[Rd] sweave provoked segfault (PR#2809)
pgilbert at bank-banque-canada.ca
pgilbert at bank-banque-canada.ca
Tue Apr 22 00:03:39 MEST 2003
This problem is with R 1.7.0 (as released) on Linux and Solaris. Details below
are from Linux, Mandrake 9.1. The problem also happened with R 1.6.2 and on
Mandrake 9.0.
Vignettes often (for me) provokes problems with the misleading error message:
* creating vignettes ... ERROR
Error in sub(pattern, replacement, x, ignore.case, extended) :
invalid argument
Error in buildVignettes(dir = ".") : Error in sub(pattern, replacement,
x, ignore.case, extended) :
invalid argument
Execution halted
This becomes a segfault with gctorture(). Output from gdb bt is copied below.
Paul Gilbert
________
R_LIBS=/home/paul/dse/src/pac/monitor/tmp.R-1.7.0:/home/paul/dse/src/pac/CHECKED.R-1.7.0/Rlibs
PADI=/home/paul/dse/src/pac/padi/exec
PATH=~/bin:/bin:/usr/bin:/usr/local/bin:/usr/X11R6/bin:/usr/games:/home/paul/dse/src/pac/padi/exec
R -d gdb
GNU gdb 5.3-22mdk (Mandrake Linux)
Copyright 2002 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you
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This GDB was configured as "i586-mandrake-linux-gnu"...
(gdb) run
Starting program: /home/paul/toolchain/R/R-1.7.0/bin/R.bin
R : Copyright 2003, The R Development Core Team
Version 1.7.0 (2003-04-16)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type `license()' or `licence()' for distribution details.
R is a collaborative project with many contributors.
Type `contributors()' for more information.
Type `demo()' for some demos, `help()' for on-line help, or
`help.start()' for a HTML browser interface to help.
Type `q()' to quit R.
library(tools)
> > library(tools)
> gctorture()
> checkVignettes(dir='/home/paul/dse/src/pac/monitor', workdir = 'cur',
keepfiles=TRUE)
Program received signal SIGSEGV, Segmentation fault.
0x080c1598 in RunGenCollect (size_needed=0) at memory.c:1210
1210 PROCESS_NODES();
(gdb) bt
#0 0x080c1598 in RunGenCollect (size_needed=0) at memory.c:1210
#1 0x080c3089 in R_gc_internal (size_needed=0) at memory.c:1865
#2 0x080c27fe in Rf_cons (car=0xbfffbf40, cdr=0x81f65a0) at
memory.c:1534
#3 0x08097e35 in Rf_duplicate (s=0x8324ff0) at duplicate.c:108
#4 0x080c9abf in GetObject (cptr=0xbfffc2d0) at objects.c:40
#5 0x080ca663 in do_usemethod (call=0x82c5d28, op=0x8209874,
args=0x82c5d44,
env=0x8f1ecd4) at objects.c:401
#6 0x080a3b28 in Rf_eval (e=0x82c5d28, rho=0x8f1ecd4) at eval.c:418
#7 0x080a3db2 in Rf_applyClosure (call=0x8324ff0, op=0x82c5c48,
arglist=0x8d05e80, rho=0x8f385f0, suppliedenv=0x81f65a0) at
eval.c:609
#8 0x080a3937 in Rf_eval (e=0x8324ff0, rho=0x8f385f0) at eval.c:453
#9 0x080a586b in Rf_evalList (el=0x8324f9c, rho=0x8f385f0) at
eval.c:1372
#10 0x080c9a3c in do_internal (call=0x8324ef4, op=0x81fb5c8,
args=0x832515c,
env=0x8f385f0) at names.c:1053
#11 0x080a3b28 in Rf_eval (e=0x8324ef4, rho=0x8f385f0) at eval.c:418
#12 0x080a3db2 in Rf_applyClosure (call=0x878ef30, op=0x8324e14,
arglist=0x8dbc92c, rho=0x8f0bb0c, suppliedenv=0x81f65a0) at
eval.c:609
#13 0x080a3937 in Rf_eval (e=0x878ef30, rho=0x8f0bb0c) at eval.c:453
#14 0x080a5685 in do_set (call=0x878efd8, op=0x8f0bb0c, args=0x878efa0,
rho=0x8f0bb0c) at eval.c:1283
#15 0x080a3b28 in Rf_eval (e=0x878efd8, rho=0x8f0bb0c) at eval.c:418
#16 0x080a4f62 in do_begin (call=0x878f4ec, op=0x81fba7c,
args=0x878eff4,
rho=0x8f0bb0c) at eval.c:1072
---Type <return> to continue, or q <return> to quit---
#17 0x080a3b28 in Rf_eval (e=0x878f4ec, rho=0x8f0bb0c) at eval.c:418
#18 0x080a3db2 in Rf_applyClosure (call=0x87a0758, op=0x86d817c,
arglist=0x8f0e3dc, rho=0x8f37ed4, suppliedenv=0x81f65a0) at
eval.c:609
