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david.reitter at gmail.com

2008-Jan-20 16:55 UTC

[Rd] read.table: wrong error message? (PR#10592)

--Apple-Mail-44--797532055
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I believe read.table may report misleading errors. In this example,  
where a header line in a file has an incorrect number of row names (28  
instead of 29), I get the error message "duplicate row.names are not  
allowed".

However, I cannot not find any duplicate row names. Fixing the header  
line by adding an extra row name, however, avoids the error.

The behavior is confusing - I would expect a different error message,  
even if I should have quoted some row names.

I am attaching a sample file that reproduces the problem with R -- 
vanilla, and then: read.table("m2").  I get it in 2.5.1 and 2.6.0.

PS.:

R version 2.6.0 (2007-10-03)
...
 > x <- read.table("m2", header=T)
Error in read.table("m2", header = T) :
   duplicate 'row.names' are not allowed
 > traceback()
2: stop("duplicate 'row.names' are not allowed")
1: read.table("m2", header = T)
 >

  
--Apple-Mail-44--797532055
Content-Disposition: attachment;
	filename=m2
Content-Type: application/octet-stream;
	x-unix-mode=0644;
	name="m2"
Content-Transfer-Encoding: 7bit

primed rule role dist starttime target.utt rule.freq primeperiod.length
dialogue.length dialogue.id words.repeated words.repeated.prop head.repeated
head.freq head.pos prime.gaze target.gaze eyecontact familiar convseq length
doc.score friend task.familiar same.specrule derivation pathlen distituent
0 vp---vbg-vp i 2 5.67 4 False 172 70 261.5322 1 0 0/7 True na None None None 1
0 1 7 135 - - 1 None - -
0 vp---to-vp r 1 6.03 4 False 758 13 261.5322 1 0 0/6 True na None None None 1 0
1 6 135 - - 1 None - -
0 vp---to-vp i 2 6.03 4 False 758 70 261.5322 1 0 0/6 True na None None None 1 0
1 6 135 - - 1 None - -
0 s---cc-s i 1 11.3 5 False 813 83 261.5322 1 0 2/9 True na None None None 1 0 1
9 135 - - 1 None - -
0 s---cc-s i 3 11.3 5 False 813 70 261.5322 1 0 0/9 True na None None None 1 0 1
9 135 - - 1 None - -
0 s---advp-s i 3 12.71 5 False 440 70 261.5322 1 0 0/8 True na None None None 1
0 1 8 135 - - 1 None - -
1 vp---ber-vp i 1 12.98 5 False 406 83 261.5322 1 0 2/7 True na None None None 1
0 1 7 135 - - 1 None - -
1 vp---vbg-vp i 1 13.11 5 False 172 83 261.5322 1 0 3/7 True na None None None 1
0 1 7 135 - - 1 None - -
1 vp---to-vp i 1 13.52 5 False 758 83 261.5322 1 0 2/6 True na None None None 1
0 1 6 135 - - 1 None - -
1 pp---ql-rp-pp i 1 14.12 5 False 282 83 261.5322 1 0 0/3 True na None None None
1 0 1 3 135 - - 1 None - -
0 pp---ql-rp-pp r 2 14.12 5 False 282 13 261.5322 1 0 0/3 True na None None None
1 0 1 3 135 - - 1 None - -
0 ap---ap r 2 18.75 5 False 120 13 261.5322 1 0 0/1 True na None None None 1 0 1
1 135 - - 1 None - -
0 pp---pp-pp i 3 22.7 6 False 429 13 261.5322 1 0 0/4 True na None None None 1 0
1 4 135 - - 1 None - -
1 pp---ql-rp r 2 22.7 6 False 505 83 261.5322 1 0 1/2 True na None None None 1 0
1 2 135 - - 1 None - -
0 pp---rp-pp r 2 23.54 6 False 1124 83 261.5322 1 0 0/2 True na None None None 1
0 1 2 135 - - 1 None - -
0 pp---pp-cc-rb-pp i 2 25.27 7 False 64 200 261.5322 1 0 1/6 True na None None
None 1 0 1 6 135 - - 1 None - -
0 pp---pp-cc-rb-pp r 4 25.27 7 False 64 13 261.5322 1 0 0/6 True na None None
None 1 0 1 6 135 - - 1 None - -
1 pp---ql-rp-pp i 2 25.99 7 False 282 200 261.5322 1 0 2/3 True na None None
None 1 0 1 3 135 - - 1 None - -
1 pp---ql-rp-pp i 3 25.99 7 False 282 83 261.5322 1 0 0/3 True na None None None
1 0 1 3 135 - - 1 None - -

