Summary: [R] read.table on Mac OS X, CARBON vs. DARWIN

Thanks a lot, James!!
The problem is fixed. On the version 1.4.0 Mac/darwin (the latest 
available version for this system) the function read.table (which is 
called from read.delim etc., too) has the bug you explained.

Inserting the row
	nlines <- nlines+1
after
	 lines <- c(lines, line)
removes this bug.
M.


On Friday, February 22, 2002, at 02:33  PM, james.holtman at convergys.com 
wrote:

If you can not the the latest 1.4.1, here is a patch (adds one line to
read.table) that will fix it on your current system.

The 'read.table' function appears to be up to 10X slower in R 1.4.0 
than

R

1.3.1 for some of the data sets I read in.  I was comparing the source

code

for the 2 versions and see that it was rewritten in R 1.4.0.

I think I found out what part of the problem might be.  I was 
comparing
R1.3.1 and R1.4.0 code and it appears that a statement is missing in 
some
of the code for R 1.4.  This is the section of code at the beginning 
of
read.table.  The loop starting with 'while (nlines < 5)' will read in 
the
entire file, because there is no increment of 'nlines' in the loop.  I
traced through the code  and this is what was happening.  It then 
does a
'pushBack' of the entire file.  In tracing through the code, this is

where

is appears to be taking the time.  With the change noted below, the 
speed
was similar to R 1.3.1 and the results were the same.

Here is the current code with what I think is the additional statement
needed:

=================part of read.table========

    nlines <- 0
    lines <- NULL
    while (nlines < 5) {
        line <- readLines(file, 1, ok = TRUE)
        if (length(line) == 0)
            break
        if (blank.lines.skip && length(grep("^[ \\t]*$", line)))
            next
        if (length(comment.char) && nchar(comment.char)) {
            pattern <- paste("^[ \\t]*", substring(comment.char,
                1, 1), sep = "")
            if (length(grep(pattern, line)))
                next
        }
        lines <- c(lines, line)
       #
       #  additional line required
       #
       nlines <- nlines+1
    }

--

Meinhard Ploner <meinhardploner at gmx.net> on 02/22/2002 03:17:34

To:   james.holtman at convergys.com
cc:
Subject:  Re: [R] read.table on Mac OS X, CARBON vs. DARWIN


Yes. Thanks a lot.
I had the 1.4.0 because on Fink the latest version (1.4.1) is not
available. However, I will download it from the CRAN.
Meinhard


On Thursday, February 21, 2002, at 10:29  PM,
james.holtman at convergys.com wrote:

read.table did have a bug in it in 1.4.0.  It was fixed in 1.4.1.  Is
that
what you are running with?

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