R help - Feb 2011 - Weird error (special character) of read.table

Hi,

I have the following input file.
$ cat main.txt
CEL_A CELL_B
1 4
2 5
2 6

Then I run read.table in R.
> f=read.table('main.txt', header=T, check.names=F, sep='\t')
> head(f)
  \ufeffCEL_A CELL_B
1    1      4
2    2      5
3    2      6
> f$CEL_A
NULL

I'm not sure where the special character \ufeff comes from. Could anybody
let me know what is the problem?

Thanks,
John

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On 22/02/2011 10:43 AM, John Edwards wrote:
> Hi,
>
> I have the following input file.
> $ cat main.txt
> CEL_A CELL_B
> 1 4
> 2 5
> 2 6
>
> Then I run read.table in R.
>
> >  f=read.table('main.txt', header=T, check.names=F,
sep='\t')
> >  head(f)
>    \ufeffCEL_A CELL_B
> 1    1      4
> 2    2      5
> 3    2      6
> >  f$CEL_A
> NULL
>
> I'm not sure where the special character \ufeff comes from. Could
anybody
> let me know what is the problem?

The Unicode character "\uFEFF" is the "byte-order mark". 
This is
commonly used in Windows systems, not so commonly on others, which tend 
to get confused by it.  You didn't say what system you are working on 
and what encoding was used for the file; those are likely both important.

Duncan Murdoch

On Tue, Feb 22, 2011 at 7:43 AM, John Edwards <jhnedwards603 at gmail.com>
wrote:
> Hi,
>
> I have the following input file.
> $ cat main.txt
> CEL_A CELL_B
> 1 4
> 2 5
> 2 6
>
> Then I run read.table in R.
>
>> f=read.table('main.txt', header=T, check.names=F,
sep='\t')
>> head(f)
> ?\ufeffCEL_A CELL_B
> 1 ? ?1 ? ? ?4
> 2 ? ?2 ? ? ?5
> 3 ? ?2 ? ? ?6
>> f$CEL_A
> NULL
>
> I'm not sure where the special character \ufeff comes from. Could
anybody
> let me know what is the problem?
Looks like the Unicode character called 'byte order mark' (BOM), cf.

  http://en.wikipedia.org/wiki/Byte_order_mark

It looks like your 'main.txt' text file was created by a software that
saves it as a Unicode-encoded text file.  If you need a plain
old-style ASCII text file, see if you can resave it as such.  With
last year's development in R, it also not unlikely that you can tell R
to read in the existing file by specifying the encoding, but since I
don't now how to do that I leave that as an search-the-help exercise
for you.

/Henrik
>
> Thanks,
> John
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

What you describe could be a bug (in which case providing your OS and R version
info per the posting guidelines would be a minimum requirement to get it fixed)
or a control character that is actually in your file (which you might need a
binary editor to see).
---------------------------------------------------------------------------
Jeff Newmiller The ..... ..... Go Live...
DCN:<jdnewmil@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/Batteries O.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---------------------------------------------------------------------------
Sent from my phone. Please excuse my brevity.

John Edwards <jhnedwards603@gmail.com> wrote:

Hi, I have the following input file. $ cat main.txt CEL_A CELL_B 1 4 2 5 2 6
Then I run read.table in R. > f=read.table('main.txt', header=T,
check.names=F, sep='\t') > head(f) \ufeffCEL_A CELL_B 1 1 4 2 2 5 3 2
6 > f$CEL_A NULL I'm not sure where the special character \ufeff comes
from. Could anybody let me know what is the problem? Thanks, John 	[[alternative
HTML version deleted]]_____________________________________________
R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and
provide commented, minimal, self-contained, reproducible code.


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