This function of SPONGEffects uses outdated software from the GSVA package.
Since Bioconductor 3.18 this has changed (copied from documentation):
Instead of gsva(expr=., gset.idx.list=., method=., ...), use a method-specific parameter object, see plageParam zscoreParam ssgseaParam gsvaParam, followed by a call to the new gsva() function, see gsva.
Probably the corresponding function in SPONGE::enrichment_modules() has to be replaced, the functionality should be identical.
This function of SPONGEffects uses outdated software from the
GSVApackage.Since Bioconductor 3.18 this has changed (copied from documentation):
Instead of gsva(expr=., gset.idx.list=., method=., ...), use a method-specific parameter object, see plageParam zscoreParam ssgseaParam gsvaParam, followed by a call to the new gsva() function, see gsva.
Probably the corresponding function in
SPONGE::enrichment_modules()has to be replaced, the functionality should be identical.