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maechler@stat.math.ethz.ch

2004-Jul-17 12:15 UTC

[Rd] gsub(*, perl=TRUE) bug incl. seg.fault (PR#7108)

Experimenting a bit further, I've "found" the following

1) the problem seems only gsub(), not sub()

  > sub(" ", "", "b c + d | a * b", perl=TRUE)
  [1] "bc + d | a * b"
  > gsub(" ", "", "b c + d | a * b", perl=TRUE)
  NULL

2) only if perl = TRUE, not otherwise

3) Also modifying the replacement string only slightly leads to a
  different (correct instead of bug) result:

  > gsub(" ", "", "bc + d | a * b", perl=TRUE)
  [1] "bc+d|a*b"
  > gsub(" ", "", "b c + d | a *", perl=TRUE)
  [1] "bc+d|a*"
  > gsub(" ", "", "b c + d | b", perl=TRUE)
  [1] "bc+d|b"

Whereas those give the bug as well :

  > gsub(" ", "", "b : : d : a : b", perl=TRUE)
  NULL
  > gsub(" ", "", "b : : : : a : b", perl=TRUE)
  NULL
  > gsub(" ", "", "b : : : : : : b", perl=TRUE)
  NULL
  > gsub(" ", "", "a : : : : : : a", perl=TRUE)
  NULL
but not this
  > gsub(" ", "", "b : : : : : : a", perl=TRUE)
  [1] "b::::::a"

But it's even worse :

  > gsub(" ", "", "a: 12345 :a", perl=TRUE)

  -> segmentation fault

and from "R -d gdb" :

    > gsub(" ", "", "a: 12345 :a", perl=TRUE)

    Program received signal SIGSEGV, Segmentation fault.
    hashIndex (symbol=0x8fd0060, table=0x823f2b8) at
    ../../../R/src/main/envir.c:599
    599	  if( !HASHASH(c) ) {
    (gdb) bt
    #0  hashIndex (symbol=0x8fd0060, table=0x823f2b8)
	at ../../../R/src/main/envir.c:599
    #1  0x080b145d in R_GetGlobalCache (symbol=0x1)
	at ../../../R/src/main/envir.c:656
    #2  0x080b1ac1 in findGlobalVar (symbol=0x8fd0060)
	at ../../../R/src/main/envir.c:923
    #3  0x080b8873 in Rf_eval (e=0x823f2b8, rho=0x823f014)
	at ../../../R/src/main/eval.c:329
    #4  0x080b88c9 in Rf_eval (e=0x8fd1e60, rho=0x821e540)
	at ../../../R/src/main/eval.c:354
    #5  0x080e1e0e in GetObject (cptr=0xbfffd400)
	at ../../../R/src/main/objects.c:88
    #6  0x080e2a3b in do_usemethod (call=0x84eb084, op=0x823be78,
args=0x84eb0a0,
	env=0x8fd1df0) at ../../../R/src/main/objects.c:381
    #7  0x080b8c33 in Rf_eval (e=0x84eb084, rho=0x8fd1df0)
	at ../../../R/src/main/eval.c:375
    #8  0x080b8f48 in Rf_applyClosure (call=0x8fd1eb4, op=0x84eafa4, 
	arglist=0x8fd1e44, rho=0x823f014, suppliedenv=0x821e540)
	at ../../../R/src/main/eval.c:559
    #9  0x080b89bf in Rf_eval (e=0x8fd1eb4, rho=0x823f014)
	at ../../../R/src/main/eval.c:410
    #10 0x0811b0f3 in Rf_PrintValueEnv (s=0x8fd1eb4, env=0x823f014)
	at ../../../R/src/main/print.c:775
    #11 0x080d55f1 in Rf_ReplIteration (rho=0x823f014, savestack=150798432, 
	browselevel=1, state=0x823f014) at ../../../R/src/main/main.c:254
    #12 0x080d578d in R_ReplConsole (rho=0x823f014, savestack=0, browselevel=0)
	at ../../../R/src/main/main.c:298
    #13 0x080d60d0 in run_Rmainloop () 
        at ../../../R/src/main/main.c:656
    #14 0x08147e90 in main (ac=150798432, av=0x8fd0060)
	at ../../../R/src/unix/system.c:99
    #15 0x42017589 in __libc_start_main () from /lib/i686/libc.so.6

(which is not directly helpful since  src/main/pcre.c  (where
the C source for gsub(*, perl=TRUE) resides)  isn't mentioned above.

