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Don't import stats::plogis

Need to use the S4 generic `plogis()` from DelayedArray. It's default method is `stats::plogis()`, so it does the right thing.

Peter Hickey authored on 28/06/2018 16:27:46
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@@ -19,7 +19,7 @@ importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
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 importFrom(stats, "approxfun", "fisher.test", "ppoints",
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            "predict", "preplot", "qchisq",
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            "qnorm", "qqplot", "qunif", "cov2cor",
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-           "plogis", "setNames")
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+           "setNames")
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 importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
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            "mtext", "par", "plot", "points", "polygon", "rect", "rug", "text")
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 import(parallel)
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@@ -341,8 +341,6 @@ BSmooth <- function(BSseq,
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 # TODOs ------------------------------------------------------------------------
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-# TODO: The @trans slot isn't getting correctly set (it's using stats::plogis
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-#       instead of DelayedArray::plogis).
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 # TODO: Use the logging facilities of BiocParallel. This is a longterm goal.
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 #       For example, we could set custom messages within .BSmooth() using the
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 #       futile.logger syntax; see the BiocParalell vignette 'Errors, Logs and