[Rd] vignette segfault bt

Paul Gilbert pgilbert at bank-banque-canada.ca
Wed Apr 16 15:48:16 MEST 2003 

The released version of R-1.7.0 builds and checks fine on Mandrake 9.1, but I am
still having trouble with my vignettes and sweave causing segfaults.
Unfortunately the segfaults with the release version are happening in tests
where I have much more difficulty trapping them. I did also build
R-1.7.0beta_2003-04-16 this morning, and for that the segfaults occurred in a
test which is much easier for me to reproduce. Below are gdb bt outputs, the
first without gctorture and the second with it. (I think they are the same.)

Paul
_____

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
are
welcome to change it and/or distribute copies of it under certain
conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for
details.
This GDB was configured as "i586-mandrake-linux-gnu"...
(gdb) run
Starting program:
/home/paul/dse/src/pac/R-test/R-1.7.0beta_2003.04.16/bin/R.bin  
 
R : Copyright 2003, The R Development Core Team
Version 1.7.0 Under development (unstable) (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)
> checkVignettes(dir='/home/paul/dse/src/pac/monitor', workdir = 'cur',
keepfiles=TRUE)
 
Program received signal SIGILL, Illegal instruction.
0x080786ff in file_fgetc (con=0xbfffc830) at connections.c:289
289             this->wpos = ftell(this->fp);
(gdb) bt
#0  0x080786ff in file_fgetc (con=0xbfffc830) at connections.c:289
#1  0x080a9ce1 in con_getc () at /ext/R/cvs/R-devel/src/main/gram.y:1130
#2  0x080a881b in xxgetc () at /ext/R/cvs/R-devel/src/main/gram.y:287
#3  0x080aa947 in SymbolValue (c=255)
    at /ext/R/cvs/R-devel/src/main/gram.y:1673
#4  0x080aab01 in token () at /ext/R/cvs/R-devel/src/main/gram.y:1744
#5  0x080aaefa in Rf_yylex () at /ext/R/cvs/R-devel/src/main/gram.y:1886
#6  0x080a87e4 in Rf_yyparse () at
/usr/local/share/bison/bison.simple:595
#7  0x080a98cd in R_Parse1 (status=0x46)
    at /ext/R/cvs/R-devel/src/main/gram.y:948
#8  0x080a9bee in R_Parse (n=-1, status=0xbfffcd68)
    at /ext/R/cvs/R-devel/src/main/gram.y:1083
#9  0x081175d1 in do_parse (call=0x883d674, op=0x8205024,
args=0x8839138,
    env=0x9207e84) at source.c:76
#10 0x080c99e4 in do_internal (call=0x883d5e8, op=0x81fb5e8,
args=0x92088bc,
    env=0x9207e84) at names.c:1056
#11 0x080a3b28 in Rf_eval (e=0x883d5e8, rho=0x9207e84) at eval.c:418
#12 0x080a4f62 in do_begin (call=0x883cdc4, op=0x81fba9c,
args=0x883d5cc,
    rho=0x9207e84) at eval.c:1072
#13 0x080a3b28 in Rf_eval (e=0x883cdc4, rho=0x9207e84) at eval.c:418
#14 0x080a3db2 in Rf_applyClosure (call=0x8954ae0, op=0x883d4ec,
    arglist=0x9207f64, rho=0x9208338, suppliedenv=0x81f65c0) at
eval.c:609
#15 0x080a3937 in Rf_eval (e=0x8954ae0, rho=0x9208338) at eval.c:453
---Type <return> to continue, or q <return> to quit---
#16 0x080a5685 in do_set (call=0x8954a8c, op=0x9208338, args=0x8954aa8,
    rho=0x9208338) at eval.c:1283
#17 0x080a3b28 in Rf_eval (e=0x8954a8c, rho=0x9208338) at eval.c:418
#18 0x080a586b in Rf_evalList (el=0x8954a1c, rho=0x9208338) at
eval.c:1372
