duplicate 'row.names' are not allowed error

This related question points out a part of the ?read.table documentation that explains your problem:

If there is a header and the first row contains one fewer field than the number of columns, the first column in the input is used for the row names. Otherwise if row.names is missing, the rows are numbered.

Your header row likely has 1 fewer column than the rest of the file and so read.table assumes that the first column is the row.names (which must all be unique), not a column (which can contain duplicated values). You can fix this by using one of the following two Solutions:

1. adding a delimiter (ie \t or ,) to the front or end of your header row in the source file, or,
2. removing any trailing delimiters in your data

The choice will depend on the structure of your data.

Example:
Here the header row is interpreted as having one fewer column than the data because the delimiters don't match:

v1,v2,v3   # 3 items!!
a1,a2,a3,  # 4 items
b1,b2,b3,  # 4 items

This is how it is interpreted by default:

   v1,v2,v3   # 3 items!!
a1,a2,a3,  # 4 items
b1,b2,b3,  # 4 items

The first column (with no header) values are interpreted as row.names: a1 and b1. If this column contains duplicates, which is entirely possible, then you get the duplicate 'row.names' are not allowed error.

If you set row.names = FALSE, the shift doesn't happen, but you still have a mismatching number of items in the header and in the data because the delimiters don't match.

Solution 1 Add trailing delimiter to header:

v1,v2,v3,  # 4 items!!
a1,a2,a3,  # 4 items
b1,b2,b3,  # 4 items

Solution 2 Remove excess trailing delimiter from non-header rows:

v1,v2,v3   # 3 items
a1,a2,a3   # 3 items!!
b1,b2,b3   # 3 items!!

Then tell read.table not to use row.names:

systems <- read.table("http://getfile.pl?test.csv", 
                      header=TRUE, sep=",", row.names=NULL)

and now your rows will simply be numbered.

Also look at read.csv which is a wrapper for read.table which already sets the sep=',' and header=TRUE arguments so that your call simplifies to

systems <- read.csv("http://getfile.pl?test.csv", row.names=NULL)

I had this error when opening a CSV file and one of the fields had commas embedded in it. The field had quotes around it, and I had cut and paste the read.table with quote="" in it. Once I took quote="" out, the default behavior of read.table took over and killed the problem. So I went from this:

systems <- read.table("http://getfile.pl?test.csv", header=TRUE, sep=",", quote="")

to this:

systems <- read.table("http://getfile.pl?test.csv", header=TRUE, sep=",")

In my case was a comma at the end of every line. By removing that worked