[Rd] [R] Repeatable, But Time Varying R GUI Crash (PR#13880)
William Dunlap
wdunlap at tibco.com
Thu Aug 6 23:36:40 CEST 2009
> -----Original Message-----
> From: r-devel-bounces at r-project.org
> [mailto:r-devel-bounces at r-project.org] On Behalf Of
> murdoch at stats.uwo.ca
> Sent: Thursday, August 06, 2009 1:45 PM
> To: r-devel at stat.math.ethz.ch
> Cc: R-bugs at 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
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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="")
> >
> > }
> >
> > }
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
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