>>>>> Pages, Herve
>>>>> on Tue, 21 Jan 2020 17:33:01 +0000 writes:
> Dear Martin,
> What's the ETA for _R_CLASS_MATRIX_ARRAY_=TRUE to become the new
> unconditional behavior in R devel? Thanks!
> H.
Thank you, Hervé, for asking / reminding.
It has been made so now, 3 days ago (svn r77714).
Martin
> 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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