--Apple-Mail-44--797532055--

Peter Dalgaard

2008-Jan-21 11:34 UTC

head link

[Rd] read.table: wrong error message? (PR#10592)

david.reitter at gmail.com wrote:> --Apple-Mail-44--797532055
> Content-Type: text/plain;
> 	charset=US-ASCII;
> 	format=flowed;
> 	delsp=yes
> Content-Transfer-Encoding: 7bit
>
> I believe read.table may report misleading errors. In this example,  
> where a header line in a file has an incorrect number of row names (28  
> instead of 29), I get the error message "duplicate row.names are not  
> allowed".
>
> However, I cannot not find any duplicate row names. Fixing the header  
> line by adding an extra row name, however, avoids the error.
>
> The behavior is confusing - I would expect a different error message,  
> even if I should have quoted some row names.
>   Arguably, read.table() is too smart for its own good at times, but this
_is_ documented behaviour:


     If 'row.names' is not specified and the header line has one less
     entry than the number of columns, the first column is taken to be
     the row names.  This allows data frames to be read in from the
     format in which they are printed.  If 'row.names' is specified and
     does not refer to the first column, that column is discarded from
     such files.

So, if your COLUMN (sic!) name count is off by one, read.table() takes
the first variable as row.names, and when this is a 0/1 variable, you
will have duplicate names.
> I am attaching a sample file that reproduces the problem with R -- 
> vanilla, and then: read.table("m2").  I get it in 2.5.1 and
2.6.0.
>
> PS.:
>
> R version 2.6.0 (2007-10-03)
> ...
>  > x <- read.table("m2", header=T)
> Error in read.table("m2", header = T) :
>    duplicate 'row.names' are not allowed
>  > traceback()
> 2: stop("duplicate 'row.names' are not allowed")
> 1: read.table("m2", header = T)
>  >
>
>   
> --Apple-Mail-44--797532055
> Content-Disposition: attachment;
> 	filename=m2
> Content-Type: application/octet-stream;
> 	x-unix-mode=0644;
> 	name="m2"
> Content-Transfer-Encoding: 7bit
>
> primed rule role dist starttime target.utt rule.freq primeperiod.length
dialogue.length dialogue.id words.repeated words.repeated.prop head.repeated
head.freq head.pos prime.gaze target.gaze eyecontact familiar convseq length
doc.score friend task.familiar same.specrule derivation pathlen distituent
> 0 vp---vbg-vp i 2 5.67 4 False 172 70 261.5322 1 0 0/7 True na None None
None 1 0 1 7 135 - - 1 None - -
> 0 vp---to-vp r 1 6.03 4 False 758 13 261.5322 1 0 0/6 True na None None
None 1 0 1 6 135 - - 1 None - -
> 0 vp---to-vp i 2 6.03 4 False 758 70 261.5322 1 0 0/6 True na None None
None 1 0 1 6 135 - - 1 None - -
> 0 s---cc-s i 1 11.3 5 False 813 83 261.5322 1 0 2/9 True na None None None
1 0 1 9 135 - - 1 None - -
> 0 s---cc-s i 3 11.3 5 False 813 70 261.5322 1 0 0/9 True na None None None
1 0 1 9 135 - - 1 None - -
> 0 s---advp-s i 3 12.71 5 False 440 70 261.5322 1 0 0/8 True na None None
None 1 0 1 8 135 - - 1 None - -
> 1 vp---ber-vp i 1 12.98 5 False 406 83 261.5322 1 0 2/7 True na None None
None 1 0 1 7 135 - - 1 None - -
> 1 vp---vbg-vp i 1 13.11 5 False 172 83 261.5322 1 0 3/7 True na None None
None 1 0 1 7 135 - - 1 None - -
> 1 vp---to-vp i 1 13.52 5 False 758 83 261.5322 1 0 2/6 True na None None
None 1 0 1 6 135 - - 1 None - -
> 1 pp---ql-rp-pp i 1 14.12 5 False 282 83 261.5322 1 0 0/3 True na None None
None 1 0 1 3 135 - - 1 None - -
> 0 pp---ql-rp-pp r 2 14.12 5 False 282 13 261.5322 1 0 0/3 True na None None
None 1 0 1 3 135 - - 1 None - -
> 0 ap---ap r 2 18.75 5 False 120 13 261.5322 1 0 0/1 True na None None None
1 0 1 1 135 - - 1 None - -
> 0 pp---pp-pp i 3 22.7 6 False 429 13 261.5322 1 0 0/4 True na None None
None 1 0 1 4 135 - - 1 None - -
> 1 pp---ql-rp r 2 22.7 6 False 505 83 261.5322 1 0 1/2 True na None None
None 1 0 1 2 135 - - 1 None - -
> 0 pp---rp-pp r 2 23.54 6 False 1124 83 261.5322 1 0 0/2 True na None None
None 1 0 1 2 135 - - 1 None - -
> 0 pp---pp-cc-rb-pp i 2 25.27 7 False 64 200 261.5322 1 0 1/6 True na None
None None 1 0 1 6 135 - - 1 None - -
> 0 pp---pp-cc-rb-pp r 4 25.27 7 False 64 13 261.5322 1 0 0/6 True na None
None None 1 0 1 6 135 - - 1 None - -
> 1 pp---ql-rp-pp i 2 25.99 7 False 282 200 261.5322 1 0 2/3 True na None
None None 1 0 1 3 135 - - 1 None - -
> 1 pp---ql-rp-pp i 3 25.99 7 False 282 83 261.5322 1 0 0/3 True na None None
None 1 0 1 3 135 - - 1 None - -
>
> --Apple-Mail-44--797532055--
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>   

