read.delim() - errors “more columns than column names” and “header and ''col.names” are of different lengths"

Question

Preliminary information OS: Windows XP Professional Version 2002 Service Pack 3; R version: R 2.12.2 (2011-02-25)

I am attempting to read a 30,000 row by 80 column, tab-delimited text file into R using the read.delim() function. This file does have column headers with following naming convention: "_". The code that I use to attempt to read the data in is:

cc <- c("integer", "character", "integer", rep("character", 3), 
        rep("integer", 73))

example_data <- read.delim(file = 'C:/example.txt', row.names = FALSE,
                           col.names = TRUE, as.is = TRUE, colClasses = cc)

After I submit this command, I receive the following error message:

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
more columns than column names
In addition: Warning message:
In read.table(file = file, header = header, sep = sep, quote = quote,  :
  header and 'col.names' are of different lengths

Information that may be important - from column 8 until column 80 the count of zeros in each column is as follows:

column 08: 29,000 zeros
column 13: 15,000 zeros
column 19: 500 zeros
column 43: 15,000 zeros
columns 65-80: 29,000 zeros for each column

Can anyone help identify reasons that I am receiving the above error messages? Any help will be greatly appreciated.

Answer 1

The cause of the problem is your use of the col.names=TRUE argument. This is supposed to be used manually to specify column names for the resulting data frame, and therefore must be a vector with the same length as there are columns in the input, one name per column.

f you want read.delim to take column names from the file, consider using header=TRUE; you may also wish to reconsider row.names=TRUE as again this is intended as a specification of the row names rather than an instruction to read them from the file.

More information is available on the help page for read.delim.

Answer 2

I also recently had the same error and it disappeared after converting the file to comma or semicolon delimited and read it with read.csv / read.csv2. I know this is not a fullfillig answer but maybe you might check that out.

Answer 3

If you want to read as character matrix then first convert your file into .csv format and use read.csv. Don't use any other declaration other than file name. e.g.;

read.csv("filepath")