Duplicate 'row.names' error reading table. row.names=NULL shifts columns

Question

This is similar to read.csv row.names and to https://stackoverflow.com/questions/12425599/duplicated-row-names , but I do not see answers that help.

Problem: Trying

Answer 1

My problem is associated with field separator for TAB-delimited file:

If I don't specify the field separator:

> condensed <- read.table("condense_report.tab", header=T)
 Error in read.table("condense_report.tab", header = T) : 
 duplicate 'row.names' are not allowed

If I add the sep=TAB

condensed <- read.table("condense_report.tab", header=TRUE, sep="\t")

Then there is no error message.

Here is my file's content (^I is the TAB character, and $ is the end of line mark):

Sample^Imethod^Ispecies^Imean_frac^Istd_frac^Imean_dep^Imean_clsz^Inumrep$ asterix_potion^Imothur^IEnterococcus faecalis^I0.32290000^I0.021755985650701942^I3293.5000^I3309.7500^I4$ asterix_potion^Imothur^IAcinetobacter baumannii^I0.28010000^I0.021539851624928375^I2869.5000^I2880.7500^I4$

The problem is with the species column. It has spaces, and R is using both space and tab as delimiters by default. So you have an extra column than the header according to R if no sep option is given. This is the root of the problem.