Dear Martin,
What's the ETA for _R_CLASS_MATRIX_ARRAY_=TRUE to become the new
unconditional behavior in R devel? Thanks!
H.
On 11/21/19 08:57, Martin Maechler wrote:
>
> TLDR: This is quite technical, still somewhat important:
> 1) R 4.0.0 will become a bit more coherent: a matrix is an array
> 2) Your package (or one you use) may be affected.
>
>
>>>>>> Martin Maechler
>>>>>> on Fri, 15 Nov 2019 17:31:15 +0100 writes:
>
>>>>>> Pages, Herve
>>>>>> on Thu, 14 Nov 2019 19:13:47 +0000 writes:
>
> >> On 11/14/19 05:47, Hadley Wickham wrote:
> >>> On Sun, Nov 10, 2019 at 2:37 AM Martin Maechler ... wrote:
>
> [................]
>
> >>>>> Note again that both "matrix" and "array" are special [see ?class]
> as
> >>>>> being of __implicit class__ and I am considering that this
> >>>>> implicit class behavior for these two should be slightly
> >>>>> changed ....
> >>>>>
> >>>>> And indeed I think you are right on spot and this would mean
> >>>>> that indeed the implicit class
> >>>>> "matrix" should rather become c("matrix", "array").
> >>>>
> >>>> I've made up my mind (and not been contradicted by my fellow R
> >>>> corers) to try go there for R 4.0.0 next April.
>
> >>> I can't seem to find the previous thread, so would you mind being a
> >>> bit more explicit here? Do you mean adding "array" to the implicit
> >>> class?
>
> >> It's late in Europe ;-)
>
> >> That's my understanding. I think the plan is to have class(matrix())
> >> return c("matrix", "array"). No class attributes added to matrix or
> >> array objects.
>
> >> It's all what is needed to have inherits(matrix(), "array") return
> TRUE
> >> (instead of FALSE at the moment) and S3 dispatch pick up the foo.array
> >> method when foo(matrix()) is called and there is no foo.matrix method.
>
> > Thank you, Hervé! That's exactly the plan.
>
> BUT it's wrong what I (and Peter and Hervé and ....) had assumed:
>
> If I just change the class
> (as I already did a few days ago, but you must activate the change
> via environment variable, see below),
>
> S3 dispatch does *NOT* at all pick it up:
> "matrix" (and "array") are even more special here (see below),
> and from Hadley's questions, in hindsight I now see that he's been aware
> of that and I hereby apologize to Hadley for not having thought
> and looked more, when he asked ..
>
> Half an hour ago, I've done another source code commit (svn r77446),
> to "R-devel" only, of course, and the R-devel NEWS now starts as
>
> ------------------------------------------------------------
>
> CHANGES IN R-devel:
>
> USER-VISIBLE CHANGES:
>
> • .... intention that the next non-patch release should be 4.0.0.
>
> • R now builds by default against a PCRE2 library ........
> ...................
> ...................
>
> • For now only active when environment variable
> _R_CLASS_MATRIX_ARRAY_ is set to non-empty, but planned to be the
> new unconditional behavior when R 4.0.0 is released:
>
> Newly, matrix objects also inherit from class "array", namely,
> e.g., class(diag(1)) is c("matrix", "array") which invalidates
> code (wrongly) assuming that length(class(obj)) == 1, a wrong
> assumption that is less frequently fulfilled now. (Currently
> only after setting _R_CLASS_MATRIX_ARRAY_ to non-empty.)
>
> S3 methods for "array", i.e., <someFun>.array(), are now also
> dispatched for matrix objects.
>
> ------------------------------------------------------------
> (where only the very last 1.5 lines paragraph is new.)
>
> Note the following
> (if you use a version of R-devel, with svn rev >= 77446; which
> you may get as a binary for Windows in about one day; everyone
> else needs to compile for the sources .. or wait a bit, maybe
> also not much longer than one day, for a docker image) :
>
>
>> Sys.unsetenv("_R_CLASS_MATRIX_ARRAY_") # ==> current R behavior
>> class(m <- diag(1))
> [1] "matrix"
>> Sys.setenv("_R_CLASS_MATRIX_ARRAY_" = "BOOH !") # ==> future R behavior
>> class(m)
> [1] "matrix" "array"
>>
>> foo <- function(x) UseMethod("foo")
>> foo.array <- function(x) "made in foo.array()"
>> foo(m)
> [1] "made in foo.array()"
>> Sys.unsetenv("_R_CLASS_MATRIX_ARRAY_")# ==> current R behavior
>> foo(m)
> Error in UseMethod("foo") :
> no applicable method for 'foo' applied to an object of class "c('matrix',
> 'double', 'numeric')"
>
>> Sys.setenv("_R_CLASS_MATRIX_ARRAY_" = TRUE) # ==> future R behavior
>> foo(m)
> [1] "made in foo.array()"
>> foo.A <- foo.array ; rm(foo.array)
>> foo(m)
> Error in UseMethod("foo") :
> no applicable method for 'foo' applied to an object of class "c('matrix',
> 'array', 'double', 'numeric')"
>>
>
> So, with my commit 77446, the _R_CLASS_MATRIX_ARRAY_
> environment variable also changes the
>
> "S3 dispatch determining class"
>
> mentioned as 'class' in the error message (of the two cases, old
> and new) above, which in R <= 3.6.x for a numeric matrix is
>
> c('matrix', 'double', 'numeric')
>
> and from R 4.0.0 on will be
>
> c('matrix', 'array', 'double', 'numeric')
>
> Note that this is *not* (in R <= 3.6.x, nor very probably in R 4.0.0)
> the same as R's class().
