Re: [Rd] file descriptor leak in getSrcLines in R 2.10.0 svn 48590

[Duncan Murdoch]

On 5/22/2009 11:17 AM, William Dunlap wrote:
... 
The idea is that if the srcfile is already open, then it 
should be left 
open; but if it is not open, it should be closed at the end.  
open() on 
an open srcfile is supposed to make no change to the srcfile, just 
return the already open connection.

> (It looks like the srcref stuff is not finished yet, as 
there are other
> problems, like print(parse(file)) not showing what it used to.)


This is an encoding problem, which looks easy to fix.  I 
think the leak 
was caused by this:  because of the encoding problem, the connections 
got opened but open.srcfile aborted before completion, so 
close.srcfile 
didn't think the srcfile was open at all, and it left the 
connections in 
existence.

That incompletely opened connection may be why after doing
this test closeAllConnections crashed R because the ex_ptr
component of an Rconnection object was a nil pointer:

I saw a crash like that once, but then couldn't reproduce it.  I'll see 
if I can do so with your code.

Duncan Murdoch


tf<-tempfile()
cat(file=tf, "1:10\nlog(log(pi))\n")
p<-parse(tf)
p
expression(<srcref: file "/tmp/RtmpazU79B/file327b23c6" chars 1:1 to 1:4>,
    <srcref: file "/tmp/RtmpazU79B/file327b23c6" chars 2:1 to 2:12>)
attr(,"srcfile")
/tmp/RtmpazU79B/file327b23c6
showConnections()
  description                    class  mode text   isopen   can read can write
3 "/tmp/RtmpazU79B/file327b23c6" "file" "rt" "text" "opened" "yes"    "no"
4 "/tmp/RtmpazU79B/file327b23c6" "file" "rt" "text" "opened" "yes"    "no"
5 "/tmp/RtmpazU79B/file327b23c6" "file" "rt" "text" "opened" "yes"    "no"
6 "/tmp/RtmpazU79B/file327b23c6" "file" "rt" "text" "opened" "yes"    "no"
closeAllConnections()

Program received signal SIGSEGV, Segmentation fault.
0x08118eff in Rf_setAttrib (vec=0x883f278, name=0x8621948, val=0x0)
    at attrib.c:226
226         if (NAMED(val)) val = duplicate(val);
(gdb) up
#1  0x08146c7b in do_getconnection (call=0x87a3b74, op=0x85f6fd8,
    args=0x87a3ca8, env=0x87a3c1c) at connections.c:4166
4166            setAttrib(ans, install("conn_id"), con->ex_ptr);
(gdb) list
4161        PROTECT(class = allocVector(STRSXP, 2));
4162        SET_STRING_ELT(class, 0, mkChar(con->class));
4163        SET_STRING_ELT(class, 1, mkChar("connection"));
4164        classgets(ans, class);
4165        if (what > 2)
4166            setAttrib(ans, install("conn_id"), con->ex_ptr);
4167        UNPROTECT(2);
4168        return ans;
4169    }
4170

(gdb) print con->ex_ptr
$3 = (void *) 0x0
(gdb) print *con
$4 = {class = 0x90c8940 "file",
  description = 0x89c5878 "/tmp/RtmpazU79B/file327b23c6", enc = 0,
  mode = "rt\000\000", text = TRUE, isopen = TRUE, incomplete = FALSE,
  canread = TRUE, canwrite = FALSE, canseek = TRUE, blocking = TRUE,
  isGzcon = FALSE, open = 0x813c4f2 <file_open>,
  close = 0x813c77b <file_close>, destroy = 0x813bcf9 <null_destroy>,
  vfprintf = 0x813c7c3 <file_vfprintf>, fgetc = 0x813bfef <dummy_fgetc>,
  fgetc_internal = 0x813c860 <file_fgetc_internal>,
  seek = 0x813c8f9 <file_seek>, truncate = 0x813caa1 <file_truncate>,
  fflush = 0x813cb8a <file_fflush>, read = 0x813cbae <file_read>,
  write = 0x813cc26 <file_write>, nPushBack = 0, posPushBack = 64256,
  PushBack = 0x204, save = -1000, save2 = -1000,
  encname = "unknown", '\0' <repeats 93 times>, "A", inconv = 0x0,
  outconv = 0x0,
  iconvbuff = " 
\036\022\tE\001\000\000F\001\000\000G\001\000\000H\001\000\000I\001\000\000J",
  oconvbuff = 
"\001\000\000K\001\000\000L\001\000\000M\001\000\000N\001\000\000O\001\000\000P\001\000\000Q\001\000\000R\001\000\000S\001\000\000T\001\000\000U\001\000\000V\001",
 next = 0x157 <Address 0x157 out of bounds>,
  init_out = 
"X\001\000\000Y\001\000\000Z\001\000\000[\001\000\000\\\001\000\000]\001\000\000^",
 navail = 0, inavail = 351, EOF_signalled = 352,
  UTF8out = FALSE, id = 0x23, ex_ptr = 0x0, private = 0x908ec78}

______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel