[R] Problem With Repeated Use Of Load/Save/Close Commands

[Marilyn & Rich Short]

Duncan,

Thank you very much for your help. Your first work-around solved my 
problem, even if the second one didn't. I'm not sure if it was the 
elimination of the file() or the close() commands, or both,  that did 
it.

You got me going again after a couple of weeks of casting about. My hat 
is off to you!

Thanks,
Rich


----- Original Message ----- 
From: "Duncan Murdoch" <murdoch at stats.uwo.ca>
To: "Marilyn & Rich Short" <rm.short at comcast.net>
Cc: <r-help at r-project.org>
Sent: Saturday, July 18, 2009 8:21 AM
Subject: Re: [R] Problem With Repeated Use Of Load/Save/Close Commands


> On 18/07/2009 11:08 AM, Duncan Murdoch wrote:
>> On 17/07/2009 7:57 PM, Marilyn & Rich Short wrote:
>>> Hello,
>>>
>>> I'm having a problem in R with repeated use of the "load", "save", 
>>> and "close" commands. 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:
>>>
>>> R version 2.9.1 (2009-06-26)
>>> i286-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
>>>
>>> I'm using the vanilla load of R, with nothing added after booting 
>>> up.
>>> The problem also occurs on my Vista machine as well.
>>>
>>> The program below will induce the problem.
>>> ------------------------------------------------------------
>>>    junk       = 1
>>>    PathA    = tempdir()
>>>    conX     = paste(PathA,"junk",sep="\\")
>>>    outJunk  = file(conX, open="wb")
>>>    save(junk, file=outJunk)
>>>    close(outJunk)
>>>    for(i in 1:4000){
>>>        outMIA = file(conX, open="rb")
>>>        load(file=outMIA)
>>>        close(outMIA)
>>>        closeAllConnections()
>>>        unlink(conX)
>>>        rm(outMIA)
>>>        rm(junk)
>>>        cat(" i = ",i,sep=" ")
>>>        gc()
>>>        zzz = showConnections(all=FALSE)
>>>        cat(" zzz = ",zzz,"\n",sep=" ")
>>>    }
>>> --------------------------------------------------------------------
>>> 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.
>>>
>>> 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); closeAllConnections(); and gc(); after 
>>> close(outMIA);  and unlink(conX);]. 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 above will allow 
>>> you to reproduce the problem.
>>>
>>> Any suggestion would be greatly appreciated.
>>
>> I've somewhat localized the problem.  load(file=outMIA) passes the 
>> outMIA connection to gzcon(), which handles decompression of the 
>> data. gzcon() re-opens the file, and it looks as though the original 
>> file handle is lost, because closing either the result of gzcon() or 
>> the original connection results in only the second file handle being 
>> closed.
>>
>> So a second workaround besides the one I sent earlier is just not to 
>> open or close outMIA.  That is, rewrite it as
>>
>>     junk       = 1
>>     PathA    = tempdir()
>>     conX     = paste(PathA,"junk",sep="\\")
>>     outJunk  = file(conX, open="wb")
>>     save(junk, file=outJunk)
>>     close(outJunk)
>>     for(i in 1:4000){
>>         outMIA = file(conX)
>>         load(file=outMIA)
>>         rm(outMIA)
>>         rm(junk)
>>         cat(" i = ",i,sep=" ")
>>         gc()
>>         zzz = showConnections(all=FALSE)
>>         cat(" zzz = ",zzz,"\n",sep=" ")
>>     }
>>
>> so that load() does the open and close, and things are fine.
>
> Oops, not quite fine.  There's a whole set of warnings...
>
> Duncan Murdoch