From bill at insightful.com  Tue Apr 29 18:29:35 2008
From: bill at insightful.com (Bill Dunlap)
Date: Tue, 29 Apr 2008 09:29:35 -0700 (PDT)
Subject: [Rd] reproducible segmentation fault caused by textConnection()
In-Reply-To: <4817280C.4050701@ebi.ac.uk>
References: <4817280C.4050701@ebi.ac.uk>
Message-ID: <Pine.GSO.4.56.0804290924510.14834@devsun3201.insightful.com>

On Tue, 29 Apr 2008, Gregoire Pau wrote:

> Dear all,
>
> It seems that textConnection() can trigger a segmentation fault. The
> following script (using two large loops) makes this bug reproducible:
>
> for (i in 1:10000) {
>    z=textConnection(NULL,open='w')
>    for (j in 1:100) {
>      write(runif(1)*1e6,file=z)
>      write('\n',file=z)
>    }
>    close(z)
> }
>
> The bug could be reproduced on R-2.6.1, R-2.7.0 and on the latest
> R-devel 2008-04-29 r45543.

valgrind shows that it uses freed memory after
a garbage collecting episode (after many iterations),
because a Routtextconn's 'data' component was freed:

   ==24210== Invalid read of size 1
   ==24210==    at 0x810B328: Rf_lengthgets (Rinlinedfuns.h:358)
   ==24210==    by 0x8121C48: text_vfprintf (connections.c:2064)
   ==24210==    by 0x809D0C1: Rvprintf (printutils.c:770)
   ==24210==    by 0x809D105: Rprintf (printutils.c:668)
   ==24210==    by 0x810A984: do_cat (builtin.c:617)
   ==24210==  Address 0x5823CD8 is 0 bytes inside a block of size 1,176 free'd
   ==24210==    at 0x40052A3: free (vg_replace_malloc.c:233)
   ==24210==    by 0x805AC3D: R_gc_internal (memory.c:769)
   ==24210==    by 0x805B873: Rf_cons (memory.c:1757)
   ==24210==    by 0x81571F6: Rf_promiseArgs (eval.c:1633)

   (gdb) where 5
   #0  Rf_lengthgets (x=0x5823cd8, len=289)
       at ../../src/include/Rinlinedfuns.h:358
   #1  0x08121c49 in text_vfprintf (con=0x500f280, format=0x81e64d8 "\n",
    ap=0xbef18b84 "?\213??") at connections.c:2064
   #2  0x0809d0c2 in Rvprintf (format=0x81e64d8 "\n", arg=0xbef18b84 "?\213??")
       at printutils.c:770
   #3  0x0809d106 in Rprintf (format=0x81e64d8 "\n") at printutils.c:668
   #4  0x0810a985 in do_cat (call=0x4ae31f0, op=0x4104eec, args=0x55bb2bc,
       rho=0x55baf20) at builtin.c:617
   (More stack frames follow...)
   (gdb) up
   #1  0x08121c49 in text_vfprintf (con=0x500f280, format=0x81e64d8 "\n",
       ap=0xbef18b84 "?\213??") at connections.c:2064
   2064                PROTECT(tmp = lengthgets(this->data, ++this->len));
   (gdb) print this->data
   $1 = 0x5823cd8
   (gdb) whatis this
   type = Routtextconn
   (gdb) whatis this->data
   type = SEXP
   (gdb) print *this->data
   $2 = {sxpinfo = {type = 16, obj = 0, named = 2, gp = 0, mark = 0, debug = 0,
     trace = 0, spare = 0, gcgen = 0, gccls = 7}, attrib = 0x40ae088,
     gengc_next_node = 0x8235270, gengc_prev_node = 0x8235270, u = {primsxp = {
     offset = 288}, symsxp = {pname = 0x120, value = 0x0,
     internal = 0x57685c0}, listsxp = {carval = 0x120, cdrval = 0x0,
     tagval = 0x57685c0}, envsxp = {frame = 0x120, enclos = 0x0,
     hashtab = 0x57685c0}, closxp = {formals = 0x120, body = 0x0,
     env = 0x57685c0}, promsxp = {value = 0x120, expr = 0x0,
     env = 0x57685c0}}}


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Bill Dunlap
Insightful Corporation
bill at insightful dot com

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[Rd] reproducible segmentation fault caused by textConnection()
Bill Dunlap