Must be a memory allocation / mismatch / end_of_string problem
somewhere.

Martin Maechler, ETH Zurich

Prof Brian Ripley

2004-Jul-26 17:47 UTC

head link

[Rd] gsub(*, perl=TRUE) bug incl. seg.fault (PR#7108)

I presume this was in R 1.9.1?

It seems that this was something I had already fixed (from another
symptom) and not been able to commit because the CVS archive was down.

I have now fixed it in R 1.9.1 patched and R-devel, and put a regression
test into the latter.

Brian

On Sat, 17 Jul 2004 maechler@stat.math.ethz.ch wrote:
> Experimenting a bit further, I've "found" the following
> 
> 1) the problem seems only gsub(), not sub()
> 
>   > sub(" ", "", "b c + d | a * b",
perl=TRUE)
>   [1] "bc + d | a * b"
>   > gsub(" ", "", "b c + d | a * b",
perl=TRUE)
>   NULL
> 
> 2) only if perl = TRUE, not otherwise
> 
> 3) Also modifying the replacement string only slightly leads to a
>   different (correct instead of bug) result:
> 
>   > gsub(" ", "", "bc + d | a * b",
perl=TRUE)
>   [1] "bc+d|a*b"
>   > gsub(" ", "", "b c + d | a *",
perl=TRUE)
>   [1] "bc+d|a*"
>   > gsub(" ", "", "b c + d | b",
perl=TRUE)
>   [1] "bc+d|b"
> 
> Whereas those give the bug as well :
> 
>   > gsub(" ", "", "b : : d : a : b",
perl=TRUE)
>   NULL
>   > gsub(" ", "", "b : : : : a : b",
perl=TRUE)
>   NULL
>   > gsub(" ", "", "b : : : : : : b",
perl=TRUE)
>   NULL
>   > gsub(" ", "", "a : : : : : : a",
perl=TRUE)
>   NULL
> but not this
>   > gsub(" ", "", "b : : : : : : a",
perl=TRUE)
>   [1] "b::::::a"
> 
> But it's even worse :
> 
>   > gsub(" ", "", "a: 12345 :a",
perl=TRUE)
> 
>   -> segmentation fault
> 
> and from "R -d gdb" :
> 
>     > gsub(" ", "", "a: 12345 :a",
perl=TRUE)
> 
>     Program received signal SIGSEGV, Segmentation fault.
>     hashIndex (symbol=0x8fd0060, table=0x823f2b8) at
>     ../../../R/src/main/envir.c:599
>     599	  if( !HASHASH(c) ) {
>     (gdb) bt
>     #0  hashIndex (symbol=0x8fd0060, table=0x823f2b8)
> 	at ../../../R/src/main/envir.c:599
>     #1  0x080b145d in R_GetGlobalCache (symbol=0x1)
> 	at ../../../R/src/main/envir.c:656
>     #2  0x080b1ac1 in findGlobalVar (symbol=0x8fd0060)
> 	at ../../../R/src/main/envir.c:923
>     #3  0x080b8873 in Rf_eval (e=0x823f2b8, rho=0x823f014)
> 	at ../../../R/src/main/eval.c:329
>     #4  0x080b88c9 in Rf_eval (e=0x8fd1e60, rho=0x821e540)
> 	at ../../../R/src/main/eval.c:354
>     #5  0x080e1e0e in GetObject (cptr=0xbfffd400)
> 	at ../../../R/src/main/objects.c:88
>     #6  0x080e2a3b in do_usemethod (call=0x84eb084, op=0x823be78,
args=0x84eb0a0,
> 	env=0x8fd1df0) at ../../../R/src/main/objects.c:381
>     #7  0x080b8c33 in Rf_eval (e=0x84eb084, rho=0x8fd1df0)
> 	at ../../../R/src/main/eval.c:375
>     #8  0x080b8f48 in Rf_applyClosure (call=0x8fd1eb4, op=0x84eafa4, 
> 	arglist=0x8fd1e44, rho=0x823f014, suppliedenv=0x821e540)
> 	at ../../../R/src/main/eval.c:559
>     #9  0x080b89bf in Rf_eval (e=0x8fd1eb4, rho=0x823f014)
> 	at ../../../R/src/main/eval.c:410
>     #10 0x0811b0f3 in Rf_PrintValueEnv (s=0x8fd1eb4, env=0x823f014)
> 	at ../../../R/src/main/print.c:775
>     #11 0x080d55f1 in Rf_ReplIteration (rho=0x823f014, savestack=150798432,
> 	browselevel=1, state=0x823f014) at ../../../R/src/main/main.c:254
>     #12 0x080d578d in R_ReplConsole (rho=0x823f014, savestack=0,
browselevel=0)
> 	at ../../../R/src/main/main.c:298
>     #13 0x080d60d0 in run_Rmainloop () 
>         at ../../../R/src/main/main.c:656
>     #14 0x08147e90 in main (ac=150798432, av=0x8fd0060)
> 	at ../../../R/src/unix/system.c:99
>     #15 0x42017589 in __libc_start_main () from /lib/i686/libc.so.6
> 
> (which is not directly helpful since  src/main/pcre.c  (where
> the C source for gsub(*, perl=TRUE) resides)  isn't mentioned above.
> 
> Must be a memory allocation / mismatch / end_of_string problem
> somewhere.
> 
> Martin Maechler, ETH Zurich
> 
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
> 
> 
-- 
Brian D. Ripley,                  ripley@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

