[Bioc-devel] today's devel build report

[Dan Tenenbaum]

Hi all,

As part of our ongoing response to Michael Love's request for more information when things happen with the build system, today in the devel (3.2) build reports we see some packages failing in response to some methods (seqapply(), mseqapply(), tseqapply(), seqsplit(), and seqby()) being removed from IRanges.

Note that these methods were deprecated a year ago, and then made defunct in the previous devel cycle, so it is appropriate that they are being removed now at the beginning of this devel cycle.

If your package uses these methods, you should replace them as suggested by the .Defunct() calls in the *release* version of IRanges:

seqapply <- function(X, FUN, ...) {
  .Defunct("as(lapply(X, FUN, ...), 'List')")
}

mseqapply <- function(FUN, ..., MoreArgs = NULL, USE.NAMES = TRUE) {
  .Defunct("as(mapply(FUN, ...), 'List')")
}

tseqapply <- function(X, INDEX, FUN = NULL, ...) {
  .Defunct("as(tapply(X, INDEX, FUN, ...), 'List')")
}

seqsplit <- function(x, f, drop=FALSE) {
  .Defunct("splitAsList")
}

seqby <- function(data, INDICES, FUN, ...) {
  .Defunct("as(by(X, INDICES, FUN, ...), 'List')")
}

Let us know if you have any questions.
Thanks,
Dan