Debugging C code

Creation Date: 8 Feb 2012; Last Edit Date: 27 Feb 2012

The following applies to non-Windows operating systems. This is not for the faint of heart, and requires some C-level familiarity.

Set-up

The first, essential, step is to write a short script that reliably and quickly reproduces the error. Call this script buggy.R.

For debugging package code at the C level, one usually starts by installing the package without any compiler optimizations, e.g., by following

RShowDoc("R-admin")

section 6.3.3. setting for instance

CFLAGS=-ggdb -O0

in .R/Makevars.

valgrind

The valgrind debugger can be used to spot memory access problems, which are a common source of faults in C code. When the bug is isolated and easily produced in buggy.R, start R with

R -d valgrind -f buggy.R

This runs quite slowly, and will flag invalid memory read and write locations. The former typically contribute to bad data, the latter to memory corruption and spectacular failures. The output will require C familiarity to interpret. It is helpful to run the buggy code with a package that has been installed without compiler optimizations. See section 4.3 of RShowDoc("R-exts")

gdb for interactive debugging

Start R with a C-level debugger such as gdb (this is an old-school command-line style debugger, not to everyone's taste)

R -d gdb -f buggy.R

You'll end up at the gdb prompt

(gdb)

and a typical operation is to (r)un or (c)ontinue execution

(gdb) r

to run buggy.R. You'll end up back in C when there is a segfault, or you press cntrl-C (^C, below), or when you've inserted a (b)reakpoint at some C-level function that you suspect is buggy, e.g.,

> ^C
(gdb) b some_buggy_fun
(gdb) c

When you do end up back in the debugger, you can print C variables or the C representation of R variables (provided R isn't too confused by this point)

(gdb) p c_var
(gdb) call Rf_PrintValue(some_R_variable)

You can also view a (b)ack(t)race of the call stack, navigate (u)p and (d)own the call stack, etc. See

(gdb) help

and our mutual friend Google for additional information.

Case study

As a case study, a colleague reported that their complicated program would, on one particular computer, produce a segmentation fault or just stop responding. The same series of actions wouldn't cause problems on other computers. This sounds like a classic memory problem, with the segfault and difficulty of reproduction.

The first advice was to develop a simple script that reproduced the problem: the original report had too many moving parts. A big insight was that the bug could be produced by running part of the code that uses RCurl, followed by a call to the garbage collector, gc(). The role of the garbage collector suggests again memory corruption of some sort, and in particular that perhaps RCurl is allocating (at the C level) an R object but not properly PROTECT'ing it from garbage collection. We suspect RCurl rather than R or libcurl (other possible players) because it is the least tested of the code. We could be wrong, of course... After many iterations, my colleague arrived at buggy24.R:

library(RCurl)

foo <- function() {
    url <- "https://google.com"
    curl <- getCurlHandle()
    opts <- list(followlocation=NULL, ssl.verifypeer=TRUE)
    d <- debugGatherer()
    getURL(url,customrequest="GET",curl=curl,debugfunction=d$update,.opts=opts)
}

execute <- function() {
    foo()
    gc()
}

execute()

This is pretty simple, and doesn't require access to any special resources (like the server that was originally being queried). This script doesn't cause a segfault when run on all systems, but running valgrind (having installed RCurl without any optimizations) shows...

> R -d valgrind -f buggy24.R
...
==10859== Conditional jump or move depends on uninitialised value(s)
==10859==    at 0x11BF00F6: getCurlPointerForData (curl.c:798)
==10859==    by 0x11BF0E80: R_curl_easy_setopt (curl.c:164)
==10859==    by 0x11BF17AD: R_curl_easy_perform (curl.c:89)
==10859==    by 0x4ED5499: do_dotcall (dotcode.c:588)
==10859==    by 0x4F1CAA4: Rf_eval (eval.c:593)
==10859==    by 0x4F2BD5C: do_set (eval.c:1828)
==10859==    by 0x4F1C8B7: Rf_eval (eval.c:567)
==10859==    by 0x4F2B957: do_begin (eval.c:1514)
==10859==    by 0x4F1C8B7: Rf_eval (eval.c:567)
==10859==    by 0x4F297E9: Rf_applyClosure (eval.c:960)
==10859==    by 0x4F1CBA5: Rf_eval (eval.c:611)
==10859==    by 0x4F2BD5C: do_set (eval.c:1828)

