[R] Memory issues in R

Neotropical bat risk assessments neotropical.bats at gmail.com
Sun Apr 26 17:20:12 CEST 2009


   How do people deal with R and memory issues?
   I have tried using gc() to see how much memory is used at each step.
   Scanned Crawley R-Book and all other R books I have available and the FAQ
   on-line but no help really found.
   Running WinXP Pro (32 bit) with 4 GB RAM.
   One SATA drive pair is in RAID 0 configuration with 10000 MB allocated as
   virtual memory.
   I do have another machine set up with Ubuntu but it only has 2 GB RAM and
   have not been able to get R installed on that system.
   I can run smaller sample data sets w/o problems and everything plots as
   needed.
   However I need to review large data sets.
   Using latest R version 2.9.0 (2009-04-17)
   My  data is in CSV format with a header row and is a big data set with
   1,200,240 rows!
   E.g. below:
   Dur,TBC,Fmax,Fmin,Fmean,Fc,S1,Sc,
   9.81,0,28.78,24.54,26.49,25.81,48.84,14.78,
   4.79,1838.47,37.21,29.41,31.76,29.52,241.77,62.83,
   4.21,5.42,28.99,26.23,27.53,27.4,76.03,11.44,
   10.69,193.48,30.53,25.4,27.69,25.4,-208.19,26.05,
   15.5,248.18,30.77,24.32,26.57,24.92,-202.76,18.64,
   14.85,217.47,31.25,24.62,26.93,25.56,-88.4,10.32,
   11.86,158.01,33.61,25.24,27.66,25.32,83.32,17.62,
   14.05,229.74,30.65,24.24,26.76,25.24,61.87,14.06,
   8.71,264.02,31.01,25.72,27.56,25.72,253.18,19.2,
   3.91,10.3,25.32,24.02,24.55,24.02,-71.67,16.83,
   16.11,242.21,29.85,24.02,26.07,24.62,79.45,19.11,
   16.81,246.48,28.57,23.05,25.46,23.81,-179.82,15.95,
   16.93,255.09,28.78,23.19,25.75,24.1,-112.21,16.38,
   5.12,107.16,32,29.41,30.46,29.41,134.45,20.88,
   16.7,150.49,27.97,22.92,24.91,23.95,42.96,16.81
   .... etc
   I am getting the following warning/error message:
   Error: cannot allocate vector of size 228.9 Mb
   Complete listing from R console below:
   > library(batcalls)
   Loading required package: ggplot2
   Loading required package: proto
   Loading required package: grid
   Loading required package: reshape
   Loading required package: plyr
   Attaching package: 'ggplot2'
           The following object(s) are masked from package:grid :
            nullGrob
   > gc()
            used (Mb) gc trigger (Mb) max used (Mb)
   Ncells 186251  5.0     407500 10.9   350000  9.4
   Vcells  98245  0.8     786432  6.0   358194  2.8
   > BR <- read.csv ("C:/R-Stats/Bat calls/Reduced bats.csv")
   > gc()
             used (Mb) gc trigger  (Mb) max used  (Mb)
   Ncells  188034  5.1     667722  17.9   378266  10.2
   Vcells 9733249 74.3   20547202 156.8 20535538 156.7
   > attach(BR)
   > library(ggplot2)
   > library(MASS)
   > library(batcalls)
   > BRC<-kde2d(Sc,Fc)
   Error: cannot allocate vector of size 228.9 Mb
   > gc()
              used  (Mb) gc trigger  (Mb)  max used  (Mb)
   Ncells   198547   5.4     667722  17.9    378266  10.2
   Vcells 19339695 147.6  106768803 814.6 124960863 953.4
   >
   Tnx for any insight,
   Bruce



More information about the R-help mailing list