#19 0x080a3a50 in Rf_eval (e=0x8954a00, rho=0x9208338) at eval.c:439
#20 0x080a5685 in do_set (call=0x89549ac, op=0x9208338, args=0x89549c8,
    rho=0x9208338) at eval.c:1283
#21 0x080a3b28 in Rf_eval (e=0x89549ac, rho=0x9208338) at eval.c:418
#22 0x080a4f62 in do_begin (call=0x8953ad0, op=0x81fba9c,
args=0x8954990,
    rho=0x9208338) at eval.c:1072
#23 0x080a3b28 in Rf_eval (e=0x8953ad0, rho=0x9208338) at eval.c:418
#24 0x080a3db2 in Rf_applyClosure (call=0x8720f1c, op=0x8958db0,
    arglist=0x9208434, rho=0x8e5d4d0, suppliedenv=0x81f65c0) at
eval.c:609
#25 0x080a3937 in Rf_eval (e=0x8720f1c, rho=0x8e5d4d0) at eval.c:453
#26 0x080a3856 in Rf_eval (e=0x9206f1c, rho=0x9206e90) at eval.c:383
#27 0x080a379f in Rf_eval (e=0x826fc38, rho=0x9206e90) at eval.c:360
#28 0x080a4f62 in do_begin (call=0x87d4f84, op=0x81fba9c,
args=0x87d4edc,
    rho=0x9206e90) at eval.c:1072
#29 0x080a3b28 in Rf_eval (e=0x87d4f84, rho=0x9206e90) at eval.c:418
#30 0x080a3b28 in Rf_eval (e=0x87d5b7c, rho=0x9206e90) at eval.c:418
#31 0x080a4f62 in do_begin (call=0x87d54c4, op=0x81fba9c,
args=0x87d5b60,
    rho=0x9206e90) at eval.c:1072
#32 0x080a3b28 in Rf_eval (e=0x87d54c4, rho=0x9206e90) at eval.c:418
---Type <return> to continue, or q <return> to quit---
#33 0x080a3db2 in Rf_applyClosure (call=0x8721018, op=0x87d5a80,
    arglist=0x9206f00, rho=0x8e5d4d0, suppliedenv=0x81f65c0) at
eval.c:609
#34 0x080a3937 in Rf_eval (e=0x8721018, rho=0x8e5d4d0) at eval.c:453
#35 0x080a5685 in do_set (call=0x8721088, op=0x8e5d4d0, args=0x8721050,
    rho=0x8e5d4d0) at eval.c:1283
#36 0x080a3b28 in Rf_eval (e=0x8721088, rho=0x8e5d4d0) at eval.c:418
#37 0x080a4f62 in do_begin (call=0x87210a4, op=0x81fba9c,
args=0x87210c0,
    rho=0x8e5d4d0) at eval.c:1072
#38 0x080a3b28 in Rf_eval (e=0x87210a4, rho=0x8e5d4d0) at eval.c:418
#39 0x080a495c in do_for (call=0x872089c, op=0x81f5fa0, args=0x8720810,
    rho=0x8e5d4d0) at eval.c:968
#40 0x080a3b28 in Rf_eval (e=0x872089c, rho=0x8e5d4d0) at eval.c:418
#41 0x080a4f62 in do_begin (call=0x8720d40, op=0x81fba9c,
args=0x87208b8,
    rho=0x8e5d4d0) at eval.c:1072
#42 0x080a3b28 in Rf_eval (e=0x8720d40, rho=0x8e5d4d0) at eval.c:418
#43 0x080a3b28 in Rf_eval (e=0x87209b4, rho=0x8e5d4d0) at eval.c:418
#44 0x080a4f62 in do_begin (call=0x8726138, op=0x81fba9c,
args=0x87209d0,
    rho=0x8e5d4d0) at eval.c:1072
#45 0x080a3b28 in Rf_eval (e=0x8726138, rho=0x8e5d4d0) at eval.c:418
#46 0x080a3db2 in Rf_applyClosure (call=0x8e5d690, op=0x86cd684,
    arglist=0x8e5d620, rho=0x820ce3c, suppliedenv=0x81f65c0) at
eval.c:609
#47 0x080a3937 in Rf_eval (e=0x8e5d690, rho=0x820ce3c) at eval.c:453
#48 0x080bd784 in Rf_ReplIteration (rho=0x820ce3c, savestack=1,
browselevel=0,
---Type <return> to continue, or q <return> to quit---
    state=0xbffff050) at main.c:236
#49 0x080bd942 in R_ReplConsole (rho=0x820ce3c, savestack=0,
browselevel=0)
    at main.c:284
#50 0x080be1ff in run_Rmainloop () at main.c:615
#51 0x08124b5c in main (ac=1, av=0xbffff524) at system.c:99
#52 0x400977f7 in __libc_start_main () from /lib/i686/libc.so.6
(gdb)
(gdb)

