thr3ads.net - R devel - [Rd] NextMethod causes R 2.2.0 to crash (PR#8416) [Dec 2005]

If this information is useful, please help other people find it:
Share via:

Bill.Venables@csiro.au

2005-Dec-21 03:32 UTC

[Rd] NextMethod causes R 2.2.0 to crash (PR#8416)

I found writing the following default method the for the generic
function "julian" causes R to crash.


julian.default <- function(x, ...) {
        x <- as.Date(x)
        NextMethod("julian", x, ...)
}

Here is a test example 
> m <- as.Date("1972-09-27") + 0:10
> m  [1] "1972-09-27" "1972-09-28" "1972-09-29"
"1972-09-30" "1972-10-01"
"1972-10-02" "1972-10-03"
 [8] "1972-10-04" "1972-10-05" "1972-10-06"
"1972-10-07"> class(m)
[1] "Date"> julian(m) [1] 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010
attr(,"origin")
[1] "1970-01-01"
> m <- as.character(m)
> class(m)[1] "character"
> julian(m)
< R crashes>

--please do not edit the information below--

Version:
 platform = i386-pc-mingw32
 arch = i386
 os = mingw32
 system = i386, mingw32
 status = 
 major = 2
 minor = 2.0
 year = 2005
 month = 10
 day = 06
 svn rev = 35749
 language = R



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/

Henrik Bengtsson

2005-Dec-21 03:48 UTC

head link

[Rd] NextMethod causes R 2.2.0 to crash (PR#8416)

Bill.Venables at csiro.au wrote:> I found writing the following default method the for the generic
> function "julian" causes R to crash.
> 
> 
> julian.default <- function(x, ...) {
>         x <- as.Date(x)
>         NextMethod("julian", x, ...)
> }
On Windows XP R 2.2.0 Patched (2005-11-21 r36410) you get:

Error: evaluation nested too deeply: infinite recursion / 
options(expressions=)?

and on Windows XP R 2.1.1 Patched (2005-09-19) you get:

Error: protect(): protection stack overflow

It seems that the R.2.2.0 revision you have does not protect against 
this.  I agree that it should not be possible to crash R, but is it 
valid to call NextMethod() in a default function? [R core, should this 
ever be allowed?]

I do not know exactly how NextMethod() is expected to work here, but I 
could imaging that 'x' has class 'Date' when NextMethod() is
called and
the "next" class will the be the default one so you call 
julian.default() again ending up in an infinite call.  This makes sense 
from the errors I get above.  Try this and see what you get in your version:

julian.default <- function(x, ...) {
   cat("In julian.default()\n")
   x <- as.Date(x)
   NextMethod("julian", x, ...)
}

Was you intention to do the following instead

  julian.default <- function(x, ...) {
    x <- as.Date(x)
    julian(x, ...)
  }

where julian() is the generic function?

Cheers

Henrik

> Here is a test example 
> 
> 
>>m <- as.Date("1972-09-27") + 0:10
>>m 
> 
>  [1] "1972-09-27" "1972-09-28" "1972-09-29"
"1972-09-30" "1972-10-01"
> "1972-10-02" "1972-10-03"
>  [8] "1972-10-04" "1972-10-05" "1972-10-06"
"1972-10-07"
> 
>>class(m)
> 
> [1] "Date"
> 
>>julian(m)
> 
>  [1] 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010
> attr(,"origin")
> [1] "1970-01-01"
> 
> 
>>m <- as.character(m)
>>class(m)
> 
> [1] "character"
> 
> 
>>julian(m)
> 
> 
> < R crashes>
> 
> --please do not edit the information below--
> 
> Version:
>  platform = i386-pc-mingw32
>  arch = i386
>  os = mingw32
>  system = i386, mingw32
>  status = 
>  major = 2
>  minor = 2.0
>  year = 2005
>  month = 10
>  day = 06
>  svn rev = 35749
>  language = R
> 
> 
> 
> 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/
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
>

Bill.Venables@csiro.au

2005-Dec-21 05:06 UTC

head link

[Rd] NextMethod causes R 2.2.0 to crash (PR#8416)

Thanks Hendrik.

My main concern is that it should not be so easy to crash R.

On whether or not NextMethod from within the default method is kosher or
not - I would have thought so, but clearly I'm wrong here.  Perhaps
NextMethod within a default method should be something that at least
attracts a warning.

