I think DESeq is a bit out of sync with the documentation/tutorial at the moment. I ran into the same problems as you, but after looking at some help pages and/or the vignette (can't remember which) I ended up using:
cds <- newCountDataSet(data, conds)
cds <- estimateSizeFactors(cds)
cds <- estimateVarianceFunctions(cds)
res <- nbinomTest(cds, "case", "control")
... which seems to work.
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