(gdb) run
The program being debugged has been started already.
Start it from the beginning? (y or n) y
 
Starting program:
/home/paul/dse/src/pac/R-test/R-1.7.0beta_2003.04.16/bin/R.bin  
 
R : Copyright 2003, The R Development Core Team
Version 1.7.0 Under development (unstable) (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)
> gctorture()
> checkVignettes(dir='/home/paul/dse/src/pac/monitor', workdir = 'cur',
keepfiles=TRUE)
 
Program received signal SIGILL, Illegal instruction.
0x080786ff in file_fgetc (con=0xbfffc830) at connections.c:289
289             this->wpos = ftell(this->fp);
(gdb) bt
#0  0x080786ff in file_fgetc (con=0xbfffc830) at connections.c:289
#1  0x080a9ce1 in con_getc () at /ext/R/cvs/R-devel/src/main/gram.y:1130
#2  0x080a881b in xxgetc () at /ext/R/cvs/R-devel/src/main/gram.y:287
#3  0x080aa947 in SymbolValue (c=255)
    at /ext/R/cvs/R-devel/src/main/gram.y:1673
#4  0x080aab01 in token () at /ext/R/cvs/R-devel/src/main/gram.y:1744
#5  0x080aaefa in Rf_yylex () at /ext/R/cvs/R-devel/src/main/gram.y:1886
#6  0x080a87e4 in Rf_yyparse () at
/usr/local/share/bison/bison.simple:595
#7  0x080a98cd in R_Parse1 (status=0x46)
    at /ext/R/cvs/R-devel/src/main/gram.y:948
#8  0x080a9bee in R_Parse (n=-1, status=0xbfffcd68)
    at /ext/R/cvs/R-devel/src/main/gram.y:1083
#9  0x081175d1 in do_parse (call=0x883d674, op=0x8205024,
args=0x8839138,
    env=0x8f403ec) at source.c:76
#10 0x080c99e4 in do_internal (call=0x883d5e8, op=0x81fb5e8,
args=0x8f38248,
    env=0x8f403ec) at names.c:1056
#11 0x080a3b28 in Rf_eval (e=0x883d5e8, rho=0x8f403ec) at eval.c:418
#12 0x080a4f62 in do_begin (call=0x883cdc4, op=0x81fba9c,
args=0x883d5cc,
    rho=0x8f403ec) at eval.c:1072
#13 0x080a3b28 in Rf_eval (e=0x883cdc4, rho=0x8f403ec) at eval.c:418
#14 0x080a3db2 in Rf_applyClosure (call=0x8954ae0, op=0x883d4ec,
    arglist=0x8f38a88, rho=0x8f32c1c, suppliedenv=0x81f65c0) at
eval.c:609
#15 0x080a3937 in Rf_eval (e=0x8954ae0, rho=0x8f32c1c) at eval.c:453
---Type <return> to continue, or q <return> to quit---
#16 0x080a5685 in do_set (call=0x8954a8c, op=0x8f32c1c, args=0x8954aa8,
    rho=0x8f32c1c) at eval.c:1283
#17 0x080a3b28 in Rf_eval (e=0x8954a8c, rho=0x8f32c1c) at eval.c:418
#18 0x080a586b in Rf_evalList (el=0x8954a1c, rho=0x8f32c1c) at
eval.c:1372
#19 0x080a3a50 in Rf_eval (e=0x8954a00, rho=0x8f32c1c) at eval.c:439
#20 0x080a5685 in do_set (call=0x89549ac, op=0x8f32c1c, args=0x89549c8,
    rho=0x8f32c1c) at eval.c:1283
#21 0x080a3b28 in Rf_eval (e=0x89549ac, rho=0x8f32c1c) at eval.c:418
#22 0x080a4f62 in do_begin (call=0x8953ad0, op=0x81fba9c,
args=0x8954990,
    rho=0x8f32c1c) at eval.c:1072
#23 0x080a3b28 in Rf_eval (e=0x8953ad0, rho=0x8f32c1c) at eval.c:418
