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hb@maths.lth.se

2002-Feb-28 16:20 UTC

[Rd] Failed file("foo", "r") keeps file open? (PR#1333)

Full_Name: Henrik Bengtsson
Version: R v1.4.0
OS: Solaris 8
Submission from: (NULL) (130.235.3.49)


When I am trying the following on Rv1.4.0 on Solaris 8, I get that the
"cannot close output sink connection":
 
 % R --vanilla

 tmpfile <- tempfile()  # Create a filename that does not exist
 for(k in 1:100) {
   cat(k, ": ");
   try(fh <- file(tmpfile, "r"))
   close(file("tmp.txt", "w"))   # Opens and closes a file
for writing.
 }
 
1 Error in file(tempfile(), "r") : cannot open file
`/tmp/fileR70d5S167e'
2 Error in file(tempfile(), "r") : cannot open file
`/tmp/fileR70d5S2781'
...
47 Error in file(tempfile(), "r") : cannot open file
`/tmp/fileR70d5S345b'
Error in close.connection(file("tmp.txt", "w")) :
        cannot close output sink connection
 
It always happens after 48 failed file openings.


To me it looks like failed 'file(tmpfile, "r")' does not
correctly
clean up after itself. And since 'fh' is never assigned it can neither
be solved by a 'close(fh)'.

FYI: Doing a cat(file="tmp.txt", k") instead of the
close(file(...)) call,
will produce a "sink stack is full" error.

FYI2: After the failure above, trying to call sink() will result in a
      "Segmentation fault" and [R] is stopped.

Background: I ran into this problem after have been running the same
script several times over several days I eventually ran into the problem.
It was hard to identify the problem, but I believe the above example shows
the core of it and I could not track the problem further.

Unfortunately, I do not have access to R v1.4.1 for Solaris 8.


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ripley@stats.ox.ac.uk

2002-Feb-28 18:00 UTC

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[Rd] Failed file("foo", "r") keeps file open? (PR#1333)

On Thu, 28 Feb 2002 hb@maths.lth.se wrote:
> Full_Name: Henrik Bengtsson
> Version: R v1.4.0
> OS: Solaris 8
> Submission from: (NULL) (130.235.3.49)
>
>
> When I am trying the following on Rv1.4.0 on Solaris 8, I get that the
> "cannot close output sink connection":
>
>  % R --vanilla
>
>  tmpfile <- tempfile()  # Create a filename that does not exist
>  for(k in 1:100) {
>    cat(k, ": ");
>    try(fh <- file(tmpfile, "r"))
>    close(file("tmp.txt", "w"))   # Opens and closes a
file for writing.
>  }
>
> 1 Error in file(tempfile(), "r") : cannot open file
`/tmp/fileR70d5S167e'
> 2 Error in file(tempfile(), "r") : cannot open file
`/tmp/fileR70d5S2781'
> ...
> 47 Error in file(tempfile(), "r") : cannot open file
`/tmp/fileR70d5S345b'
> Error in close.connection(file("tmp.txt", "w")) :
>         cannot close output sink connection
>
> It always happens after 48 failed file openings.
>
>
> To me it looks like failed 'file(tmpfile, "r")' does not
correctly
> clean up after itself. And since 'fh' is never assigned it can
neither
> be solved by a 'close(fh)'.
It does correctly clean up: it should leave a connection which is not
opened.  That may not be the best design, but it is the design.

Take a look at closeAllConnections.

It's better to call file() and then open(), which will avoid the problem.

> FYI: Doing a cat(file="tmp.txt", k") instead of the
close(file(...)) call,
> will produce a "sink stack is full" error.
>
> FYI2: After the failure above, trying to call sink() will result in a
>       "Segmentation fault" and [R] is stopped.
>
> Background: I ran into this problem after have been running the same
> script several times over several days I eventually ran into the problem.
> It was hard to identify the problem, but I believe the above example shows
> the core of it and I could not track the problem further.
>
> Unfortunately, I do not have access to R v1.4.1 for Solaris 8.
>
>
>
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> r-devel mailing list -- Read
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>
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>
-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


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hb@maths.lth.se

2002-Feb-28 19:16 UTC

head link

[Rd] Failed file("foo", "r") keeps file open? (PR#1333)

