I'm seeing an error in devel branch related to DESeqResults, which contains DataFrame. And I think I can trace it to S4Vectors.

I have this minimal example:

setClass("myDataFrame", contains="DataFrame")
d <- DataFrame(x=1:5)
dd <- new("myDataFrame", d)
d$y <- 1:5
dd$y <- 1:5
Error in concatenateObjects(x, objects, ignore.mcols = ignore.mcols) : 
  the objects to concatenate must be myDataFrame objects (or NULLs)
Calls: $<- ... c -> .local -> concatenateObjects -> concatenateObjects

For sessionInfo() and more context, see this original post:

C: results function of DESeq2 devel fails

It looks like this is fixed for me in S4Vectors version 0.17.22.