irlba Bug When Attempting to RunUMAP()

[jwalewski]

Hello,

I am attempting to use the RunUMAP() function on some test data I have and I am getting the following error:

Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'

I am currently using Seurat v.4.4.0 and SeuratObject v4.1.4. Even after explicitly importing irlba I get the same error. RunTSNE(), however, works exactly as expected. Do you guys have any idea about what's going on here, or is more information needed?

[LiorLuo]

I solved this by running following scripts install.packages("Matrix", type = "source") install.packages("irlba", type = "source")

[jwalewski]

install.packages("Matrix", type = "source") install.packages("irlba", type = "source")

Luckily, this seems to have worked for me. Thank you!

[Rym12345]

I solved this by running following scripts install.packages("Matrix", type = "source") install.packages("irlba", type = "source")

this also seems to have worked for me. thank you when I use the Seurat V5, this eror don’t happen. However ,it happens when I use the Seurat V4. I don‘t understand the reason

[Evenlyeven]

I solved this by running following scripts install.packages("Matrix", type = "source") install.packages("irlba", type = "source")

this also seems to have worked for me. thank you when I use the Seurat V5, this eror don’t happen. However ,it happens when I use the Seurat V4. I don‘t understand the reason

I am using Seurat V5 and saw the error ...

[yukixuen]

I solved this by running following scripts install.packages("Matrix", type = "source") install.packages("irlba", type = "source")

Worked too. Thank you!

[cetinsz]

I solved this by running following scripts install.packages("Matrix", type = "source") install.packages("irlba", type = "source")

This doesn´t work for me in Seurar V4 unfortunately.

[zhuldyzhanzak]

This does not work for me as well. Can anyone please help?

My Seurat is 4.3.0.1 SeuratObject is 4.0.3 Matrix is 1.6-4

[fisheryu2022]

Hello,

I am attempting to use the RunUMAP() function on some test data I have and I am getting the following error:

Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'

I am currently using Seurat v.4.4.0 and SeuratObject v4.1.4. Even after explicitly importing irlba I get the same error. RunTSNE(), however, works exactly as expected. Do you guys have any idea about what's going on here, or is more information nee

This does not work for me as well. Can anyone please help?

My Seurat is 4.3.0.1 SeuratObject is 4.0.3 Matrix is 1.6-4

It doesn't work for me either. Are you using M1 too?

[zhuldyzhanzak]

Hello, I am attempting to use the RunUMAP() function on some test data I have and I am getting the following error:

Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'

I am currently using Seurat v.4.4.0 and SeuratObject v4.1.4. Even after explicitly importing irlba I get the same error. RunTSNE(), however, works exactly as expected. Do you guys have any idea about what's going on here, or is more information nee

This does not work for me as well. Can anyone please help? My Seurat is 4.3.0.1 SeuratObject is 4.0.3 Matrix is 1.6-4

It doesn't work for me either. Are you using M1 too?

It started to work recently. Try to install a package called RSpectra. It helped me

[fisheryu2022]

Thank you to both Cinzialo and zhuldyzhanzak! I have now solved the problem. Here is my solution: 1. Go to https://cran.r-project.org/bin/macosx/tools/, download an installer package gfortran-12.2-universal.pkg 2. In R: install.packages("Matrix", type = "source") 3. In R: install.packages("irlba", type = "source")

[menage95]

I have an M1 and am running into the error as well, but the below solution does not work:

2. In R: install.packages("Matrix", type = "source")
3. In R: install.packages("irlba", type = "source")

Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) : function 'as_cholmod_sparse' not provided by package 'Matrix'

[fisheryu2022]

I have an M1 and am running into the error as well, but the below solution does not work:

2. In R: install.packages("Matrix", type = "source")
3. In R: install.packages("irlba", type = "source")

Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) : function 'as_cholmod_sparse' not provided by package 'Matrix'

Here, there, before installing Matrix and irlba, you could do this first : Go to https://cran.r-project.org/bin/macosx/tools/, download an installer package gfortran-12.2-universal.pkg

[menage95]

I have an M1 and am running into the error as well, but the below solution does not work:

2. In R: install.packages("Matrix", type = "source")
3. In R: install.packages("irlba", type = "source")

Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) : function 'as_cholmod_sparse' not provided by package 'Matrix'

Here, there, before installing Matrix and irlba, you could do this first : Go to https://cran.r-project.org/bin/macosx/tools/, download an installer package gfortran-12.2-universal.pkg

that worked thanks!!!

[HappinessEricst]

RSpectra

Thanks this worked for me without needing to downgrade my matrix from 1.5.4.1

[jpcartailler]

Having the same issue trying to run RunSVD

Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'

The system is Win10:

Seurat         4.3.0
SeuratObject   5.0.1
Matrix         1.6-5
irlba          2.3.5.1

I tried this but it did not work (like @cetinsz reported)

install.packages("Matrix", type = "source")
install.packages("irlba", type = "source")

and I tried installing RSpectra but the issue persists.

[fisheryu2022]

Here, there, before installing Matrix and irlba, you could do this first : Go to https://cran.r-project.org/bin/macosx/tools/, download an installer package gfortran-12.2-universal.pkg

[Elham-adabi]

I had the same issue and could solve it with updating to R4.3.2 and Running: install.packages("Matrix", type = "source") install.packages("irlba", type = "source")

[apal6]

Hi,

I am having the same issue. Any advice?

Code and error: install.packages("Matrix",type="source") install.packages("irlba",type="source") cds<-preprocess_cds(cds,num_dim=50)

error: Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix'

[HappinessEricst]

Hi,

I am having the same issue. Any advice?

Code and error: install.packages("Matrix",type="source") install.packages("irlba",type="source") cds<-preprocess_cds(cds,num_dim=50)

error: Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix'

I had to install the package "RSpectra" this solved mine. Hope this works for you

[alicekao1118]

Solved the problem by installing RSpectra

Below are some of my package and env info: R 4.1.0 Seurat 4.4.0 I'm using server on Linux

[shiranss]

Here, there, before installing Matrix and irlba, you could do this first : Go to https://cran.r-project.org/bin/macosx/tools/, download an installer package gfortran-12.2-universal.pkg

I tried this followed by install.packages("Matrix", type = "source") install.packages("irlba", type = "source")

but I still have the same error.

I also installed RSpectra and loaded it which still gives the same error. Could anyone help with this?

R version 4.3.3 (2024-02-29) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.4.1 Seurat_5.0.3
SeuratObject_5.0.1
Matrix_1.6-5
irlba_2.3.5.1

[ScienceComputing]

Here, there, before installing Matrix and irlba, you could do this first : Go to https://cran.r-project.org/bin/macosx/tools/, download an installer package gfortran-12.2-universal.pkg

I tried this followed by install.packages("Matrix", type = "source") install.packages("irlba", type = "source")

but I still have the same error.

I also installed RSpectra and loaded it which still gives the same error. Could anyone help with this?

R version 4.3.3 (2024-02-29) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.4.1 Seurat_5.0.3 SeuratObject_5.0.1 Matrix_1.6-5 irlba_2.3.5.1

Maybe you can try R 4.4.0 for Mac, and re-install Matrix. I do not see irlba bug anymore. Hope it helps.

[igrabski]

Hi all, these issues should be resolved using the most up-to-date versions of Seurat, SeuratObject, and Matrix, and by installing Matrix and irlba from source as suggested as above. If problems persist, please feel free to open a new issue.

[sugarballer]

Matrix 1.6-1 solves this problem.