#19 0x080a3937 in Rf_eval (e=0x87a0758, rho=0x8f37ed4) at eval.c:453
#20 0x080a5685 in do_set (call=0x87a07e4, op=0x8f37ed4, args=0x87a07c8,
rho=0x8f37ed4) at eval.c:1283
#21 0x080a3b28 in Rf_eval (e=0x87a07e4, rho=0x8f37ed4) at eval.c:418
#22 0x080a4f62 in do_begin (call=0x87a0aac, op=0x81fba7c,
args=0x87a08c4,
rho=0x8f37ed4) at eval.c:1072
#23 0x080a3b28 in Rf_eval (e=0x87a0aac, rho=0x8f37ed4) at eval.c:418
#24 0x080a3b28 in Rf_eval (e=0x879b778, rho=0x8f37ed4) at eval.c:418
#25 0x080a3b28 in Rf_eval (e=0x879b970, rho=0x8f37ed4) at eval.c:418
#26 0x080a4f62 in do_begin (call=0x879b98c, op=0x81fba7c,
args=0x879b9e0,
rho=0x8f37ed4) at eval.c:1072
#27 0x080a3b28 in Rf_eval (e=0x879b98c, rho=0x8f37ed4) at eval.c:418
#28 0x080a495c in do_for (call=0x879ba6c, op=0x81f5f80, args=0x879ba50,
rho=0x8f37ed4) at eval.c:968
#29 0x080a3b28 in Rf_eval (e=0x879ba6c, rho=0x8f37ed4) at eval.c:418
#30 0x080a4f62 in do_begin (call=0x87a8554, op=0x81fba7c,
args=0x879baa4,
rho=0x8f37ed4) at eval.c:1072
#31 0x080a3b28 in Rf_eval (e=0x87a8554, rho=0x8f37ed4) at eval.c:418
#32 0x080a3db2 in Rf_applyClosure (call=0x8721b18, op=0x86e693c,
arglist=0x8f37fd0, rho=0x8f38e74, suppliedenv=0x81f65a0) at
eval.c:609
---Type <return> to continue, or q <return> to quit---
#33 0x080a3937 in Rf_eval (e=0x8721b18, rho=0x8f38e74) at eval.c:453
#34 0x080a3856 in Rf_eval (e=0x8f37ef0, rho=0x8f38cfc) at eval.c:383
#35 0x080a379f in Rf_eval (e=0x826fbf8, rho=0x8f38cfc) at eval.c:360
#36 0x080a4f62 in do_begin (call=0x87d4f44, op=0x81fba7c,
args=0x87d4e9c,
rho=0x8f38cfc) at eval.c:1072
#37 0x080a3b28 in Rf_eval (e=0x87d4f44, rho=0x8f38cfc) at eval.c:418
#38 0x080a3b28 in Rf_eval (e=0x87d5b3c, rho=0x8f38cfc) at eval.c:418
#39 0x080a4f62 in do_begin (call=0x87d5484, op=0x81fba7c,
args=0x87d5b20,
rho=0x8f38cfc) at eval.c:1072
#40 0x080a3b28 in Rf_eval (e=0x87d5484, rho=0x8f38cfc) at eval.c:418
#41 0x080a3db2 in Rf_applyClosure (call=0x8721bf8, op=0x87d5a40,
arglist=0x8f37f0c, rho=0x8f38e74, suppliedenv=0x81f65a0) at
eval.c:609
#42 0x080a3937 in Rf_eval (e=0x8721bf8, rho=0x8f38e74) at eval.c:453
#43 0x080a5685 in do_set (call=0x8721c68, op=0x8f38e74, args=0x8721c4c,
rho=0x8f38e74) at eval.c:1283
#44 0x080a3b28 in Rf_eval (e=0x8721c68, rho=0x8f38e74) at eval.c:418
#45 0x080a4f62 in do_begin (call=0x8721c84, op=0x81fba7c,
args=0x8721d48,
rho=0x8f38e74) at eval.c:1072
#46 0x080a3b28 in Rf_eval (e=0x8721c84, rho=0x8f38e74) at eval.c:418
#47 0x080a3b28 in Rf_eval (e=0x87214d0, rho=0x8f38e74) at eval.c:418
#48 0x080a4f62 in do_begin (call=0x8722908, op=0x81fba7c,
args=0x8721540,
rho=0x8f38e74) at eval.c:1072
#49 0x080a3b28 in Rf_eval (e=0x8722908, rho=0x8f38e74) at eval.c:418
---Type <return> to continue, or q <return> to quit---
#50 0x080a495c in do_for (call=0x8721604, op=0x81f5f80, args=0x87215cc,
rho=0x8f38e74) at eval.c:968
#51 0x080a3b28 in Rf_eval (e=0x8721604, rho=0x8f38e74) at eval.c:418
#52 0x080a4f62 in do_begin (call=0x87260f8, op=0x81fba7c,
args=0x8721620,
rho=0x8f38e74) at eval.c:1072
#53 0x080a3b28 in Rf_eval (e=0x87260f8, rho=0x8f38e74) at eval.c:418
#54 0x080a3db2 in Rf_applyClosure (call=0x8f38ec8, op=0x86cd644,
arglist=0x8f38f38, rho=0x820ce1c, suppliedenv=0x81f65a0) at
eval.c:609
#55 0x080a3937 in Rf_eval (e=0x8f38ec8, rho=0x820ce1c) at eval.c:453
#56 0x080bd784 in Rf_ReplIteration (rho=0x820ce1c, savestack=16,
browselevel=0, state=0xbffff0f0) at main.c:236
#57 0x080bd942 in R_ReplConsole (rho=0x820ce1c, savestack=0,
browselevel=0)
at main.c:284
#58 0x080be1ff in run_Rmainloop () at main.c:615
#59 0x08124b5c in main (ac=1, av=0xbffff5c4) at system.c:99
#60 0x400977f7 in __libc_start_main () from /lib/i686/libc.so.6
(gdb)
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