Unable to find an inherited method for function ‘gsva’ for signature ‘"missing", "missing"’

ncborcherding / escape

Easy single cell analysis platform for enrichment

https://www.borch.dev/uploads/screpertoire/articles/running_escape

MIT License

149 stars 20 forks source link

Unable to find an inherited method for function ‘gsva’ for signature ‘"missing", "missing"’ #128

Closed kangjiajinlong closed 1 month ago

kangjiajinlong commented 1 month ago

Hello,

I ran escape using the following code but encountered errors that I cannot resolve:

library(escape) H <- getGeneSets(library="H")

DefaultAssay(obj.sub) <- "RNA" obj.sub <- runEscape(obj.sub, method = "ssGSEA",gene.sets = H, groups = 5000, min.size = 5,new.assay.name="escape.H")

[1] "Using sets of 5000 cells. Running 17 times." Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘gsva’ for signature ‘"missing", "missing"’

Could you kindly look into this issue?

Jack

ncborcherding commented 1 month ago

Hey Jack,

You will need to update your version of GSVA - please check out #88

Nick

kangjiajinlong commented 1 month ago

Thanks I will try.

kangjiajinlong commented 1 month ago

I tried your suggesting devtools::install_github("rcastelo/GSVA"). The process crashed when install "SpatialExperiment":

installing source package ‘SpatialExperiment’ ... using staged installation R inst byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/jkang5/R/ubuntu/4.3.1/magick/libs/magick.so': libMagick++-6.Q16.so.8: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted