On 5/21/2009 2:17 PM, William Dunlap wrote:
I noticed the following file descriptor leak when I couldn't remove
a package unless I shut down the R session that had loaded and
used it. The function that triggered the problem printed the output
of a call to parse(). Each time one prints a srcref a connection is
opened and not closed. It looks like it happens in
as.character.srcref's
call to getSrcLines, which has some logic I don't understand about
closing 'srcfile' on exit only if !.is.Open(srcfile):
getSrcLines
function (srcfile, first, last)
{
if (first > last)
return(character(0L))
if (!.isOpen(srcfile))
on.exit(close(srcfile))
conn <- open(srcfile, first)
lines <- readLines(conn, n = last - first + 1L, warn = FALSE)
srcfile$line <- first + length(lines)
return(lines)
}
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.
The encoding problem came because "unknown" is not a legal encoding to
pass to file(). It needs to be changed to "" or "native.enc".
Thanks for the report; I'll commit a fix after some more testing.
Duncan Murdoch
This is on Linux, compiled by me with an ancient version of gcc.
% R
R version 2.10.0 Under development (unstable) (2009-05-21 r48590)
...
showConnections()
description class mode text isopen can read can write
tf<-tempfile()
cat(file=tf, "1:7\nlog(pi)\n")
showConnections()
description class mode text isopen can read can write
p<-parse(tf)
showConnections()
description class mode text isopen can read can write
p
expression(<srcref: file "/tmp/RtmpZ1llo5/file327b23c6" chars 1:1 to
1:3>,
<srcref: file "/tmp/RtmpZ1llo5/file327b23c6" chars 2:1 to 2:7>)
attr(,"srcfile")
/tmp/RtmpZ1llo5/file327b23c6
showConnections()
description class mode text isopen can read
can write
3 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
4 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
5 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
6 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
tf
[1] "/tmp/RtmpZ1llo5/file327b23c6"
z<-attr(p,"srcref")[[2]]
showConnections()
description class mode text isopen can read
can write
3 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
4 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
5 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
6 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
zz<-as.character(z)
showConnections()
description class mode text isopen can read
can write
3 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
4 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
5 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
6 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
7 "/tmp/RtmpZ1llo5/file327b23c6" "file" "rt" "text" "opened" "yes"
"no"
zz
[1] "<srcref: file \"/tmp/RtmpZ1llo5/file327b23c6\" chars 2:1 to 2:7>"
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
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