-- 
   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

ripley at stats.ox.ac.uk

2008-Jan-21 11:40 UTC

head link

[Rd] read.table: wrong error message? (PR#10592)

On Sun, 20 Jan 2008, david.reitter at gmail.com wrote:
>
> --Apple-Mail-44--797532055
> Content-Type: text/plain;
> 	charset=US-ASCII;
> 	format=flowed;
> 	delsp=yes
> Content-Transfer-Encoding: 7bit
>
> I believe read.table may report misleading errors. In this example,
> where a header line in a file has an incorrect number of row names (28
> instead of 29), I get the error message "duplicate row.names are not
> allowed".
The first column of your file repeats 0 and 1, and your specification 
asked for the first column to be taken as the row names: from the help 
file

      If 'row.names' is not specified and the header line has one less
      entry than the number of columns, the first column is taken to be
      the row names.
> However, I cannot not find any duplicate row names. Fixing the header
> line by adding an extra row name, however, avoids the error.
An extra *column* name?  The behaviour of header=TRUE depends on the 
number of fields on the header line: see the quote above.
> The behavior is confusing - I would expect a different error message,
> even if I should have quoted some row names.
It may have confused you, but it has been in R/S for 20 years and is 
described in the help, the 'R Data Import/Export Manual', most books on 
R/S ....

It is fortunate that you did get an error message: if you give an input 
format different from what you intended it can easily be valid but not 
that you intended.