> Hadley calls this long class vector the 'implicit class' -- which
> is a good term but somewhat conflicting with R's (i.e. R-core's)
> "definition" used in the ?class help page (for ca. 11 years).
>
> R's internal C code has a nice function class R_data_class2()
> which computes this 'S3-dispatch-class' character (vector) for
> any R object, and R_data_class2() is indeed called from (the
> underlying C function of) R's UseMethod().
>
> Using the above fact of an error message,
> I wrote a nice (quite well tested) function my.class2() which
> returns this S3_dispatch_class() also in current versions of R:
>
> my.class2 <- function(x) { # use a fn name not used by any sane ..
> foo.7.3.343 <- function(x) UseMethod("foo.7.3.343")
> msg <- tryCatch(foo.7.3.343(x), error=function(e) e$message)
> clm <- sub('"$', '', sub(".* of class \"", '', msg))
> if(is.language(x) || is.function(x))
> clm
> else {
> cl <- str2lang(clm)
> if(is.symbol(cl)) as.character(cl) else eval(cl)
> }
> }
>
> ## str2lang() needs R >= 3.6.0:
> if(getRversion() < "3.6.0") ## substitute for str2lang(), good enough here:
> str2lang <- function(s) parse(text = s, keep.source=FALSE)[[1]]
>
>
> Now you can look at such things yourself:
>
> ## --------------------- the "interesting" cases : ---
> ## integer and double
> my.class2( pi) # == c("double", "numeric")
> my.class2(1:2) # == c("integer", "numeric")
> ## matrix and array [also combined with int / double ] :
> my.class2(matrix(1L, 2,3)) # == c(matrixCL, "integer", "numeric") <<<
> my.class2(matrix(pi, 2,3)) # == c(matrixCL, "double", "numeric") <<<
> my.class2(array("A", 2:3)) # == c(matrixCL, "character") <<<
> my.class2(array(1:24, 2:4)) # == c("array", "integer", "numeric")
> my.class2(array( pi , 2:4)) # == c("array", "double", "numeric")
> my.class2(array(TRUE, 2:4)) # == c("array", "logical")
> my.class2(array(letters, 2:4)) # == c("array", "character")
> my.class2(array(1:24 + 1i, 2)) # == c("array", "complex")
>
> ## other cases
> my.class2(NA) # == class(NA) : "logical"
> my.class2("A") # == class("B"): "character"
> my.class2(as.raw(0:2)) # == "raw"
> my.class2(1 + 2i) # == "complex"
> my.class2(USJudgeRatings)#== "data.frame"
> my.class2(class) # == "function" # also for a primitive
> my.class2(globalenv()) # == "environment"
> my.class2(quote(sin(x)))# == "call"
> my.class2(quote(sin) ) # == "name"
> my.class2(quote({})) # == class(*) == "{"
> my.class2(quote((.))) # == class(*) == "("
>
> -----------------------------------------------------
>
> note that of course, the lines marked "<<<" above, contain
> 'matrixCL' which is "matrix" in "old" (i.e. current) R,
> and is c("matrix", "array") in "new" (i.e. future) R.
>
> Last but not least: It's quite trivial (only few words need to
> be added to the sources; more to the documentation) to add an R
> function to base R which provides the same as my.class2() above,
> (but much more efficiently, not via catching error messages !!),
> and my current proposal for that function's name is .class2()
> {it should start with a dot ("."), as it's not for the simple
> minded average useR ... and you know how I'm happy with
> function names that do not need one single [Shift] key ...}
>
> The current plan contains
>
> 1) Notify CRAN package maintainers (ca 140) whose packages no
> longer pass R CMD check when the feature is turned on
> (via setting the environment variable) in R-devel.
>
> 2a) (Some) CRAN team members set _R_CLASS_MATRIX_ARRAY_ (to non-empty),
> as part of the incoming checks, at least for all new CRAN submissions
>
> 2b) set the _R_CLASS_MATRIX_ARRAY_ (to non-empty), as part of
> ' R CMD check --as-cran <pkg>'
>
> 3) Before the end of 2019, change the R sources (for R-devel)
> such that it behaves as it behaves currently when the environment
> variable is set *AND* abolish this environment variable from
> the sources. {read on to learn *why*}
>
> Consequently (to 3), R 4.0.0 will behave as indicated, unconditionally.
>
> Note that (as I've shown above in the first example set) this is
> set up in such a manner that you can change the environment
> variable during a *running* R session, and observe the effect immediately.
> This however lead to some slow down of quite a bit of the R
> code, because actually the environment variable has to be
> checked quite often (easily dozens of times for simple R calls).
>
> For that reason, we want to do "3)" as quickly as possible.
>
> Please do not hesitate to ask or comment
> -- here, not on Twitter, please -- noting that I'll be
> basically offline for an extended weekend within 24h, now.
>
> I hope this will eventually to lead to clean up and clarity in
> R, and hence should be worth the pain of broken
> back-compatibility and having to adapt your (almost always only
> sub-optimally written ;-)) R code,
> see also my Blog
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bit.ly_R-5Fblog-5Fclass-5Fthink-5F2x&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=xAGXmo1FhJxT-qBfj-McDEn3sqWhqJHNV-IPpN7g6oA&s=yUUwdjl5LE90V0tLTM3FZYZ0zHf8coHo49Vt95O7IwQ&e=
>
> Martin Maechler
> ETH Zurich and R Core team
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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