From this.is.mvw at gmail.com  Sat Jul 17 01:24:53 2010
From: this.is.mvw at gmail.com (Mike Williamson)
Date: Fri, 16 Jul 2010 16:24:53 -0700
Subject: [Rd] garbage collection & memory leaks in 'R', it seems...
Message-ID: <AANLkTikMqpyyCKq_6WXxG6F70zd2YsZQyjWZPxDFzIK4@mail.gmail.com>

Hello developers,

    I noticed that if I am running 'R', type "rm(list=objects())" and
"gc()", 'R' will still be consuming (a lot) more memory than when I then
close 'R' and re-open it.  In my ignorance, I'm presuming this is something
in 'R' where it doesn't really do a great job of garbage collection... at
least not nearly as well as Windows or unix can do garbage collection.
    Am I right?  If so, is there any better way to "clean up" the memory
that 'R' is using?  I have a script that runs a fairly large job, and I
cannot keep it going on its own in a convenient way because of these
remnants of garbage that pile up and eventually leave so little memory
remaining that the script crashes.

    I have attached a screen shot of the "system performance" screen on the
64-bit windows machine (with 64-bit 'R') that I am using.  I labeled
portions of it before closing 'R' and after re-opening it (loading up the
same saved image) to show the large difference in memory being consumed.
Below are the details of my version of 'R'.  Thanks for any help!!

                                Thanks,
                                        Mike


R version:  Win-64bit version, 2.11.1  (the machine I'm using has 20 GB of
memory, so that's my memory limit since it's 64 bit version)
packages:  see below...



             Package        Version
brew         "brew"         "1.0-3"
colorspace   "colorspace"   "1.0-1"
corpcor      "corpcor"      "1.5.6"
digest       "digest"       "0.4.2"
fdrtool      "fdrtool"      "1.2.6"
GeneCycle    "GeneCycle"    "1.1.1"
ggplot2      "ggplot2"      "0.8.7"
longitudinal "longitudinal" "1.1.5"
MASS         "MASS"         "7.3-6"
plyr         "plyr"         "0.1.9"
proto        "proto"        "0.3-8"
qvalue       "qvalue"       "1.22.0"
R.methodsS3  "R.methodsS3"  "1.2.0"
R.oo         "R.oo"         "1.7.3"
R.utils      "R.utils"      "1.4.3"
randomForest "randomForest" "4.5-35"
RColorBrewer "RColorBrewer" "1.0-2"
reshape      "reshape"      "0.8.3"
RODBC        "RODBC"        "1.3-1"
sos          "sos"          "1.3-0"
base         "base"         "2.11.1"
boot         "boot"         "1.2-42"
class        "class"        "7.3-2"
cluster      "cluster"      "1.12.3"
codetools    "codetools"    "0.2-2"
datasets     "datasets"     "2.11.1"
foreign      "foreign"      "0.8-40"
graphics     "graphics"     "2.11.1"
grDevices    "grDevices"    "2.11.1"
grid         "grid"         "2.11.1"
KernSmooth   "KernSmooth"   "2.23-3"
lattice      "lattice"      "0.18-8"
MASS         "MASS"         "7.3-6"
Matrix       "Matrix"       "0.999375-39"
methods      "methods"      "2.11.1"
mgcv         "mgcv"         "1.6-2"
nlme         "nlme"         "3.1-96"
nnet         "nnet"         "7.3-1"
rpart        "rpart"        "3.1-46"
spatial      "spatial"      "7.3-2"
splines      "splines"      "2.11.1"
stats        "stats"        "2.11.1"
stats4       "stats4"       "2.11.1"
survival     "survival"     "2.35-8"
tcltk        "tcltk"        "2.11.1"
tools        "tools"        "2.11.1"
utils        "utils"        "2.11.1"




"Telescopes and bathyscaphes and sonar probes of Scottish lakes,
Tacoma Narrows bridge collapse explained with abstract phase-space maps,
Some x-ray slides, a music score, Minard's Napoleanic war:
The most exciting frontier is charting what's already here."
  -- xkcd

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[Rd] garbage collection & memory leaks in 'R', it seems...
Mike Williamson