FindNeighbors Error

[s-e-h]

Dear Satijalab,
have run
I have recently updated my Seurat to Version 5.0.0 and have been getting this error every time I have tried to run the FindNeighbors() function:

SO <- FindNeighbors(SO, dims = 1:5)
Computing nearest neighbor graph
Computing SNN
Error in validObject(.Object) :
invalid class “Graph” object: superclass "mMatrix" not defined in the environment of the object's class

My Matrix Package is version 1.6-2

For reference:

sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

I saw there was an issue similar to this in 2021 but that had been resolved. Any help with this would be greatly appreciated.

[shanshenbing]

Get the same error. The error is correlated with #4445. Hope for help. Finally, I re-instal Matrix 1.6-1.1 will solve the bug. I was inspired by #7986.
you can try:
devtools::install_version("Matrix",version = "1.6-1.1")

[sinanugur]

Downgrading Matrix version may help, for example to 1.5_3

[s-e-h]

@shanshenbing this worked, thanks very much for the help!

[shanshenbing]

Happily know it works.

[zijianni]

Encountered similar problem. Seems there is an incompatibility issue between Seurat v5 and Matrix 1.6-2, and it's being reported by multiple users, e.g. here, #7983 , and this issue.

Does Seurat maintainer team have any plan to resolve the conflict?

[ellefeg]

I had the same issue with FindNeighbors and was struggling to downgrade Matrix due to gfortran issues. In case anyone else has the same problem, here's what I did. First confirm you have gfortran installed:

du -sh /usr/local/gfortran/

And then follow the instructions on this post to point R in the right direction. Copy the following into a file called ~/.R/Makevars

FC      = usr/local/opt/gcc/bin/gfortran
F77     = /usr/local/opt/gcc/bin/gfortran
FLIBS   = -L/usr/local/opt/gcc/lib

Restart R and install Matrix:

devtools::install_version("Matrix",version = "1.6-1.1")

I haven't run the whole Seurat pipeline yet but the FindNeighbors step works now.

[longmanz]

Hi All,
Thanks everyone for reporting this and answering this issue. This is a confirmed issue for Seurat (SeuratObject) when using Matrix 1.6-2 (satijalab/seurat-object#145). Please down-grade your Matrix package back to 1.6-1.1 to avoid this. remotes::install_version("Matrix", version = "1.6-1.1")

[HelloWorldLTY]

Hi, I cannot resolve thisd question becuase it seems that we cannot use matrix lower than 1.6.3 for seurat:

namespace ‘Matrix’ 1.6-1 is already loaded, but >= 1.6.3 is required

Could you please help me? Thanks.

Update: It seems that this bug has been resolved in Seurat v5.

[Lil-Psilocybe]

I had the same issue with FindNeighbors and was struggling to downgrade Matrix due to gfortran issues. In case anyone else has the same problem, here's what I did. First confirm you have gfortran installed:

du -sh /usr/local/gfortran/

And then follow the instructions on this post to point R in the right direction. Copy the following into a file called ~/.R/Makevars

FC      = usr/local/opt/gcc/bin/gfortran
F77     = /usr/local/opt/gcc/bin/gfortran
FLIBS   = -L/usr/local/opt/gcc/lib

Restart R and install Matrix:

devtools::install_version("Matrix",version = "1.6-1.1")

I haven't run the whole Seurat pipeline yet but the FindNeighbors step works now.

This was still helpful in 2024!