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]]
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
