I have just committed bsseq 0.9.4 to the devel branch of Biconductor.

This update changes the underlying representation of objects of class
'BSseq' to use a SummarizedExperiment backend, and should make for a
smoother ride when very large objects are manipulated.

There are likely to be further updates in the coming days as potential bugs
are found and removed (although it does pass all unitTests, all vignettes
build and all examples run).

Old serialized (saved) objects can be updated using
  x <- updateObject(x)

Best,
Kasper

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