From mail at joeconway.com  Wed Jul  4 22:56:01 2007
From: mail at joeconway.com (Joe Conway)
Date: Wed, 04 Jul 2007 13:56:01 -0700
Subject: [Rd] problem with findFun call from embedded R
Message-ID: <468C0961.9020804@joeconway.com>

I was debugging a problem reported to me regarding PL/R, and found that 
I can duplicate it using only R sources. It might be characterized as 
possibly a misuse of the findFun() function, but I leave that for the R 
devel experts to decide.

The below results are all with R-2.5.1 (I can't seem to download 
r-patched at the moment, but didn't see anything in the 2.5.1-patched 
release notes indicating this issue had been noticed) on Fedora Core 6 
x86_64 (also duplicated with R-2.5.0 on FC7 i386).

Steps to reproduce:
8<------------------------
  configure, make, make install from source tree
  cd tests/Embedding/
  make RNamedCall
  ./RNamedCall  #works as expected
  mv foo.R foo.R.orig
  ./RNamedCall  #segfaults
8<------------------------

output:
8<------------------------
Error in file(file, "r", encoding = encoding) :
         unable to open connection
In addition: Warning message:
cannot open file 'foo.R', reason 'No such file or directory' in: 
file(file, "r", encoding = encoding)
Error: could not find function "foo"

  *** caught segfault ***
address (nil), cause 'memory not mapped'

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 1
aborting ...
Segmentation fault
8<------------------------

The problem comes from RNamedCall starting at line 54:
8<------------------------
   fun = findFun(install("foo"), R_GlobalEnv);
   if(fun == R_NilValue) {
	fprintf(stderr, "No definition for function foo.
                          Source foo.R and save the session.\n");
   UNPROTECT(1);
   exit(1);
   }
8<------------------------

If foo.R was not found and never sourced, meaning that the object "foo" 
does not exist, findFun never returns. Instead the segfault occurs at 
line 719 in errors.c at the LONGJMP statement. Setting a breakpoint at 
erros.c:719, the backtrace looks like this (will wrap poorly):

8<------------------------
Breakpoint 2, jump_to_top_ex (traceback=TRUE, tryUserHandler=TRUE, 
processWarnings=TRUE, resetConsole=TRUE,
     ignoreRestartContexts=FALSE) at errors.c:719
719         LONGJMP(R_ToplevelContext->cjmpbuf, 0);
(gdb) bt
#0  jump_to_top_ex (traceback=TRUE, tryUserHandler=TRUE, 
processWarnings=TRUE, resetConsole=TRUE,
     ignoreRestartContexts=FALSE) at errors.c:719
#1  0x00002aaaaab77e5d in verrorcall_dflt (call=0x609d78, 
format=0x2aaaaace4a4d "%s", ap=0x7fffa13a94c0)
     at errors.c:516
#2  0x00002aaaaab7814a in Rf_errorcall (call=0x609d78, 
format=0x2aaaaace4a4d "%s") at errors.c:551
#3  0x00002aaaaab78347 in Rf_error (format=0x2aaaaace42da "could not 
find function \"%s\"") at errors.c:578
#4  0x00002aaaaab708e5 in Rf_findFun (symbol=0xc64f20, rho=0x649fa0) at 
envir.c:1244
#5  0x0000000000400e0c in bar1 () at RNamedCall.c:54
#6  0x0000000000400d59 in main (argc=1, argv=0x7fffa13ab838) at 
RNamedCall.c:16
8<------------------------

And then stepping into line 719 generates the segfault:
8<------------------------
(gdb) s

Program received signal SIGSEGV, Segmentation fault.
0x00002aaaaab701ce in Rf_findVar (symbol=0x6c12b8, rho=0x0) at envir.c:998
998         if (TYPEOF(rho) == NILSXP)
8<------------------------

I believe this is happening because findFun() was not executed inside a 
valid context, and therefore R_ToplevelContext->cjmpbuf is invalid.

My question is -- is the above an abuse of findFun() by RNamedCall.c 
(meaning I should avoid the same pattern)? Or maybe it should be wrapped 
in something similar to R_ToplevelExec?

==========================

On a related note, I found during my PL/R debugging that the segfault 
was causing the same console based, interactive, "*** caught segfault 
***" logic to execute. I was able to confirm that R_Interactive was set 
to TRUE in my PL/R session.

It seems that Rf_initEmbeddedR() sets R_Interactive to TRUE and depends 
on the output of isatty() to change it to FALSE in Rf_initialize_R() if 
there is no tty. Unfortunately, the most common methods for starting 
Postgres leave the tty attached (stdout and stderr are directed to the 
log file). I ended up explicitly writing "R_Interactive = FALSE" just 
after running Rf_initEmbeddedR() -- is this a safe and reasonable thing 
to do?

Thanks,

Joe



[Rd] problem with findFun call from embedded R
Joe Conway