On Thu, 28 Feb 2002, Prof Brian Ripley wrote:
> On Thu, 28 Feb 2002 hb@maths.lth.se wrote:
> 
> > Full_Name: Henrik Bengtsson
> > Version: R v1.4.0
> > OS: Solaris 8
> > Submission from: (NULL) (130.235.3.49)
> >
> >
> > When I am trying the following on Rv1.4.0 on Solaris 8, I get that the
> > "cannot close output sink connection":
> >
> >  % R --vanilla
> >
> >  tmpfile <- tempfile()  # Create a filename that does not exist
> >  for(k in 1:100) {
> >    cat(k, ": ");
> >    try(fh <- file(tmpfile, "r"))
> >    close(file("tmp.txt", "w"))   # Opens and
closes a file for writing.
> >  }
> >
> > 1 Error in file(tempfile(), "r") : cannot open file
`/tmp/fileR70d5S167e'
> > 2 Error in file(tempfile(), "r") : cannot open file
`/tmp/fileR70d5S2781'
> > ...
> > 47 Error in file(tempfile(), "r") : cannot open file
`/tmp/fileR70d5S345b'
> > Error in close.connection(file("tmp.txt", "w")) :
> >         cannot close output sink connection
> >
> > It always happens after 48 failed file openings.
> >
> >
> > To me it looks like failed 'file(tmpfile, "r")' does
not correctly
> > clean up after itself. And since 'fh' is never assigned it can
neither
> > be solved by a 'close(fh)'.
> 
> It does correctly clean up: it should leave a connection which is not
> opened.  That may not be the best design, but it is the design.
> 
> Take a look at closeAllConnections.
Accepting the design, calling file(tempfile(), open="r"), will, as
you say, create a "closed" connection as seen by
showConnections(all=TRUE) and it can be deleted by identifying the
connection id from the list and the closing it with

  fh <- getConnection(id)
  close(fh)

or one could call closeAllConnections(), which is not always what you
want. However, if one creates TOO MANY failed connections as above,
neither of the above works:

  % R --vanilla

  K <- 48; # K <- 47 is ok.
  tmpfile <- tempfile()
  for(k in 1:K) try(fh <- file(tmpfile, "r"))

will make [R] stall when closeAllConnections() is called. Doing Ctrl+C and
trying do anything, e.g. "ls() [ENTER]", will generate a
"Segmentation
fault" or "0 [ENTER]" will generate a "Bus error".
Trying to use

  fh <- getConnection(id)
  close(fh)

gives "Error in close.connection(fh) : cannot close output sink
connection". In this case there is not fatal quitting of [R].

I don't think it is a common thing to end up in this situation, but even
with the design you refer to, I still think something should be fixed
since it is possible to force [R] into an instable and unleavable state,
which is likely to crash [R].
> It's better to call file() and then open(), which will avoid the
problem.
I definitely agree, now when you have told me.
 > > FYI: Doing a cat(file="tmp.txt", k") instead of the
close(file(...)) call,
> > will produce a "sink stack is full" error.
> >
> > FYI2: After the failure above, trying to call sink() will result in a
> >       "Segmentation fault" and [R] is stopped.
> >
> > Background: I ran into this problem after have been running the same
> > script several times over several days I eventually ran into the
problem.
> > It was hard to identify the problem, but I believe the above example
shows
> > the core of it and I could not track the problem further.
> >
> > Unfortunately, I do not have access to R v1.4.1 for Solaris 8.
> >
> >
> >
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> > r-devel mailing list -- Read
http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
> > Send "info", "help", or "[un]subscribe"
> > (in the "body", not the subject !)  To:
r-devel-request@stat.math.ethz.ch
> >
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> >
> 
> -- 
> Brian D. Ripley,                  ripley@stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272860 (secr)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
Thanks

Henrik Bengtsson

Dept. of Mathematical Statistics @ Centre for Mathematical Sciences 
Lund Institute of Technology/Lund University, Sweden (+2h UTC)
Office: P316, +46 46 222 9611 (phone), +46 46 222 4623 (fax)
h b @ m a t h s . l t h . s e, http://www.maths.lth.se/bioinformatics/




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