From mtmorgan at fhcrc.org  Fri Oct  5 02:56:08 2012
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Thu, 04 Oct 2012 17:56:08 -0700
Subject: [Rd] identical() fails to compare isS4(<S4 instance>) to TRUE
In-Reply-To: <506E1641.2030405@gmail.com>
References: <506DF82E.7080507@fhcrc.org> <506DFE56.30501@gmail.com>
	<506E04B3.7030101@fhcrc.org> <506E1641.2030405@gmail.com>
Message-ID: <506E3028.7090405@fhcrc.org>

On 10/04/2012 04:05 PM, Duncan Murdoch wrote:
> On 12-10-04 5:50 PM, Martin Morgan wrote:
>> On 10/04/2012 02:23 PM, Duncan Murdoch wrote:
>>> On 12-10-04 4:57 PM, Martin Morgan wrote:
>>>>
>>>>    > setClass("A", "integer")
>>>>    > isS4(new("A"))
>>>> [1] TRUE
>>>>    > identical(isS4(new("A")), TRUE)
>>>> [1] FALSE
>>>>
>>>>    > sessionInfo()
>>>> R Under development (unstable) (2012-10-04 r60876)
>>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>
>>>> locale:
>>>>     [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>>     [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>>     [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>>     [7] LC_PAPER=C                 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
>>>>
>>>
>>> I can confirm this in R-devel, but it doesn't happen in R-patched.  In R-devel,
>>> isS4 is returning a vector marked as LGLSXP, but containing the value 16, not
>>> the usual 1 for TRUE.
>>>
>>>   > .Internal(inspect(isS4(new("A"))))
>>> @4bfbed8 10 LGLSXP g0c1 [] (len=1, tl=0) 16
>>>
>>> I'm not going to have time to track this down and fix it.
>>
>> The bit is set at src/include/Rinternals.h:278
>>
>>    39103        jmc #define IS_S4_OBJECT(x) ((x)->sxpinfo.gp & S4_OBJECT_MASK)
>>
>> but it's identical that has changed; it looks as though there are other similar
>> operations in that header and probably elsewhere.
>
> In R-patched, it returned the value 1 for TRUE, so I'm not sure identical() has
> changed.

R version 2.15.1 Patched (2012-09-24 r60798) has

 > isS4
function (object)
.Call("R_isS4Object", object, PACKAGE = "base")

with objects.c:1531

SEXP R_isS4Object(SEXP object)
{
     /* wanted: return isS4(object) ? mkTrue() : mkFalse(); */
     return IS_S4_OBJECT(object) ? mkTrue() : mkFalse(); ;
}

where R-devel has

 > isS4
function (object)  .Primitive("isS4")

with coerce.c:1843

     case 51:		/* isS4 */
	LOGICAL(ans)[0] = IS_S4_OBJECT(CAR(args));
	break;

made in r60395

Martin

>
> Duncan Murdoch
>
>>
>> Martin
>>
>>>
>>> Duncan Murdoch
>>
>>
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793



[Rd] identical() fails to compare isS4(<S4 instance>) to TRUE
Martin Morgan