R help - Jan 2002 - problem with read.table -- example

Hi,

I have not get much response for my question about read.table for couple of
days ago.  As I said, the problem is that read.delim() do not want to read
more than 51 lines of data, with longer file it reads the first column as
row names, although I have not noticed any special binary symbols around
line 51 either.  This problem seems to happen with this particular file, I
could easily read in a 12000 rows x 22 cols table.

I add my problematic file (it is really small) here, in a uuencoded gziped
form.  What I did was:
> a <- read.delim("tab20.and")
Error in "row.names<-.data.frame"(*tmp*, value = row.names) :
	duplicate row.names are not allowed

I am interested if anybody (specially on RH 7.1) is able to read the table
in the same way.

Thanks in advance,

Ott Toomet


My R-version is 1.4.0 without any patches I am aware of:

platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    1
minor    4.0
year     2001
month    12
day      19
language R

And the table itself:

begin 664 tab20.and.gz
M'XL("%'M3SP``W1A8C(P+F%N9`"=T\L. at
D`,!=`U_(N3ON;1_W&O,?Y_!$$'
M>M$869&3MA<FG?MPO5W.8TTT/P,E8M9&-#H(:XIB4:2`>)0L,$<I?4P7<9]$
M:PIB#.)1-EFK,'L*D]>LTT3JN<Y%:]B6'$@:4!4 at
QT:FY\'MB)&6C]^31A(N
M6-43LY69"@-Y`Y)^ZI0UTTPY16I(VANKR?*+*4JO*;;,!M&_Q$`:"/=E>:4+
MB(+4*`I="EV:HQC4'(A%87I?BU5R7]5IATQI>._\AJ17$=7G^\B;Q?QFPC]:
31=.&9D>YR_7:V0/)#`.YB`0`````
`
end

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On Fri, 25 Jan 2002, Ott Toomet wrote:
> I have not get much response for my question about read.table for couple of
> days ago.  As I said, the problem is that read.delim() do not want to read
There is no problem with this example using R-patched or if you edit
read.table to apply the patch I posted on R-help:

Date: Tue, 15 Jan 2002 09:48:21 +0000 (GMT)
Subject: Re: [R] Lower performance execution in read.table()  in R-1.4.0
vs. R-1.3.1.. ?

which you will be find at
http://www.r-project.org/nocvs/mail/r-help/2002/0335.html

[...]

-- 
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 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Ott Toomet <siim at obs.ee> writes:
> Hi,
> 
> I have not get much response for my question about read.table for couple of
> days ago.  As I said, the problem is that read.delim() do not want to read
> more than 51 lines of data, with longer file it reads the first column as
> row names, although I have not noticed any special binary symbols around
> line 51 either.  This problem seems to happen with this particular file, I
> could easily read in a 12000 rows x 22 cols table.
> 
> I add my problematic file (it is really small) here, in a uuencoded gziped
> form.  What I did was:
> 
> > a <- read.delim("tab20.and")
> Error in "row.names<-.data.frame"(*tmp*, value = row.names) :
> 	duplicate row.names are not allowed
> 
> I am interested if anybody (specially on RH 7.1) is able to read the table
> in the same way.
The error message is unduly cryptic, but the problem seems to be this:
> count.fields("tab20.and",sep="\t")
 [1] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[39] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 2 2 2 2 2 2 2 2 2
                                 ! !

(lines 53 and 54 have an extra TAB at the end)

Interestingly,
> read.table("tab20.and",head=T,sep="\t")
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
        line 1 did not have 3 elements

which is not exactly pinpointing the problem, but gives a better clue.
(I.e., fill=T is making things confused)

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907
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