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satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression
GNU General Public License v3.0
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Issue with calling "glmGamPoi" to work #192

Closed Joy8Liu closed 6 months ago

Joy8Liu commented 6 months ago

Hi, there is a issue I've encountered when using sctransform. I'd like to ask this problem for help. I've installed 'glmGamPoi', and the answer to 'glmGamPoi' %in% installed.packages() is True.

But when I run the code Pre3 <- SCTransform(Pre3, verbose = FALSE), The response is the following information:

`vst.flavor` is set to 'v2' but could not find glmGamPoi installed.
Please install the glmGamPoi package for much faster estimation.
--------------------------------------------
install.packages('BiocManager')
BiocManager::install('glmGamPoi')
--------------------------------------------
Falling back to native (slower) implementation.

I wonder how I can resolve this problem. Thank you so much for your help in advance.

Originally posted by @Joy8Liu in https://github.com/satijalab/seurat/issues/5585#issuecomment-2095827086

Joy8Liu commented 6 months ago

Find a solution already, never mind.

cgorozco commented 4 months ago

What was the solution?

Joy8Liu commented 4 months ago

What was the solution?

I couldn't remember it clearly. But the reason is one dependency of "glmGampoi" is not installed. I seemed to find this dependency by the Error occurred when I library(glmGamPoi)? So someone may find hints from the error message.