[R] Too many open files

[Marilyn & Rich Short]

Hello,

I'm having a problem in R. I'm getting an error message that reads, "Too 
many open files". I'm opening files and closing them (and unlinking 
them), but when I go through that process 509 times, the program halts 
and I get this error message: "cannot open the connection" with warning 
messages: "Too many open files".  I've been working on this problem for 
a couple of weeks and have gleaned a bit of info from different internet 
threads, but no solutions yet.

I'm using Windows XP, SP3 and R 2.9.1.
Here is my session info:

> sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

(The problem also occurs on my Vista machine as well.)

There is some talk on the internet that some windows systems have a 
limit of 512 files that can be open at one time. Even though I'm closing 
my files each time, something is keeping track of how many times I've 
opened and closed a file in a session. I've talked to Microsoft and run 
a test program in Visual Studio C#, and, at the moment, it looks like 
the problem does not lie in the Microsoft arena. The C# program 
performed a similar task 10,000 times without a problem. I'm not totally 
convinced, but the current evidence says to look elsewhere.

I've attached a script that will induce the problem. However, be warned 
that, if you use it, you will have to get out of R after you run it. R 
will no longer be able to access files such as help or sessionInfo(). 
This can be solved by getting out of the R GUI and back in. Also, I'm 
using my pathname, "MyPathnameA", so you'll probably want to edit it 
with your own.

R E-mails from as far back as 2006 ask for help on the issue. There have 
been several suggestions, but no confirmed solution that I can find. You 
will see my attempt at these suggestions in the script [ 
rm(outMIA);rm(junk); and gc(); after close(outMIA); and 
unlink(FileNameMIA);]. For me, this becomes important because it limits 
the total number if iterations in nested do-loops. This is where I ran 
into the problem. The program below is a distillation from the original 
program.

Any suggestion would be greatly appreciated.

I'm a retired engineer and am picking up R to use on a genetic algorithm 
I want to play with.

Thanks for your attention,
Rich Short

# This script induces an error: "cannot open the connection" with

# warnings: "Too many open files".

?

# ---------------- Create a junk file and "save" it for use further into 
the program ---

junk                <- 1

MyPathnameA <- "C:\\Documents and Settings\\All 
Users\\Documents\\SIREPO\\DBFS-0150"

connectionX     <- paste(MyPathnameA,"junk",sep="\\")

outJunk           <- file(connectionX, open="wb")

save(junk, file=outJunk)

close(outJunk)






# The next two lines are a repeat from above. They will be useful if you 
want to run

# this script again after "junk" has been loaded.

MyPathnameA <- "C:\\Documents and Settings\\All 
Users\\Documents\\SIREPO\\DBFS-0150"

connectionX     <- paste(MyPathnameA,"junk",sep="\\")

FileNameMIA   <- connectionX

for(i in 1:4000){

   # ----------------- Load "junk" ---------------------------------

   outMIA <- file(FileNameMIA, open="rb")

   load(file=outMIA)                           # load a file

   # ----------------- close "junk"; unlink; remove; ----------------

   close(outMIA)                              # close the file

   unlink(FileNameMIA)                    # Unlink

   rm(outMIA)                          # This should be unnecessary. I 
tried it just to be sure the retention of the variable was

   rm(junk)                              # not causing the connection to 
be kept open.

   cat(" i = ",i,sep=" ")             # Show what iteration we are on.

   gc()                                    # Garbage collection. This 
should be unnecessary. Another failed attempt at a work-around.

   zzz <- showConnections(all=FALSE)

   cat(" zzz = ",zzz,"\n",sep=" ")  # This screen print shows that there 
are no open files

}

?