gctorture and proc.time (PR#10600)

In R version 2.6.1 (2007-11-26)
and R version 2.6.1 Patched (2008-01-19 r44061)
on openSUSE 10.2 (X86-64)
gctorture()
proc.time()
Error: protect(): protection stack overflow

The problem with this is that then

R CMD check --use-gct foo

ALWAYS FAILS with
cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
Error in proc.time() - get("ptime", pos = "CheckExEnv") :
  non-numeric argument to binary operator

This does not happen in R version 2.4.1 (2006-12-18)

I was going to have my computing class try out --use-gct.
I guess not until this is fixed.
Charles Geyer
Professor, School of Statistics
University of Minnesota
charlie at stat.umn.edu
In R version 2.6.1 (2007-11-26)
and R version 2.6.1 Patched (2008-01-19 r44061)
on openSUSE 10.2 (X86-64)

gctorture()
proc.time()

Error: protect(): protection stack overflow

The problem with this is that then

R CMD check --use-gct foo

ALWAYS FAILS with

cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")

Error in proc.time() - get("ptime", pos = "CheckExEnv") :
  non-numeric argument to binary operator

This does not happen in R version 2.4.1 (2006-12-18)

I was going to have my computing class try out --use-gct.
I guess not until this is fixed.

I can reproduce this on SUSE 10.2 64 bit and Fedora 7 64 bit, but not on 
SUSE 10.3 32 bit and Fedora 8 32 bit. (The OS versions are likely not 
relevant, I bet it is a 64 bit issue somewhere).
O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907
I'm not sure if this is connected but in R2.6.1 do_proctime is missing some
PROTECTs. The current code is

 SEXP ans = allocVector(REALSXP, 5), nm = allocVector(STRSXP, 5);

and should be

    SEXP ans, nm;
    PROTECT(ans = allocVector(REALSXP, 5));
    PROTECT(nm = allocVector(STRSXP, 5));

A good way of finding these missing PROTECTs is to write say 0xEE to memory
as it is freed (i.e. one must modify the source of memory.c). Then with gc
torture enabled it more obvious if  someone uses a just freed SEXP.  There
is a similar issue in a few other places which I haven't tracked down yet
which I will submit to r-bugs in due course.  These were found using the
0xEE trick and running make check-all.

Steve
www.milbo.users.sonic.net

----- Original Message ----- 
From: "Peter Dalgaard" <p.dalgaard at biostat.ku.dk>
To: <charlie at stat.umn.edu>
Cc: <R-bugs at biostat.ku.dk>; <r-devel at stat.math.ethz.ch>
Sent: Tuesday, January 22, 2008 9:56 AM
Subject: Re: [Rd] gctorture and proc.time (PR#10600)
In R version 2.6.1 (2007-11-26)
and R version 2.6.1 Patched (2008-01-19 r44061)
on openSUSE 10.2 (X86-64)

gctorture()
proc.time()

Error: protect(): protection stack overflow

The problem with this is that then

R CMD check --use-gct foo

ALWAYS FAILS with

cat("Time elapsed: ", proc.time() - get("ptime", pos =
'CheckExEnv'),"\n")

Error in proc.time() - get("ptime", pos = "CheckExEnv") :
  non-numeric argument to binary operator

This does not happen in R version 2.4.1 (2006-12-18)

I was going to have my computing class try out --use-gct.
I guess not until this is fixed.

I can reproduce this on SUSE 10.2 64 bit and Fedora 7 64 bit, but not on
SUSE 10.3 32 bit and Fedora 8 32 bit. (The OS versions are likely not
relevant, I bet it is a 64 bit issue somewhere).
O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

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charlie at stat.umn.edu wrote:
In R version 2.6.1 (2007-11-26)
and R version 2.6.1 Patched (2008-01-19 r44061)
on openSUSE 10.2 (X86-64)

gctorture()
proc.time()

Error: protect(): protection stack overflow

The problem with this is that then

R CMD check --use-gct foo

ALWAYS FAILS with

cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")

Error in proc.time() - get("ptime", pos = "CheckExEnv") :
  non-numeric argument to binary operator

This does not happen in R version 2.4.1 (2006-12-18)

I was going to have my computing class try out --use-gct.
I guess not until this is fixed.

I can reproduce this on SUSE 10.2 64 bit and Fedora 7 64 bit, but not on 
SUSE 10.3 32 bit and Fedora 8 32 bit. (The OS versions are likely not 
relevant, I bet it is a 64 bit issue somewhere).
I can be a bit more precise - I have both 32-bit R and 64-bit R built 
and installed on fedora 8 64-bit, just one and same box.

32-bit R finishes quite quickly with:

 > proc.time()
    user  system elapsed
   0.772   0.032  10.147

64-bit R takes up 49s CPU time (from ps). This is long compared to 
either 10s (elapse) or 1s (user+sys). And it ends with:
Error: protect(): protection stack overflow

So yes, it looks like a 64-bit R specific bug.
Such things are normally easy to find with valgrind and an instrumented 
build of R (see 'Writing R Extensions'), and so was this.  Interestingly I 
got a different error immediately:
gctorture(TRUE)
proc.time()
Error: REAL() can only be applied to a 'numeric', not a 'character'

and setting a breakpoint on that message traced it back.

It was a missing PROTECT, and has now been fixed.

Peter Dalgaard wrote:
charlie at stat.umn.edu wrote:
In R version 2.6.1 (2007-11-26)
and R version 2.6.1 Patched (2008-01-19 r44061)
on openSUSE 10.2 (X86-64)

gctorture()
proc.time()

Error: protect(): protection stack overflow

The problem with this is that then

R CMD check --use-gct foo

ALWAYS FAILS with

cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")

Error in proc.time() - get("ptime", pos = "CheckExEnv") :
  non-numeric argument to binary operator

This does not happen in R version 2.4.1 (2006-12-18)

I was going to have my computing class try out --use-gct.
I guess not until this is fixed.

I can reproduce this on SUSE 10.2 64 bit and Fedora 7 64 bit, but not on
SUSE 10.3 32 bit and Fedora 8 32 bit. (The OS versions are likely not
relevant, I bet it is a 64 bit issue somewhere).
I can be a bit more precise - I have both 32-bit R and 64-bit R built
and installed on fedora 8 64-bit, just one and same box.

32-bit R finishes quite quickly with:

proc.time()
   user  system elapsed
  0.772   0.032  10.147

64-bit R takes up 49s CPU time (from ps). This is long compared to
either 10s (elapse) or 1s (user+sys). And it ends with:
Error: protect(): protection stack overflow

So yes, it looks like a 64-bit R specific bug.

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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