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
[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. > > > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- > 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 > _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ >-- 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 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- 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 _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
hb@maths.lth.se
2002-Feb-28 19:16 UTC
[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. > > > > > > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- > > 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 > > _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ > > > > -- > 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 272595Thanks 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/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- 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 _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._