#24 0x080a3db2 in Rf_applyClosure (call=0x8720f1c, op=0x8958db0,
    arglist=0x8f33e5c, rho=0x8f38794, suppliedenv=0x81f65c0) at
eval.c:609
#25 0x080a3937 in Rf_eval (e=0x8720f1c, rho=0x8f38794) at eval.c:453
#26 0x080a3856 in Rf_eval (e=0x8dbce88, rho=0x8f348a0) at eval.c:383
#27 0x080a379f in Rf_eval (e=0x826fc38, rho=0x8f348a0) at eval.c:360
#28 0x080a4f62 in do_begin (call=0x87d4f84, op=0x81fba9c,
args=0x87d4edc,
    rho=0x8f348a0) at eval.c:1072
#29 0x080a3b28 in Rf_eval (e=0x87d4f84, rho=0x8f348a0) at eval.c:418
#30 0x080a3b28 in Rf_eval (e=0x87d5b7c, rho=0x8f348a0) at eval.c:418
#31 0x080a4f62 in do_begin (call=0x87d54c4, op=0x81fba9c,
args=0x87d5b60,
    rho=0x8f348a0) at eval.c:1072
#32 0x080a3b28 in Rf_eval (e=0x87d54c4, rho=0x8f348a0) at eval.c:418
---Type <return> to continue, or q <return> to quit---
#33 0x080a3db2 in Rf_applyClosure (call=0x8721018, op=0x87d5a80,
    arglist=0x8d178e8, rho=0x8f38794, suppliedenv=0x81f65c0) at
eval.c:609
#34 0x080a3937 in Rf_eval (e=0x8721018, rho=0x8f38794) at eval.c:453
#35 0x080a5685 in do_set (call=0x8721088, op=0x8f38794, args=0x8721050,
    rho=0x8f38794) at eval.c:1283
#36 0x080a3b28 in Rf_eval (e=0x8721088, rho=0x8f38794) at eval.c:418
#37 0x080a4f62 in do_begin (call=0x87210a4, op=0x81fba9c,
args=0x87210c0,
    rho=0x8f38794) at eval.c:1072
#38 0x080a3b28 in Rf_eval (e=0x87210a4, rho=0x8f38794) at eval.c:418
#39 0x080a495c in do_for (call=0x872089c, op=0x81f5fa0, args=0x8720810,
    rho=0x8f38794) at eval.c:968
#40 0x080a3b28 in Rf_eval (e=0x872089c, rho=0x8f38794) at eval.c:418
#41 0x080a4f62 in do_begin (call=0x8720d40, op=0x81fba9c,
args=0x87208b8,
    rho=0x8f38794) at eval.c:1072
#42 0x080a3b28 in Rf_eval (e=0x8720d40, rho=0x8f38794) at eval.c:418
#43 0x080a3b28 in Rf_eval (e=0x87209b4, rho=0x8f38794) at eval.c:418
#44 0x080a4f62 in do_begin (call=0x8726138, op=0x81fba9c,
args=0x87209d0,
    rho=0x8f38794) at eval.c:1072
#45 0x080a3b28 in Rf_eval (e=0x8726138, rho=0x8f38794) at eval.c:418
#46 0x080a3db2 in Rf_applyClosure (call=0x8f387e8, op=0x86cd684,
    arglist=0x8f38858, rho=0x820ce3c, suppliedenv=0x81f65c0) at
eval.c:609
#47 0x080a3937 in Rf_eval (e=0x8f387e8, rho=0x820ce3c) at eval.c:453
#48 0x080bd784 in Rf_ReplIteration (rho=0x820ce3c, savestack=1,
browselevel=0,
---Type <return> to continue, or q <return> to quit---
    state=0xbffff050) at main.c:236
#49 0x080bd942 in R_ReplConsole (rho=0x820ce3c, savestack=0,
browselevel=0)
    at main.c:284
#50 0x080be1ff in run_Rmainloop () at main.c:615
#51 0x08124b5c in main (ac=1, av=0xbffff524) at system.c:99
#52 0x400977f7 in __libc_start_main () from /lib/i686/libc.so.6
(gdb)

More information about the R-devel mailing list