On 05/04/2019 10:46 a.m., Therneau, Terry M., Ph.D. wrote:
On 4/5/19 9:39 AM, Duncan Murdoch wrote:
On 05/04/2019 10:19 a.m., Therneau, Terry M., Ph.D. wrote:
Duncan, ?? I should have included it in my original note, but ??? ? all.equal(unclass(t0x), unclass(t1x)) returns TRUE as well.? I had tried that as well. ? But a further look at all.equal.default shows the following line right near the top: ???? if (is.language(target) || is.function(target)) ???????? return(all.equal.language(target, current, ...)) and that path explicitly ignores attributes.
Which R version are you using?? I see deparse(target) and deparse(current) in all.equal.language(), and those should not be ignoring attributes according to the documentation.
I'm using today's version of R-devel on Ubuntu.? (svn up this AM) But I agree, both target and current appear.
That's not what I said. I said that the attributes should not be
ignored in that function. I don't see anything in the R-devel version
of it that ignores attributes:
> all.equal.language
function (target, current, ...)
{
mt <- mode(target)
mc <- mode(current)
if (mt == "expression" && mc == "expression")
return(all.equal.list(target, current, ...))
ttxt <- paste(deparse(target), collapse = "\n")
ctxt <- paste(deparse(current), collapse = "\n")
msg <- c(if (mt != mc) paste0("Modes of target, current: ",
mt, ", ", mc), if (ttxt != ctxt) {
if (pmatch(ttxt, ctxt, 0L)) "target is a subset of current"
else if (pmatch(ctxt,
ttxt, 0L)) "current is a subset of target" else "target,
current do not match when deparsed"
})
if (is.null(msg))
TRUE
else msg
}
<bytecode: 0x7fd9e792f1e0>
<environment: namespace:base>
Duncan Murdoch
Duncan Murdoch
I'll change my original original title to "all.equal was not a good tool for testing certain code issues". Thanks for the pointer, Terry On 4/5/19 9:00 AM, Duncan Murdoch wrote:
On 05/04/2019 9:03 a.m., Therneau, Terry M., Ph.D. via R-devel wrote:
This arose in testing [.terms and has me confused. data(esoph)?? # use a standard data set t0x <- terms(model.frame( ~ tobgp, data=esoph)) t1 <-? terms(model.frame(ncases ~ agegp + tobgp, data=esoph)) t1x <- (delete.response(t1))[-1] ? > all.equal(t0x, t1x) [1] TRUE # the above is wrong, because they actually are not the same ? > all.equal(attr(t0x, 'dataClasses'), attr(t1x, 'dataClasses')) [1] "Names: 1 string mismatch" [2] "Lengths (1, 2) differ (string compare on first 1)"
As documented, all.equal() is generic, with methods for different classes.? The
classes of both t0x and t1x are
?c("terms","formula")
with no all.equal.terms method, so all.equal.formula is called. That method isn't
specifically documented, but you can see its definition as
function (target, current, ...)
{
??? if (length(target) != length(current))
??????? return(paste0("target, current differ in having response: ",
??????????? length(target) == 3L, ", ", length(current) == 3L))
??? if (!identical(deparse(target), deparse(current)))
??????? "formulas differ in contents"
??? else TRUE
}
So the issue is that deparse(t0x) and deparse(t1x) give the same strings with no
attributes shown, even though "showAttributes" is set by default.?? I haven't traced
through the C code to see where things are going wrong.
Duncan Murdoch
? > sessionInfo() R Under development (unstable) (2019-04-05 r76323) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.2 LTS Matrix products: default BLAS:?? /usr/local/src/R-devel/lib/libRblas.so LAPACK: /usr/local/src/R-devel/lib/libRlapack.so locale: ? ?[1] LC_CTYPE=en_US.UTF-8?????? LC_NUMERIC=C ? ?[3] LC_TIME=en_US.UTF-8??????? LC_COLLATE=C ? ?[5] LC_MONETARY=en_US.UTF-8??? LC_MESSAGES=en_US.UTF-8 ? ?[7] LC_PAPER=en_US.UTF-8?????? LC_NAME=C ? ?[9] LC_ADDRESS=C?????????????? LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats???? graphics? grDevices utils???? datasets methods base loaded via a namespace (and not attached): [1] compiler_3.7.0 tools_3.7.0 ????[[alternative HTML version deleted]]
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