If you want to be safer, supply the argument 'row.names'.
> I am attaching a sample file that reproduces the problem with R --
> vanilla, and then: read.table("m2").  I get it in 2.5.1 and
2.6.0.
Also 2.6,1 and R-devel, as it is the documented behaviour.
>
> PS.:
>
> R version 2.6.0 (2007-10-03)
> ...
> > x <- read.table("m2", header=T)
> Error in read.table("m2", header = T) :
>   duplicate 'row.names' are not allowed
> > traceback()
> 2: stop("duplicate 'row.names' are not allowed")
> 1: read.table("m2", header = T)
> >
>
>
> --Apple-Mail-44--797532055
> Content-Disposition: attachment;
> 	filename=m2
> Content-Type: application/octet-stream;
> 	x-unix-mode=0644;
> 	name="m2"
> Content-Transfer-Encoding: 7bit
>
> primed rule role dist starttime target.utt rule.freq primeperiod.length
dialogue.length dialogue.id words.repeated words.repeated.prop head.repeated
head.freq head.pos prime.gaze target.gaze eyecontact familiar convseq length
doc.score friend task.familiar same.specrule derivation pathlen distituent
> 0 vp---vbg-vp i 2 5.67 4 False 172 70 261.5322 1 0 0/7 True na None None
None 1 0 1 7 135 - - 1 None - -
> 0 vp---to-vp r 1 6.03 4 False 758 13 261.5322 1 0 0/6 True na None None
None 1 0 1 6 135 - - 1 None - -
> 0 vp---to-vp i 2 6.03 4 False 758 70 261.5322 1 0 0/6 True na None None
None 1 0 1 6 135 - - 1 None - -
> 0 s---cc-s i 1 11.3 5 False 813 83 261.5322 1 0 2/9 True na None None None
1 0 1 9 135 - - 1 None - -
> 0 s---cc-s i 3 11.3 5 False 813 70 261.5322 1 0 0/9 True na None None None
1 0 1 9 135 - - 1 None - -
> 0 s---advp-s i 3 12.71 5 False 440 70 261.5322 1 0 0/8 True na None None
None 1 0 1 8 135 - - 1 None - -
> 1 vp---ber-vp i 1 12.98 5 False 406 83 261.5322 1 0 2/7 True na None None
None 1 0 1 7 135 - - 1 None - -
> 1 vp---vbg-vp i 1 13.11 5 False 172 83 261.5322 1 0 3/7 True na None None
None 1 0 1 7 135 - - 1 None - -
> 1 vp---to-vp i 1 13.52 5 False 758 83 261.5322 1 0 2/6 True na None None
None 1 0 1 6 135 - - 1 None - -
> 1 pp---ql-rp-pp i 1 14.12 5 False 282 83 261.5322 1 0 0/3 True na None None
None 1 0 1 3 135 - - 1 None - -
> 0 pp---ql-rp-pp r 2 14.12 5 False 282 13 261.5322 1 0 0/3 True na None None
None 1 0 1 3 135 - - 1 None - -
> 0 ap---ap r 2 18.75 5 False 120 13 261.5322 1 0 0/1 True na None None None
1 0 1 1 135 - - 1 None - -
> 0 pp---pp-pp i 3 22.7 6 False 429 13 261.5322 1 0 0/4 True na None None
None 1 0 1 4 135 - - 1 None - -
> 1 pp---ql-rp r 2 22.7 6 False 505 83 261.5322 1 0 1/2 True na None None
None 1 0 1 2 135 - - 1 None - -
> 0 pp---rp-pp r 2 23.54 6 False 1124 83 261.5322 1 0 0/2 True na None None
None 1 0 1 2 135 - - 1 None - -
> 0 pp---pp-cc-rb-pp i 2 25.27 7 False 64 200 261.5322 1 0 1/6 True na None
None None 1 0 1 6 135 - - 1 None - -
> 0 pp---pp-cc-rb-pp r 4 25.27 7 False 64 13 261.5322 1 0 0/6 True na None
None None 1 0 1 6 135 - - 1 None - -
> 1 pp---ql-rp-pp i 2 25.99 7 False 282 200 261.5322 1 0 2/3 True na None
None None 1 0 1 3 135 - - 1 None - -
> 1 pp---ql-rp-pp i 3 25.99 7 False 282 83 261.5322 1 0 0/3 True na None None
None 1 0 1 3 135 - - 1 None - -
>
> --Apple-Mail-44--797532055--
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

david.reitter at gmail.com

2008-Jan-21 11:55 UTC

head link

[Rd] read.table: wrong error message? (PR#10592)

--Apple-Mail-1--729254567
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	charset=US-ASCII;
	format=flowed;
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On 21 Jan 2008, at 11:38, Prof Brian Ripley wrote:>
> The first column of your file repeats 0 and 1, and your  
> specification asked for the first column to be taken as the row  
> names: from the help file
>
>     If 'row.names' is not specified and the header line has one
less
>     entry than the number of columns, the first column is taken to be
>     the row names.
I understand now. Thanks for the explanation.

I would have figured it out myself had I paid attention to the fact  
that the error message reports "row names" rather than "column
names",
or had the error message actually contained the conflicting names  
(either "0" or "1") or the full set of read names.

--
David Reitter
ICCS/HCRC, Informatics, University of Edinburgh
http://www.david-reitter.com





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--Apple-Mail-1--729254567--

Prof Brian Ripley

2008-Jan-21 14:16 UTC

head link

[Rd] read.table: wrong error message? (PR#10592)

On Mon, 21 Jan 2008, David Reitter wrote:
> On 21 Jan 2008, at 11:38, Prof Brian Ripley wrote:
>> 
>> The first column of your file repeats 0 and 1, and your specification
asked
>> for the first column to be taken as the row names: from the help file
>>
>>    If 'row.names' is not specified and the header line has one
less
>>    entry than the number of columns, the first column is taken to be
>>    the row names.
>
> I understand now. Thanks for the explanation.
>
> I would have figured it out myself had I paid attention to the fact that
the
> error message reports "row names" rather than "column
names", or had the
> error message actually contained the conflicting names (either
"0" or "1") or
> the full set of read names.
We can fairly easily do something along those lines: I've added code to 
R-devel to do
> library(MASS)
> row.names(hills)[35] <- "Lomonds"Error in `row.names<-.data.frame`(`*tmp*`, value = c("Greenmantle",
"Carnethy",  :
   duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique value when setting 'row.names': ?Lomonds?

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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