Regards,

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/ 



-----Original Message-----
From: Henrik Bengtsson [mailto:hb at maths.lth.se] 
Sent: Wednesday, 21 December 2005 1:48 PM
To: Venables, Bill (CMIS, Cleveland)
Cc: r-devel at stat.math.ethz.ch; R-bugs at biostat.ku.dk
Subject: Re: [Rd] NextMethod causes R 2.2.0 to crash (PR#8416)


Bill.Venables at csiro.au wrote:> I found writing the following default method the for the generic
> function "julian" causes R to crash.
> 
> 
> julian.default <- function(x, ...) {
>         x <- as.Date(x)
>         NextMethod("julian", x, ...)
> }
On Windows XP R 2.2.0 Patched (2005-11-21 r36410) you get:

Error: evaluation nested too deeply: infinite recursion / 
options(expressions=)?

and on Windows XP R 2.1.1 Patched (2005-09-19) you get:

Error: protect(): protection stack overflow

It seems that the R.2.2.0 revision you have does not protect against 
this.  I agree that it should not be possible to crash R, but is it 
valid to call NextMethod() in a default function? [R core, should this 
ever be allowed?]

I do not know exactly how NextMethod() is expected to work here, but I 
could imaging that 'x' has class 'Date' when NextMethod() is
called and
the "next" class will the be the default one so you call 
julian.default() again ending up in an infinite call.  This makes sense 
from the errors I get above.  Try this and see what you get in your
version:

julian.default <- function(x, ...) {
   cat("In julian.default()\n")
   x <- as.Date(x)
   NextMethod("julian", x, ...)
}

Was you intention to do the following instead

  julian.default <- function(x, ...) {
    x <- as.Date(x)
    julian(x, ...)
  }

where julian() is the generic function?

Cheers

Henrik

> Here is a test example 
> 
> 
>>m <- as.Date("1972-09-27") + 0:10
>>m 
> 
>  [1] "1972-09-27" "1972-09-28" "1972-09-29"
"1972-09-30" "1972-10-01"
> "1972-10-02" "1972-10-03"
>  [8] "1972-10-04" "1972-10-05" "1972-10-06"
"1972-10-07"
> 
>>class(m)
> 
> [1] "Date"
> 
>>julian(m)
> 
>  [1] 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010
> attr(,"origin")
> [1] "1970-01-01"
> 
> 
>>m <- as.character(m)
>>class(m)
> 
> [1] "character"
> 
> 
>>julian(m)
> 
> 
> < R crashes>
> 
> --please do not edit the information below--
> 
> Version:
>  platform = i386-pc-mingw32
>  arch = i386
>  os = mingw32
>  system = i386, mingw32
>  status = 
>  major = 2
>  minor = 2.0
>  year = 2005
>  month = 10
>  day = 06
>  svn rev = 35749
>  language = R
> 
> 
> 
> 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/
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
>

ripley@stats.ox.ac.uk

2005-Dec-21 09:48 UTC

head link

[Rd] NextMethod causes R 2.2.0 to crash (PR#8416)

Bill,

This is a 2.2.0 Windows problem, solved in 2.2.1.  What happened was that 
someone trying to be helpful increased the evaluation nesting limit in 
2.1.0, and Windows has a small C stack (2Mb) which can easily be exceeded.
I now get
> julian(m)
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?

as I should.  The nesting limit has been reduced and the C stack size 
increased.

It is legitimate to call NextMethod in a default method, but it is all too 
easy to get loops.  In your case you want the Date method, not the next 
method (which since there is only one class will be the default).

I would advise Windows users of 2.2.0 to

1) update
2) if that is not possible, set options(expressions=1000).

Brian

On Wed, 21 Dec 2005 Bill.Venables at csiro.au wrote:
> I found writing the following default method the for the generic
> function "julian" causes R to crash.
>
>
> julian.default <- function(x, ...) {
>        x <- as.Date(x)
>        NextMethod("julian", x, ...)
> }
>
> Here is a test example
>
>> m <- as.Date("1972-09-27") + 0:10
>> m
> [1] "1972-09-27" "1972-09-28" "1972-09-29"
"1972-09-30" "1972-10-01"
> "1972-10-02" "1972-10-03"
> [8] "1972-10-04" "1972-10-05" "1972-10-06"
"1972-10-07"
>> class(m)
> [1] "Date"
>> julian(m)
> [1] 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010
> attr(,"origin")
> [1] "1970-01-01"
>
>> m <- as.character(m)
>> class(m)
> [1] "character"
>
>> julian(m)
>
> < R crashes>
>
> --please do not edit the information below--
>
> Version:
> platform = i386-pc-mingw32
> arch = i386
> os = mingw32
> system = i386, mingw32
> status > major = 2
> minor = 2.0
> year = 2005
> month = 10
> day = 06
> svn rev = 35749
> language = R
>
>
>
> 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/
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Seemingly Similar Threads

Search for more possibly parallel threads

R devel - Dec 2005 - NextMethod causes R 2.2.0 to crash (PR#8416)

[Rd] NextMethod causes R 2.2.0 to crash (PR#8416)

[Rd] NextMethod causes R 2.2.0 to crash (PR#8416)

[Rd] NextMethod causes R 2.2.0 to crash (PR#8416)

[Rd] NextMethod causes R 2.2.0 to crash (PR#8416)

Seemingly Similar Threads