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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______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.