maechler@stat.math.ethz.ch

2004-Jul-26 18:17 UTC

head link

[Rd] gsub(*, perl=TRUE) bug incl. seg.fault (PR#7108)

>>>>> "BDR" == Prof Brian Ripley
<ripley@stats.ox.ac.uk>
>>>>>     on Mon, 26 Jul 2004 16:11:51 +0100 (BST) writes:
    BDR> I presume this was in R 1.9.1?  

yes and R-patched (and R-devel) of that time -- of course not
containing your "off line" fixes.

Thanks a lot for taking care of it!
Martin

    BDR> I presume this was in R 1.9.1?  It seems that this was
    BDR> something I had already fixed (from another symptom)
    BDR> and not been able to commit because the CVS archive was
    BDR> down.

    BDR> I have now fixed it in R 1.9.1 patched and R-devel, and
    BDR> put a regression test into the latter.

    BDR> Brian

    BDR> On Sat, 17 Jul 2004 maechler@stat.math.ethz.ch wrote:

    >> Experimenting a bit further, I've "found" the
following
    >> 
    >> 1) the problem seems only gsub(), not sub()
    >> 
    >> > sub(" ", "", "b c + d | a * b",
perl=TRUE) [1] "bc + d
    >> | a * b" > gsub(" ", "", "b c + d
| a * b", perl=TRUE)
    >> NULL
    >> 
    >> 2) only if perl = TRUE, not otherwise
    >> 
    >> 3) Also modifying the replacement string only slightly
    >> leads to a different (correct instead of bug) result:
    >> 
    >> > gsub(" ", "", "bc + d | a * b",
perl=TRUE) [1]
    >> "bc+d|a*b" > gsub(" ", "", "b
c + d | a *", perl=TRUE)
    >> [1] "bc+d|a*" > gsub(" ", "",
"b c + d | b", perl=TRUE)
    >> [1] "bc+d|b"
    >> 
    >> Whereas those give the bug as well :
    >> 
    >> > gsub(" ", "", "b : : d : a : b",
perl=TRUE) NULL >
    >> gsub(" ", "", "b : : : : a : b",
perl=TRUE) NULL > gsub("
    >> ", "", "b : : : : : : b", perl=TRUE) NULL
> gsub(" ", "",
    >> "a : : : : : : a", perl=TRUE) NULL but not this >
gsub("
    >> ", "", "b : : : : : : a", perl=TRUE) [1]
"b::::::a"
    >> 
    >> But it's even worse :
    >> 
    >> > gsub(" ", "", "a: 12345 :a",
perl=TRUE)
    >> 
    -> segmentation fault
    >>  and from "R -d gdb" :
    >> 
    >> > gsub(" ", "", "a: 12345 :a",
perl=TRUE)
    >> 
    >> Program received signal SIGSEGV, Segmentation fault.
    >> hashIndex (symbol=0x8fd0060, table=0x823f2b8) at
    >> ../../../R/src/main/envir.c:599 599 if( !HASHASH(c) ) {
    >> (gdb) bt #0 hashIndex (symbol=0x8fd0060, table=0x823f2b8)
    >> at ../../../R/src/main/envir.c:599 #1 0x080b145d in
    >> R_GetGlobalCache (symbol=0x1) at
    >> ../../../R/src/main/envir.c:656 #2 0x080b1ac1 in
    >> findGlobalVar (symbol=0x8fd0060) at
