isSpike function in SingleCellExperiment package is deprecated?
isSpike was provided by SingleCellExperiment. It is now deprecated. The notes in SingleCellExperiment indicate that one should use altExps

I am struggling with a similar problem. Can't compile a package (powsimR) because a dependency uses isSpike (not used in the code directly), so I have to hunt down where it is used by one of a very long list of dependencies.