[R] Memory leak in system() command?

[Rob Steele]

You're quite right; the problem lies in an SQL query ("LOAD DATA INFILE").

Thanks!


On 9/7/2010 6:50 AM, Duncan Murdoch wrote:
> Rob Steele wrote:
>> I run an external program a few hundred times via
>>
>> status <- system(command = "blah blah blah")
>>
>> and pretty soon Linux thinks R is using tons of memory.  R doesn't think
>> so, at least not according to gc().  I'm also opening, reading and
>> closing files but I don't think that's where the problem lies.
>> Eventually the system command fails with a status of -1 and a message
>> like:
>>
>> cannot popen 'blah blah blah', probable reason 'Cannot allocate memory'
>>   
> 
> I think you need to put together a reproducible example.  When I try
> 
> repeat {
>  system(command = "echo hello")
> }
> 
> It just goes on printing hello over and over again, without growing the
> allocation.  This is on MacOSX, so your problem might be a Redhat thing,
> but just as likely it's something specific about your loop.
> 
> Duncan Murdoch
>> Any ideas?
>> Thanks!
>>
>>  
>>> R.Version()
>>>     
>> $platform
>> [1] "x86_64-redhat-linux-gnu"
>>
>> $arch
>> [1] "x86_64"
>>
>> $os
>> [1] "linux-gnu"
>>
>> $system
>> [1] "x86_64, linux-gnu"
>>
>> $status
>> [1] ""
>>
>> $major
>> [1] "2"
>>
>> $minor
>> [1] "11.1"
>>
>> $year
>> [1] "2010"
>>
>> $month
>> [1] "05"
>>
>> $day
>> [1] "31"
>>
>> $`svn rev`
>> [1] "52157"
>>
>> $language
>> [1] "R"
>>
>> $version.string
>> [1] "R version 2.11.1 (2010-05-31)"
>>
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>> and provide commented, minimal, self-contained, reproducible code.
>>
>