[Rd] sweave/gc segfault bt

Fri Apr 4 23:38:18 MEST 2003

Below is a gdb bt from a segfault provoke by my vignette for dse2. This seems to
be relatively reproducible in the sense that I got a segfault three times
(without gctorture) on Mandrake 9.0 and also caught it in Mandrake 9.1, at what
looks to my untrained eye to be about the same place (actual at
connections.c:293 in Mandrake 9.1). This is the build from Friday morning.

Paul Gilbert

R_LIBS=/home/paul/dse/src/pac/dse2/tmp.R-1.7.0:/home/paul/dse/CHECKED.R-1.7.0/Rlibs 
PADI=/home/paul/dse/src/pac/padi/exec
PATH=/usr//bin:/bin:/usr/bin::/usr/local/bin:/usr/X11R6/bin:/usr/games:~/bin:~/bin:/home/paul/dse/src/pac/padi/exec
R -d gdb 
GNU gdb 5.2.1-2mdk (Mandrake Linux)
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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 Under development (unstable) (2003-04-04)

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> library(tools)
> checkVignettes(dir='/home/paul/dse/src/pac/dse2', workdir = 'cur',
keepfiles=TRUE)

Program received signal SIGSEGV, Segmentation fault.
0x080784ff in file_fgetc (con=0xbfffc8a0) at connections.c:291
291             fseek(this->fp, this->rpos, SEEK_SET);
(gdb) bt
#0  0x080784ff in file_fgetc (con=0xbfffc8a0) at connections.c:291
#1  0x080a9f12 in con_getc () at /ext/R/cvs/R-devel/src/main/gram.y:1130
#2  0x080a8a2b in xxgetc () at /ext/R/cvs/R-devel/src/main/gram.y:287
#3  0x080aab78 in SymbolValue (c=0) at
/ext/R/cvs/R-devel/src/main/gram.y:1673
#4  0x080aad30 in token () at /ext/R/cvs/R-devel/src/main/gram.y:1744
#5  0x080ab12a in Rf_yylex () at /ext/R/cvs/R-devel/src/main/gram.y:1886
#6  0x080a89f4 in Rf_yyparse () at
/usr/local/share/bison/bison.simple:595
#7  0x080a9afd in R_Parse1 (status=0x46)
    at /ext/R/cvs/R-devel/src/main/gram.y:948
#8  0x080a9e1e in R_Parse (n=-1, status=0xbfffcdf8)
    at /ext/R/cvs/R-devel/src/main/gram.y:1083
#9  0x080a9fa3 in R_ParseConn (con=0x1, n=-1, status=0xbfffcdf8)
    at /ext/R/cvs/R-devel/src/main/gram.y:1147
#10 0x08117b61 in do_parse (call=0x883dc90, op=0x8205704,
args=0x88397c0, 
    env=0x94f5cf0) at source.c:76
#11 0x080c9e24 in do_internal (call=0x883dc04, op=0x81fbcc8,
args=0x94f52d4, 
    env=0x94f5cf0) at names.c:1056
#12 0x080a3d18 in Rf_eval (e=0x883dc04, rho=0x94f5cf0) at eval.c:418
#13 0x080a5172 in do_begin (call=0x883d3e0, op=0x81fc17c,
args=0x883dbe8, 
    rho=0x94f5cf0) at eval.c:1072
#14 0x080a3d18 in Rf_eval (e=0x883d3e0, rho=0x94f5cf0) at eval.c:418
#15 0x080a3fa5 in Rf_applyClosure (call=0x8955188, op=0x883db08, 
    arglist=0x94f5bbc, rho=0x94f57b0, suppliedenv=0x81f6ca0) at
eval.c:609
---Type <return> to continue, or q <return> to quit---
#16 0x080a3b27 in Rf_eval (e=0x8955188, rho=0x94f57b0) at eval.c:453
#17 0x080a5895 in do_set (call=0x8955134, op=0x94f57b0, args=0x8955150, 
    rho=0x94f57b0) at eval.c:1283
#18 0x080a3d18 in Rf_eval (e=0x8955134, rho=0x94f57b0) at eval.c:418
#19 0x080a5a7b in Rf_evalList (el=0x89550c4, rho=0x94f57b0) at
eval.c:1372
