R help - Dec 2011 - ff object in lapply function

Hello. I'm using as.ffdf(mydataframe) to create ffdf objects inside an
lapply
loop and returning that. I then use crbind to combine the lapply results
into allData. 

So...simplified flow looks like this. 

res <- lapply(1:nchunks, function(n)
          {
                blah blah with nth chunk
                mydataframe <- data.frame(blah blah)
               dat <- as.ffdf(mydataframe)
               return(dat)
          })

allDat <- do.call('crbind',res)
              
> allDat
     virtual physical row.names
[1,] List,7  List,4   NULL
[2,] List,7  List,4   NULL
[3,] List,7  List,4   NULL
[4,] List,7  List,4   NULL
[5,] List,7  List,4   NULL
[6,] List,7  List,4   NULL
[7,] List,7  List,4   NULL
[8,] List,7  List,4   NULL
> is.ffdf(allDat)
[1] FALSE
>is.ffdf(allDat[1,])
[1] FALSE

I can access the physical data.  After accessing allDat with calls like
below within another function

ffDat <- allDat[1,]
nEvents <- length(ffDat$physical$position)
pos <- ffDat$physical$position[1:nEvents]

several times to retrieve information, I encounter segmentation faults which
forces me to abort out of R. I'm wondering what I should be doing to prevent
the segmentation faults.

Thanks for any advice!



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On 22.12.2011 07:56, khai wrote:
> Hello. I'm using as.ffdf(mydataframe) to create ffdf objects inside an
lapply
> loop and returning that. I then use crbind to combine the lapply results
> into allData.
>
> So...simplified flow looks like this.
>
> res<- lapply(1:nchunks, function(n)
>            {
>                  blah blah with nth chunk
>                  mydataframe<- data.frame(blah blah)
>                 dat<- as.ffdf(mydataframe)
>                 return(dat)
>            })
>
> allDat<- do.call('crbind',res)
>
>> allDat
>       virtual physical row.names
> [1,] List,7  List,4   NULL
> [2,] List,7  List,4   NULL
> [3,] List,7  List,4   NULL
> [4,] List,7  List,4   NULL
> [5,] List,7  List,4   NULL
> [6,] List,7  List,4   NULL
> [7,] List,7  List,4   NULL
> [8,] List,7  List,4   NULL
>
>> is.ffdf(allDat)
> [1] FALSE
>
>> is.ffdf(allDat[1,])
> [1] FALSE
>
> I can access the physical data.  After accessing allDat with calls like
> below within another function
>
> ffDat<- allDat[1,]
> nEvents<- length(ffDat$physical$position)
> pos<- ffDat$physical$position[1:nEvents]
>
> several times to retrieve information, I encounter segmentation faults
which
> forces me to abort out of R. I'm wondering what I should be doing to
prevent
> the segmentation faults.
Try to find a simple and for others reproducible example that reproduces 
the error / segfault. If it is related to a package like ff, report to 
its maintainer, if it is related to R, report to R-devel and if you are 
really (!) sure it is in R rather than in a contributed package, report 
to the bugtraking system.

Uwe Ligges


>
> Thanks for any advice!
>
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/ff-object-in-lapply-function-tp4224441p4224441.html
> Sent from the R help mailing list archive at Nabble.com.
>
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