function "as_cholmod_sparse" not provided by package "Matrix"

compbiomed / singleCellTK

Interactively analyze single cell genomic data

https://camplab.net/sctk/

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function "as_cholmod_sparse" not provided by package "Matrix" #745

Closed Prsisteer8591 closed 7 months ago

Prsisteer8591 commented 8 months ago

Screenshot 2024-02-04 at 08 27 34 I have tried to use the QC function (scrublet and doubletfinder ) in the shiny app to run my sample. It worked fine previously. But not this time.

joshua-d-campbell commented 7 months ago

Hi @Prsisteer8591, thanks for using our tool. Could you let us know the version of the "Matrix" package you are using? If you try upgrading it, that may solve the issue. We are also nearly complete with an update that will allow for use of the Seurat V5 package. This may also help resolve the issue. It should be up in the next few days.

joshua-d-campbell commented 7 months ago

This issue should be fixed by upgrading R to v4.3, installing singleCellTK v2.12.2, and installing the latest versions of the Seurat and Matrix packages. You can re-install the package directly from GitHub:

library(devtools)
install_github("compbiomed/singleCellTK")

We will also push this version to Bioconductor soon. Let us know if you have more troubles.

FionaMoon commented 2 months ago

I tried re-install singleCellTK from github but I still get error. My Matrix version is ‘1.6.5’. My R is 4.3.2.