even with Matrix_1.6-1 installed). You may want to see the discussion here (#6746), in which it is recommended to remove the Matrix package by manually removing the folder or try loading Matrix BEFORE loading any other packages.

Hope this helps, and please feel free to comment if you continue having issues.

I have tried both of these methods, but they still did not resolve the problem.

[HarrisHan2k]

Please try to load Matrix before loading Seurat.

This works for me after numerous uninstall and reinstall the Matrix package.

[nick-robo]

After upgrading Matrix, this error started occurring for me.

[HarrisHan2k]

After upgrading Matrix, this error started occurring for me.

Installing an earlier version of the Matrix (e.g. 1.5.4) package may help. It worked for me.

[nick-robo]

Various other packages require the latest version of Matrix, so I think this solution is not viable.

[HarrisHan2k]

Various other packages require the latest version of Matrix, so I think this solution is not viable.

Maybe you need to find another way to make Seurat and Matrix work then. At least an earlier version of Matrix works for me. Try isolating different versions of the Matrix package into different environments?

[darkcircle]

I still cannot upgrade Matrix over 1.5.x, my system users argued me why there is so many errors occurred and increased today..

Many functions in the Matrix package has been disappeared and/or changed, and Seurat should follow that.