On 1/27/20 23:51, Martin Maechler wrote:
>>>>>> 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).
Yep, I've seen that. Already deployed on the Bioconductor build
machines. Thanks!
H.
>
> 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
>
--
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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