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

[kangjiajinlong]

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]

Hey Jack,

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

Nick

[kangjiajinlong]

Thanks I will try.

[kangjiajinlong]

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