[Bioc-devel] [Rd] For integer vectors, `as(x, "numeric")` has no effect.

Martin Maechler <maechler at stat.math.ethz.ch>
   on Tue, 8 Dec 2015 15:25:21 +0100 writes:

John Chambers <jmc at r-project.org>
   on Mon, 7 Dec 2015 16:05:59 -0800 writes:

We do need an explicit method here, I think.
The issue is that as() uses methods for the generic function coerce() but cannot use inheritance in the usual way (if it did, you would be immediately back with no change, since "integer" inherits from "numeric").

Copying in the general method for coercing to "numeric" as an explicit method for "integer" gives the expected result:

setMethod("coerce", c("integer", "numeric"), getMethod("coerce", c("ANY", "numeric")))

[1] "coerce"

typeof(as(1L, "numeric"))

[1] "double"

Seems like a reasonable addition to the code, unless someone sees a problem.
John

I guess that that some package checks (in CRAN + Bioc + ... -
land) will break,
but I still think we should add such a coercion to R.

Martin

Hmm...  I've tried to add the above to R
and do notice that there are consequences that may be larger than
anticipated:

Here is example code:

  myN   <- setClass("myN",   contains="numeric")
  myNid <- setClass("myNid", contains="numeric", representation(id="character"))
  NN <-    setClass("NN", representation(x="numeric"))

  (m1 <- myN  (1:3))
  (m2 <- myNid(1:3, id = "i3"))
  tools::assertError(NN (1:3))# in all R versions

  ##                     # current R  |  new R
  ##                     # -----------|----------
  class(getDataPart(m1)) # integer    |  numeric
  class(getDataPart(m2)) # integer    |  numeric


In other words, with the above setting, the traditional
gentleperson's agreement in S and R,

 __ "numeric" sometimes conveniently means "integer" or "double"  __

will be slightly less often used ... which of course may be a
very good thing.

However, it breaks strict back compatibility also in cases where
the previous behavior may have been preferable:
After all integer vectors need only have the space of doubles.

Shall we still go ahead and do apply this change to R-devel
and then all package others will be willing to update where necessary?

As this may affect the many hundreds of bioconductor packages
using S4 classes, I am -- exceptionally -- cross posting to the
bioc-devel list.

Martin Maechler

On Dec 7, 2015, at 3:37 PM, Benjamin Tyner <btyner at gmail.com> wrote:

Perhaps it is not that surprising, given that

mode(1L)

[1] "numeric"

and

is.numeric(1L)

[1] TRUE

On the other hand, this is curious, to say the least:

is.double(as(1L, "double"))

[1] FALSE

Here's the surprising behavior:

x <- 1L
xx <- as(x, "numeric")
class(xx)
## [1] "integer"

It occurs because the call to `as(x, "numeric")` dispatches the coerce
S4 method for the signature `c("integer", "numeric")`, whose body is
copied in below.

function (from, to = "numeric", strict = TRUE)
if (strict) {
class(from) <- "numeric"
from
} else from

This in turn does nothing, even when strict=TRUE, because that
assignment to class "numeric" has no effect:

x <- 10L
class(x) <- "numeric"
class(x)
[1] "integer"

Is this the desired behavior for `as(x, "numeric")`?