Look around the C source code in RCurl's curl.c, as suggested by the backtrace, just to get oriented. Then do

R -d gdb -f buggy24.R

to run the script under gdb. Run our test script

(gdb) r

No error. Don't give up, set a break point

(gdb) b curl.c:798

and run again

(gdb) r
Breakpoint 1, getCurlPointerForData (el=0x79e038,
    option=CURLOPT_WRITEFUNCTION, isProtected=FALSE, curl=0x1d9bdc0)
    at curl.c:798
798    curl.c: No such file or directory.
(gdb)

That 'no such file' means that gdb doesn't know where to find the RCurl package src/ directory, so tell it and (l)ist the context, and (p)rint the value of the C variable isProtected, which seems to be the source of the valgrind warning

(gdb) dir ~/tmp/RCurl/src
(gdb) l
793                        }
794                    }
795                }
796                break;
797              case CLOSXP:
798              (gdb) l
793                        }
794                    }
795                }
796                break;
797              case CLOSXP:
798                  if(!isProtected) {
799                R_PreserveObject(el);
800                }
801                ptr = (void *) el;
802                break;
(gdb) p isProtected
$5 = FALSE

isProtected has a value (it has to!), and furthermore the value of FALSE results in PROTECT'ing the object el across C calls (this is what R_PreserveObject does). This is pretty interesting, because we're aware that garbage collection triggers the segfault. valgrind is telling us that the value of isProtected isn't actually the result of an assignment, it could be the result of accessing an array out of bounds. Let's head up the call stack and see where this value is coming from

(gdb) up
#1  0x00007ffff426e273 in R_curl_easy_setopt (handle=0x15d9600,
    values=0x1445788, opts=0xf3d418, isProtected=0xb7d308, encoding=0x776db0)
    at curl.c:164
164            val = getCurlPointerForData(el, opt, LOGICAL(isProtected)[ i % n ], obj);
(gdb) l
159        /* Loop over all the options we are setting. */
160        for(i = 0; i < n; i++) {
161            opt = INTEGER(opts)[i];
162            el = VECTOR_ELT(values, i);
163                 /* Turn the R value into something we can use in libcurl. */
164            val = getCurlPointerForData(el, opt, LOGICAL(isProtected)[ i % n ], obj);
165   
166                    if(opt == CURLOPT_WRITEFUNCTION && TYPEOF(el) == CLOSXP) {
167                data->fun = val; useData++;
168                status =  curl_easy_setopt(obj, CURLOPT_WRITEFUNCTION, &R_curl_write_data);
(gdb)

We're entering the function getCurlPointerForData with the value LOGICAL(isProtected)[ i % n ]. Here, isProtected is now an R object, not a C variable. Looking at the surrounding code, that i % n doesn't look right -- it's probably meant to recycle isProtected in the case where a shorter logical variable is provided than the vector of elements requiring protection, but the value of n is not necessarily the length of isProtected. Let's have a look at what we've got, using a C-level R function Rf_PrintValue to print R values (SEXP's) in an R fashion

(gdb) p isProtected
$1 = (SEXP) 0xaad8a0
(gdb) call Rf_PrintValue(isProtected )
[1] FALSE

isProtected is a logical vector of length 1.

(gdb) p i
$7 = 1
(gdb) p n
$8 = 6
(gdb) p i % n
$9 = 1

...and we're trying to access element 1 of it. But the C representation of R vectors is zero-based, so the only valid value of the index is 0 -- we're out of bounds! This could well be our bug, and it's time to try fixing it (naively, LOGICAL(isProtected)[ i % LENGTH(isProtected) ]) to confirm our diagnosis, or report to the packageDescription("RCurl")$Maintainer who might have a better sense of the overall structure and intention of the code.

Fred Hutchinson Cancer Research Center