[R] segfault debugging

[Duncan Murdoch]

On 12-12-01 6:56 AM, Donatella Quagli wrote:
> Thank you so far. Here is an excerpt from the gdb session after a crash:
>    Program received signal SIGSEGV, Segmentation fault.
>
>    0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so
>    (gdb) backtrace
>    #0  0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so
>    #1  0xb744b64c in ?? () from /usr/lib/R/lib/libR.so
>    #2  0xb74c58bf in ?? () from /usr/lib/R/lib/libR.so
>    #3  0xb74c9c62 in Rf_eval () from /usr/lib/R/lib/libR.so
>    #4  0xb74ce60f in Rf_applyClosure () from /usr/lib/R/lib/libR.so
>    #5  0xb74c9f29 in Rf_eval () from /usr/lib/R/lib/libR.so
>    #6  0xb7503002 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so
>    #7  0xb7503298 in ?? () from /usr/lib/R/lib/libR.so
>    #8  0xb7503812 in run_Rmainloop () from /usr/lib/R/lib/libR.so
>    #9  0xb7503839 in Rf_mainloop () from /usr/lib/R/lib/libR.so
>    #10 0x08048768 in main ()
>    #11 0xb728de46 in __libc_start_main (main=0x8048730 <main>, argc=8, ubp_av=0xbfdb7824, init=0x80488a0 <__libc_csu_init>,
>        fini=0x8048890 <__libc_csu_fini>, rtld_fini=0xb7784590, stack_end=0xbfdb781c) at libc-start.c:228
>    #12 0x08048791 in _start ()
>
> It seems to me that the error is in frame #0. Does it mean that there is a bug in libR.so?  What can I do next?

It means that the error was detected when trying to do a memory 
allocation.  That could be a bug in R, but more likely something else 
has damaged the memory management system structures, e.g. a function 
writing to memory that it doesn't own.

Bugs like this are hard to track down, because the damage could have 
occurred a long time before it showed up, and small changes to your 
script could affect it.

I would try to narrow it down to a single statement in your script.  You 
might be able to deduce that from the last line printed before the 
crash.  If you don't have any printing, you could try adding some, but 
as I mentioned above, that might make the bug behave differently.

Another approach is to cut off statements at the end of your script. 
That probably won't affect the bug until you cut off the statement that 
actually triggered it (but it might, which is why this kind of bug is so 
frustrating to track down).

If you find the bad statement, then look at calls to external code in 
it, or recently executed before it.  See if any of them look like they 
contain errors.  Common errors are to write to an array without 
allocating it, or to write beyond the bounds of an array, or (in .Call() 
code) to allocate something and then fail to protect it from garbage 
collection.

You could also figure out what the problem is that caused the seg fault 
in frame 0.  It might be because some particular variable contains a 
garbage value.  Then in a new run, you can ask gdb to break when that 
memory location takes on the garbage value.  This is usually effective 
if you really can identify the bad value, but doing that can be hard, 
especially when you aren't familiar with how things normally work.

Good luck!

Duncan Murdoch