[Rd] [EXTERNAL] Re: Re: all.equal failure

[Duncan Murdoch]

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 using r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>
>>>>
>>>
>>
>