From james.holtman@convergys.com  Sat Dec 29 20:29:28 2001
From: james.holtman@convergys.com (james.holtman@convergys.com)
Date: Sat, 29 Dec 2001 21:29:28 +0100 (MET)
Subject: [Rd] Slow 'read.table' in R 1.4.0 (PR#1232)
Message-ID: <200112292029.VAA26005@pubhealth.ku.dk>

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
    }
    nlines <- length(lines)
    if (!nlines) {
        if (missing(col.names))
            stop("no lines available in input")
        else {
            tmp <- vector("list", length(col.names))
            names(tmp) <- col.names
            class(tmp) <- "data.frame"
            return(tmp)
        }
    }
    if (all(nchar(lines) == 0))
        stop("empty beginning of file")
    pushBack(c(lines, lines), file)

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[Rd] Slow 'read.table' in R 1.4.0 (PR#1232)
james.holtman@convergys.com