#20 0x080a3c40 in Rf_eval (e=0x89550a8, rho=0x94f57b0) at eval.c:439
#21 0x080a5895 in do_set (call=0x8955054, op=0x94f57b0, args=0x8955070, 
    rho=0x94f57b0) at eval.c:1283
#22 0x080a3d18 in Rf_eval (e=0x8955054, rho=0x94f57b0) at eval.c:418
#23 0x080a5172 in do_begin (call=0x8954178, op=0x81fc17c,
args=0x8955038, 
    rho=0x94f57b0) at eval.c:1072
#24 0x080a3d18 in Rf_eval (e=0x8954178, rho=0x94f57b0) at eval.c:418
#25 0x080a3fa5 in Rf_applyClosure (call=0x8e217b8, op=0x8959458, 
    arglist=0x94f5698, rho=0x8ef6f8c, suppliedenv=0x81f6ca0) at
eval.c:609
#26 0x080a3b27 in Rf_eval (e=0x8e217b8, rho=0x8ef6f8c) at eval.c:453
#27 0x080a3a46 in Rf_eval (e=0x94f66e8, rho=0x94f6790) at eval.c:383
#28 0x080a398f in Rf_eval (e=0x82702e0, rho=0x94f6790) at eval.c:360
#29 0x080a5172 in do_begin (call=0x87d55a0, op=0x81fc17c,
args=0x87d54f8, 
    rho=0x94f6790) at eval.c:1072
#30 0x080a3d18 in Rf_eval (e=0x87d55a0, rho=0x94f6790) at eval.c:418
#31 0x080a3d18 in Rf_eval (e=0x87d6198, rho=0x94f6790) at eval.c:418
#32 0x080a5172 in do_begin (call=0x87d5ae0, op=0x81fc17c,
args=0x87d617c, 
    rho=0x94f6790) at eval.c:1072
---Type <return> to continue, or q <return> to quit---
#33 0x080a3d18 in Rf_eval (e=0x87d5ae0, rho=0x94f6790) at eval.c:418
#34 0x080a3fa5 in Rf_applyClosure (call=0x8e2172c, op=0x87d609c, 
    arglist=0x94f6720, rho=0x8ef6f8c, suppliedenv=0x81f6ca0) at
eval.c:609
#35 0x080a3b27 in Rf_eval (e=0x8e2172c, rho=0x8ef6f8c) at eval.c:453
#36 0x080a5895 in do_set (call=0x8e216d8, op=0x8ef6f8c, args=0x8e216f4, 
    rho=0x8ef6f8c) at eval.c:1283
#37 0x080a3d18 in Rf_eval (e=0x8e216d8, rho=0x8ef6f8c) at eval.c:418
#38 0x080a5172 in do_begin (call=0x8e216bc, op=0x81fc17c,
args=0x8e216a0, 
    rho=0x8ef6f8c) at eval.c:1072
#39 0x080a3d18 in Rf_eval (e=0x8e216bc, rho=0x8ef6f8c) at eval.c:418
#40 0x080a4b3c in do_for (call=0x8e21390, op=0x81f6680, args=0x8e213ac, 
    rho=0x8ef6f8c) at eval.c:968
#41 0x080a3d18 in Rf_eval (e=0x8e21390, rho=0x8ef6f8c) at eval.c:418
#42 0x080a5172 in do_begin (call=0x8e2187c, op=0x81fc17c,
args=0x8e21374, 
    rho=0x8ef6f8c) at eval.c:1072
#43 0x080a3d18 in Rf_eval (e=0x8e2187c, rho=0x8ef6f8c) at eval.c:418
#44 0x080a3d18 in Rf_eval (e=0x8e222b4, rho=0x8ef6f8c) at eval.c:418
#45 0x080a5172 in do_begin (call=0x8e1e5ac, op=0x81fc17c,
args=0x8e22298, 
    rho=0x8ef6f8c) at eval.c:1072
#46 0x080a3d18 in Rf_eval (e=0x8e1e5ac, rho=0x8ef6f8c) at eval.c:418
#47 0x080a3fa5 in Rf_applyClosure (call=0x8ef714c, op=0x8e407d8, 
    arglist=0x8ef70dc, rho=0x820d51c, suppliedenv=0x81f6ca0) at
eval.c:609
#48 0x080a3b27 in Rf_eval (e=0x8ef714c, rho=0x820d51c) at eval.c:453
---Type <return> to continue, or q <return> to quit---
#49 0x080bdbc7 in Rf_ReplIteration (rho=0x820d51c, savestack=1,
browselevel=0, 
    state=0xbffff0e0) at main.c:236
#50 0x080bdd82 in R_ReplConsole (rho=0x820d51c, savestack=0,
browselevel=0)
    at main.c:284
#51 0x080be64f in run_Rmainloop () at main.c:615
#52 0x081251ec in main (ac=1, av=0xbffff5c4) at system.c:99
#53 0x4009a082 in __libc_start_main () from /lib/i686/libc.so.6
(gdb)