-----Original Message-----
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of William Dunlap
Sent: Thursday, August 06, 2009 2:37 PM
To: murd...@stats.uwo.ca; r-de...@stat.math.ethz.ch
Cc: r-b...@r-project.org
Subject: Re: [Rd] [R] Repeatable, But Time Varying R GUI
Crash (PR#13880)
-----Original Message-----
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of
murd...@stats.uwo.ca
Sent: Thursday, August 06, 2009 1:45 PM
To: r-de...@stat.math.ethz.ch
Cc: r-b...@r-project.org
Subject: Re: [Rd] [R] Repeatable, But Time Varying R GUI
Crash (PR#13880)
On 8/6/2009 4:11 PM, Marilyn & Rich Short wrote:
Hello,
I'm having a problem in R. The R GUI is crashing with a
message to
contact Microsoft for the solution. I've contacted
Microsoft and they
are of no help. Below is a distilled set of code that will
cause the
crash. As you will see, there are two do-loops within which
is a "load"
command. The crash usually occurs after 200*400 (=80,000) to
2,000*400(=800,000) iterations.
Do you have any suggestions on work-arounds?
I can confirm it in R-patched as well. It happens on the
very first
time through if you set gctorture() on, so it looks like
somewhere in
there is a missing PROTECT, and the garbage collector is reclaiming
something that it shouldn't.
I'll try to track it down, but I'm not sure how quick I'll be.
On Linux with R-2.10.0(devel) valgrind shows:
gctorture()
problem2()
==9777== Invalid read of size 1
==9777== at 0x805DD5C: SETCAR (memory.c:2712)
==9777== by 0x8156463: Rf_defineVar (envir.c:1353)
==9777== by 0x80B3B16: RestoreToEnv (saveload.c:2022)
==9777== by 0x80B4913: do_loadFromConn2 (saveload.c:2346)
==9777== by 0x8065CF4: do_internal (names.c:1160)
==9777== by 0x816629F: Rf_eval (eval.c:464)
==9777== by 0x816815D: do_begin (eval.c:1244)
==9777== by 0x816629F: Rf_eval (eval.c:464)
==9777== by 0x8169853: Rf_applyClosure (eval.c:698)
==9777== by 0x81661D7: Rf_eval (eval.c:508)
==9777== by 0x816815D: do_begin (eval.c:1244)
==9777== by 0x816629F: Rf_eval (eval.c:464)
==9777== Address 0x4516A1B is 3 bytes inside a block of size 2,584
free'd
==9777== at 0x40052A3: free (vg_replace_malloc.c:233)
==9777== by 0x805B121: R_gc_internal (memory.c:784)
==9777== by 0x805C1CF: Rf_allocVector (memory.c:2022)
==9777== by 0x80B3AD2: RestoreToEnv (saveload.c:2017)
==9777== by 0x80B4913: do_loadFromConn2 (saveload.c:2346)
==9777== by 0x8065CF4: do_internal (names.c:1160)
==9777== by 0x816629F: Rf_eval (eval.c:464)
==9777== by 0x816815D: do_begin (eval.c:1244)
==9777== by 0x816629F: Rf_eval (eval.c:464)
==9777== by 0x8169853: Rf_applyClosure (eval.c:698)
==9777== by 0x81661D7: Rf_eval (eval.c:508)
==9777== by 0x816815D: do_begin (eval.c:1244)
==9777==
==9777== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- y
starting debugger
==9777== starting debugger with cmd: /usr/bin/gdb -nw
/proc/9802/fd/1014
9802
GNU gdb Red Hat Linux (6.3.0.0-1.96rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public
License, and you
are
welcome to change it and/or distribute copies of it under certain
conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for
details.
This GDB was configured as "i386-redhat-linux-gnu"...Using host
libthread_db library "/lib/tls/libthread_db.so.1".
Attaching to program: /proc/9802/fd/1014, process 9802
SETCAR (x=0x5565da0, y=0x4516a18) at memory.c:2712
2712 CHECK_OLD_TO_NEW(x, y);
(gdb) up
#1 0x08156464 in Rf_defineVar (symbol=0x4f5eee0, value=0x4516a18,
rho=0x559a77c) at envir.c:1353
1353 SET_BINDING_VALUE(frame, value);
(gdb) list
1348 if (HASHTAB(rho) == R_NilValue) {
1349 /* First check for an existing binding */
1350 frame = FRAME(rho);
1351 while (frame != R_NilValue) {
1352 if (TAG(frame) == symbol) {
1353 SET_BINDING_VALUE(frame, value);
1354 SET_MISSING(frame, 0); /*
Over-ride */
1355 return;
1356 }
1357 frame = CDR(frame);
(gdb) up
#2 0x080b3b17 in RestoreToEnv (ans=0x54876b4, aenv=0x559a77c)
at saveload.c:2022
2022 defineVar(TAG(a), CAR(a), aenv);
(gdb) list
2017 PROTECT(names = allocVector(STRSXP, cnt));
2018 cnt = 0;
2019 PROTECT(a = ans);
2020 while (a != R_NilValue) {
2021 SET_STRING_ELT(names, cnt++, PRINTNAME(TAG(a)));
2022 defineVar(TAG(a), CAR(a), aenv);
2023 if(R_seemsOldStyleS4Object(CAR(a)))
2024 warningcall(R_NilValue,
2025 _("'%s' looks like a pre-2.4.0 S4
object: please recreate it"),
2026 CHAR(PRINTNAME(TAG(a))));
It again complains about the call to R_seemsOldStyleS4Object().
Memory in 'a' may have been freed. Shouldn't the
PROTECT(a=ans)
be done earlier, when ans is allocated, instead of when
the pointer is copied?
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
(My
house is full of contractors right now, so not a very nice
place to work.)
I don't know any workaround other than "avoid doing the
buggy thing".
But I can't tell you what that is....
Duncan Murdoch
Once you start the function with the "problem2()" command,
the function
will print to the screen once every 400 iterations. You can
monitor the
progress by clicking the scroll button. The R GUI should
crash somewhere
between i=200 and i=2000. Although the problem is
repeatable, the time
at which the crash occurs is random.
Thanks in advance for your attention,
Rich Short
I'm using Windows XP, SP3 and R 2.9.1.
Here is my session info:
sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets
methods base
(The problem occurs on my Vista machine as well.)
*******************************************
# This script induces the R GUI to crash.
problem2 = function(){
junk = mat.or.vec(8,40)
junk[] = 1
mjunk = mat.or.vec(8,40)
mjunk[] = -1
PathA = tempdir()
conX = paste(PathA,"junkx",sep="\\")
conY = paste(PathA,"junky",sep="\\")
outJunk = file(conX, open="wb")
save(junk, file=outJunk)
close(outJunk)
outJunkY = file(conY, open="wb")
save(mjunk, file=outJunkY)
close(outJunkY)
sign = 1
for(i in 1:4000){
for(ii in 1:400){
sign = -sign
if(sign<0){
load(file=conX)
}else{
load(file=conY)
}
sum = junk[1,5] + mjunk[3,30]
}
cat(" junk = ",junk[1,5],sep="")
cat(" mjunk = ",mjunk[3,30],sep="")
cat(" sum = ",sum,sep="")
cat(" i = ",i,"\n",sep="")
}
}
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