    >> ../../../R/src/main/envir.c:923 #3 0x080b8873 in Rf_eval
    >> (e=0x823f2b8, rho=0x823f014) at
    >> ../../../R/src/main/eval.c:329 #4 0x080b88c9 in Rf_eval
    >> (e=0x8fd1e60, rho=0x821e540) at
    >> ../../../R/src/main/eval.c:354 #5 0x080e1e0e in GetObject
    >> (cptr=0xbfffd400) at ../../../R/src/main/objects.c:88 #6
    >> 0x080e2a3b in do_usemethod (call=0x84eb084, op=0x823be78,
    >> args=0x84eb0a0, env=0x8fd1df0) at
    >> ../../../R/src/main/objects.c:381 #7 0x080b8c33 in
    >> Rf_eval (e=0x84eb084, rho=0x8fd1df0) at
    >> ../../../R/src/main/eval.c:375 #8 0x080b8f48 in
    >> Rf_applyClosure (call=0x8fd1eb4, op=0x84eafa4,
    >> arglist=0x8fd1e44, rho=0x823f014, suppliedenv=0x821e540)
    >> at ../../../R/src/main/eval.c:559 #9 0x080b89bf in
    >> Rf_eval (e=0x8fd1eb4, rho=0x823f014) at
    >> ../../../R/src/main/eval.c:410 #10 0x0811b0f3 in
    >> Rf_PrintValueEnv (s=0x8fd1eb4, env=0x823f014) at
    >> ../../../R/src/main/print.c:775 #11 0x080d55f1 in
    >> Rf_ReplIteration (rho=0x823f014, savestack=150798432,
    >> browselevel=1, state=0x823f014) at
    >> ../../../R/src/main/main.c:254 #12 0x080d578d in
    >> R_ReplConsole (rho=0x823f014, savestack=0, browselevel=0)
    >> at ../../../R/src/main/main.c:298 #13 0x080d60d0 in
    >> run_Rmainloop () at ../../../R/src/main/main.c:656 #14
    >> 0x08147e90 in main (ac=150798432, av=0x8fd0060) at
    >> ../../../R/src/unix/system.c:99 #15 0x42017589 in
    >> __libc_start_main () from /lib/i686/libc.so.6
    >> 
    >> (which is not directly helpful since src/main/pcre.c
    >> (where the C source for gsub(*, perl=TRUE) resides) isn't
    >> mentioned above.
    >> 
    >> Must be a memory allocation / mismatch / end_of_string
    >> problem somewhere.
    >> 
    >> Martin Maechler, ETH Zurich
    >> 
    >> ______________________________________________
    >> R-devel@stat.math.ethz.ch mailing list
    >> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
    >> 
    >> 

    BDR> -- Brian D. Ripley, ripley@stats.ox.ac.uk Professor of
    BDR> Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
    BDR> University of Oxford, Tel: +44 1865 272861 (self) 1
    BDR> South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG,
    BDR> UK Fax: +44 1865 272595

R devel - Jul 2004 - gsub(*, perl=TRUE) bug incl. seg.fault (PR#7108)

[Rd] gsub(*, perl=TRUE) bug incl. seg.fault (PR#7108)

[Rd] gsub(*, perl=TRUE) bug incl. seg.fault (PR#7108)

[Rd] gsub(*, perl=TRUE) bug incl. seg.fault (PR#7108)

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