From Bill.Venables at csiro.au  Sat Dec 23 02:11:10 2006
From: Bill.Venables at csiro.au (Bill.Venables at csiro.au)
Date: Sat, 23 Dec 2006 11:11:10 +1000
Subject: [Rd] substitute creates an object which prints incorrectly
	(PR#9427)
Message-ID: <B998A44C8986644EA8029CFE6396A924840A87@exqld2-bne.qld.csiro.au>

Thanks Peter.  I see the dilemma.  It is serious in my view, though,
even if I can't see an elegant way round it.

I guess the only possibilities are

1. Only keep the source in printing or, much more seriously, dumping, if
the source attribute parses to an object structually identical to the
function itself (even I can see this is going to be impractical)

2. Make the default keep.source option FALSE rather than TRUE and warn
people that switching it on can be unsafe in language manipulation.
This would be practical, I suggest, if comments were kept as part of the
function itself, as well as in the source attribute, but if comments are
only kept in the source attribute (as appears to be the case now) I
concede this becomes impractical.

3. Modify substitute() so that it strips source attributes (or anything
else apparently visible that it will not manipulate) from objects.
Sorry folks, too dangerous.  (I concede this appears to be a bit of an
overkill, too.)

Perhaps the compromise has to be to warn people that keep.source=TRUE
can be dangerous in this way, both in the help informaton for options()
and for substitute().

?

Bill Venables.

-----Original Message-----
From: Peter Dalgaard [mailto:p.dalgaard at biostat.ku.dk] 
Sent: Friday, 22 December 2006 9:47 PM
To: Venables, Bill (CMIS, Cleveland)
Cc: r-devel at stat.math.ethz.ch; R-bugs at biostat.ku.dk
Subject: Re: [Rd] substitute creates an object which prints incorrectly
(PR#9427)

Bill.Venables at csiro.au wrote:
> The function "substitute" seems to fail to make a genuine
> substitution, although the printed verision seems fine.  Here is an
> example.
>
>   
>> m <- substitute(Y <- function(x) FUN(x+1), 
>>     
> + list(Y = as.name("y"), FUN = as.name("sin")))
>   
>> m
>>     
> y <- function(x) sin(x + 1)
>   
>> eval(m)
>> y
>>     
> function(x) FUN(x+1)
>
> However the story doesn't end there.  The substitution appears to have
> been made, even though the printed version, this time, suggests
> otherwise.
>
>   
>> y(pi)
>>     
> [1] -0.841471
>   
>> sin(pi+1)
>>     
> [1] -0.841471
>   
>
>   
Yes, this is (fairly) well known. It has to do with the retention of 
function source.

The thing to notice is that it is only the printing of y that is really 
confused. If you do

dput(y)
attr(y, "source")
attr(y, "source") <- NULL
y

then you should see the point. The tricky bit is that the "source" 
attribute exists in an intermediate form inside m. Notice that m 
contains, not the function itself, but a call to the function `function`

which creates the function when eval'ed. This call contains the function

source as its 4th element (look at m[[3]][[4]] in your example), and you

might try setting it to NULL and see how things will clear up.

The issue with substitute is that it cannot sensibly substitute into 
character vectors, so it just leaves  the source as is, which gives the 
symptoms you see. It could, however, and probably should, recognize 
calls to `function` and NULL out their 4th element. It cannot be done 
completely failsafe though (`function` could result from a computation, 
or even be part of the substitution), so one has to decide that the 
extreme cases are too extreme worry about them.
 
-pd

> Bill Venables 
> CMIS, CSIRO Laboratories, 
> PO Box 120, Cleveland, Qld. 4163 
> AUSTRALIA 
> Office Phone (email preferred): +61 7 3826 7251 
> Fax (if absolutely necessary):    +61 7 3826 7304 
> Mobile (rarely used):                +61 4 1963 4642 
> Home Phone:                          +61 7 3286 7700 
> mailto:Bill.Venables at csiro.au 
> http://www.cmis.csiro.au/bill.venables/ 
>
>
> --please do not edit the information below--
>
> Version:
>  platform = i386-pc-mingw32
>  arch = i386
>  os = mingw32
>  system = i386, mingw32
>  status = 
>  major = 2
>  minor = 4.1
>  year = 2006
>  month = 12
>  day = 18
>  svn rev = 40228
>  language = R
>  version.string = R version 2.4.1 (2006-12-18)
>
> Windows XP Professional (build 2600) Service Pack 2.0
>
> Locale:
>
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
>
ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
> Search Path:
>  .GlobalEnv, .R_Store, package:RODBC, package:xlsReadWrite,
> package:cluster, package:vegan, package:ASOR, package:stats,
> package:graphics, package:grDevices, package:utils, package:datasets,
> .R_Data, .R_Utils, package:svIDE, package:tcltk, package:methods,
> Autoloads, package:base
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] substitute creates an object which prints incorrectly (PR#9427)
Bill.Venables at csiro.au