Reading large fixed format text file in r - r

Question

I am trying to input a large (> 70 MB) fixed format text file into r. For a smaller file (< 1MB), I can use the read.fwf() function as shown below.
condodattest1a <- read.fwf(impfile1,widths=testcsv3$Varlen,col.names=testcsv3$Varname)
When I try to run the line of code below,
condodattest1 <- read.fwf(impfile,widths=testcsv3$Varlen,col.names=testcsv3$Varname)
I get the following error message:
Error: cannot allocate vector of size 2 Kb
The only difference between the 2 lines is the size of the input file.
The formatting for the file I want to import is given in the dataframe called testcsv3. I show a small snippet of the dataframe below:
> head(testcsv3)
Varlen Varname Varclass Varsep Varforfmt
1 2 "V1" "character" 2 "A2.0"
2 15 "V2" "character" 17 "A15.0"
3 28 "V3" "character" 45 "A28.0"
4 3 "V4" "character" 48 "F3.0"
5 1 "V5" "character" 49 "A1.0"
6 3 "V6" "character" 52 "A3.0"
At least part of my problem is that I am reading in all the data as factors when I use read.fwf() and I end up exceeding the memory limit on my computer.
I tried to use read.table() as a way of formatting each variable but it seems I need a text delimiter with that function. There is a suggestion in section 3.3 in the link below that I could use sep to identify the column where every variable starts.
http://data.princeton.edu/R/readingData.html
However, when I use the command below:
condodattest1b <- read.table(impfile1,sep=testcsv3$Varsep,col.names=testcsv3$Varname, colClasses=testcsv3$Varclass)
I get the following error message:
Error in read.table(impfile1, sep = testcsv3$Varsep, col.names = testcsv3$Varname, : invalid 'sep' argument
Finally, I tried to use:
condodattest1c <- read.fortran(impfile1,lengths=testcsv3$Varlen, format=testcsv3$Varforfmt, col.names=testcsv3$Varname)
but I get the following message:
Error in processFormat(format) : missing lengths for some fields
In addition: Warning messages:
1: In processFormat(format) : NAs introduced by coercion
2: In processFormat(format) : NAs introduced by coercion
3: In processFormat(format) : NAs introduced by coercion
All I am trying to do at this point is format the data when they come into r as something other than factors. I am hoping this will limit the amount of memory I am using and allow me to actually input the file. I would appreciate any suggestions about how I can do this. I know the Fortran formats for all the variables and the column at which each variable begins.
Thank you,
Warren

Answer 1

Maybe this code works for you. You have to fill varlen with the field sizes and add the corresponding type strings (e.g. numeric, character, integer) to colclasses
my.readfwf <- function(filename,varlen,colclasses) {
sidx <- cumsum(c(1,varlen[1:(length(varlen)-1)]))
eidx <- sidx+varlen-1
filecontent <- scan(filename,character(0),sep="\n")
if (any(diff(nchar(filecontent))!=0))
stop("line lengths differ!")
nlines <- length(filecontent)
res <- list()
for (i in seq_along(varlen)) {
res[[i]] <- sapply(filecontent,substring,first=sidx[i],last=eidx[i])
mode(res[[i]]) <- colclasses[i]
}
attributes(res) <- list(names=paste("V",seq_along(res),sep=""),row.names=seq_along(res[[1]]),class="data.frame")
return(res)
}