[R] Out of memory issue

[David Winsemius]

On Apr 24, 2009, at 10:40 PM, David Winsemius wrote:

>
> On Apr 24, 2009, at 9:06 PM, Neotropical bat risk assessments wrote:
>
>>
>>  Hi all,
>>  Julian just reminded me I need to include the lines of code so  
>> here it is
>>  below.
>>  I am trying to run some plots on data, but when loading the CSV  
>> data file it
>>  doss that but in ggplot R is stopping and I am getting an out of  
>> memory
>>  error.
>>>
>>> d <- read.csv batcalls.rda
>>  Error: unexpected symbol in "d <- read.csv batcalls.rda"
>
> If you really do have a data file called batcalls.rda, then the  
> proper way to get it into memory is with:
>
> load("C:/Rainey//batcalls.rda")  # replace path with the actual path  
> on your system and remember not to use "\"'s
# .. and don't  ^^ use // where only / is needed
>
>
>>
>>> attach(d)
>>  Error in attach(d) : object "d" not found
>
> Because of the error ... nothing got done.
>
>>
>>> library(ggplot2)
>>> print(qplot(Sc, Fc))
>>  Error in eval(expr, envir, enclos) : object "Sc" not found
>
> You cannot do anything on something that isn't there
>>
>>> data(batcalls)
>>>   attach(batcalls)
>>>   print(qplot(Fc,geom="density"))
>>>   b<-kmeans(Fc,c(10,15,18,30))
>>>  print(qplot(Sc,Fc,colour=as.factor(b$cluster)))
>>>
>>> print(qplot(Dur,geom="density"))
>>>   b<-kmeans(Dur,c(10,15,18,30))
>>>  print(qplot(Dur,Fc,colour=as.factor(b$cluster)))
>>>
>>> d <- read.csv ("C:/Rainey/RainyAllbats.csv")
>
> OK, that appears to have run without error, so it fits into memory.  
> Now you should run:
> str(d)   # and report the results
>
>>>
>>> attach(d)
>>         The following object(s) are masked from batcalls :
>>          Dc Dur Fc Fk Fmax Fmean Fmin Qk Qual S1 Sc st TBC Tc Tk
>>> library(ggplot2)
>>> print(qplot(Sc, Fc))
>>  Warning messages:
>>  1: In data.frame(..., check.names = FALSE) :
>>    Reached total allocation of 1535Mb: see help(memory.size)
>>  2: In data.frame(..., check.names = FALSE) :
>>    Reached total allocation of 1535Mb: see help(memory.size)
>>  3: Removed 1200249 rows containing missing values (geom_point).
>>> data(d)
>>  Warning message:
>>  In data(d) : data set 'd' not found
>>>   attach(d)
>>         The following object(s) are masked from d ( position 3 ) :
>>          Dc Dur Fc Filename Fk Fmax Fmean Fmin Qk Qual S1 Sc st TBC  
>> Tc Tk
>>         The following object(s) are masked from batcalls :
>>          Dc Dur Fc Fk Fmax Fmean Fmin Qk Qual S1 Sc st TBC Tc Tk
>>>   print(qplot(Fc,geom="density"))
>>  There were 15 warnings (use warnings() to see them)
>>>   b<-kmeans(Fc,c(10,15,18,30))
>>  Error in switch(nmeth, { : NA/NaN/Inf in foreign function call  
>> (arg 1)
>>> f=jpeg(file="Sc x Fc.jpg")
>>>  print(qplot(Sc,Fc,colour=as.factor(b$cluster)))
>>  Error in data.frame(colour = c(3L, 4L, 4L, 4L, 4L, 1L, 4L, 2L, 1L,  
>> 1L, :
>>    arguments imply differing number of rows: 9404, 2400489
>
> You seem to be ignoring all the informative error message.
>>
>>> dev.off()
>>  Anyway to tweak this somehow to get it to run?
>>  Using WinXP with 4 GB RAM
>
> WinXP in its default state can only use around 2.5GB and that may  
> require upping the memory limits:
> <http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-a-limit-on-the-memory-it-uses_0021 
> >
>
> And read the material in the links from that page as well.
>
> -- 
>
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>
> ______________________________________________
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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.

David Winsemius, MD
Heritage Laboratories
West Hartford, CT