Dear Bill,
Thanks for having had a look on this bug. I am now using an anonymous
file() connection to store my stuffs instead of textConnection(): it is
much faster and doesn't raise any seg faults.
Regards,
Greg
---
Gregoire Pau
EMBL/EBI Cambridge, UK
http://www.ebi.ac.uk/~gpau
Bill Dunlap wrote:
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}}}
----------------------------------------------------------------------------
Bill Dunlap
Insightful Corporation
bill at insightful dot com
"All statements in this message represent the opinions of the author and do
not necessarily reflect Insightful Corporation policy or position."
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