R help - Sep 2009 - Working around 256 byte variable names? + trouble opening large file

Dear R users,

I am trying to read in a file with 105 columns, and when trying to attach 
it, get an error as follows:
> vc1<-read.table("P:\\R\\Everything-I.txt", header=T,
sep=" ", dec=".",
na.strings=NA, strip.white=T)
> attach(vc1)
Error in attach(vc1) : variable names are limited to 256 bytes

Is there a way to get around this, and make R accept the given variable 
names? Or will I have to shorten them?


Also, when I try to read in a much larger file with 430 columns, I get the 
error:

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, 
:
  line 397 did not have 431 elements

Is it that R isn't dealing too well with Excel-converted-to-text files? Is 
it a function of file size?

I have double-checked the 430 column file and all data seems to be in place.


Thanks for your help!

Aditi




----------------------
A Singh
Aditi.Singh at bristol.ac.uk
School of Biological Sciences
University of Bristol

Well the first suspicious thing seems to be  the 256 byte variable names.  Do
you really have a 256 byte variable name? If so, why?  It sounds like R is
reading the entire header line as one variable.

Why not try exporting the Exce file as a csv file and loading that?  




--- On Mon, 9/21/09, A Singh <Aditi.Singh at bristol.ac.uk> wrote:
> From: A Singh <Aditi.Singh at bristol.ac.uk>
> Subject: [R] Working around 256 byte variable names? + trouble opening
large file
> To: r-help at r-project.org
> Received: Monday, September 21, 2009, 4:04 PM
> Dear R users,
> 
> I am trying to read in a file with 105 columns, and when
> trying to attach it, get an error as follows:
> 
> > vc1<-read.table("P:\\R\\Everything-I.txt",
> header=T, sep=" ", dec=".", 
> na.strings=NA, strip.white=T)
> > attach(vc1)
> Error in attach(vc1) : variable names are limited to 256
> bytes
> 
> Is there a way to get around this, and make R accept the
> given variable names? Or will I have to shorten them?
> 
> 
> Also, when I try to read in a much larger file with 430
> columns, I get the error:
> 
> Error in scan(file, what, nmax, sep, dec, quote, skip,
> nlines, na.strings, :
>  line 397 did not have 431 elements
> 
> Is it that R isn't dealing too well with
> Excel-converted-to-text files? Is it a function of file
> size?
> 
> I have double-checked the 430 column file and all data
> seems to be in place.
> 
> 
> Thanks for your help!
> 
> Aditi
> 
> 
> 
> 
> ----------------------
> A Singh
> Aditi.Singh at bristol.ac.uk
> School of Biological Sciences
> University of Bristol
> 
> ______________________________________________
> 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.
>

On Sep 21, 2009, at 4:04 PM, A Singh wrote:
> Dear R users,
>
> I am trying to read in a file with 105 columns, and when trying to  
> attach it, get an error as follows:
>
>> vc1<-read.table("P:\\R\\Everything-I.txt", header=T,
sep=" ",
>> dec=".",
> na.strings=NA, strip.white=T)
>> attach(vc1)
> Error in attach(vc1) : variable names are limited to 256 bytes
>
> Is there a way to get around this, and make R accept the given  
> variable names? Or will I have to shorten them?
>
It's my guess that you have an unmatched quote in your header  
somewhere. The error is reported when the length of a SINGLE variable  
name is over the 256 character limit, and not when the total number of  
characters in all of the variable names is over 256. Shirley, you  
cannot have a variable name that want to be that long.
> Also, when I try to read in a much larger file with 430 columns, I  
> get the error:
>
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,  
> na.strings, :
> line 397 did not have 431 elements
>
> Is it that R isn't dealing too well with Excel-converted-to-text  
> files? Is it a function of file size?
R is not the problem. It is capable of "filling".
>
> I have double-checked the 430 column file and all data seems to be  
> in place.
Again, probably a misplaced quote character.

-- 

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

Hi Aditi,

On Sep 21, 2009, at 4:04 PM, A Singh wrote:
> Dear R users,
>
> I am trying to read in a file with 105 columns, and when trying to  
> attach it, get an error as follows:
>
>> vc1<-read.table("P:\\R\\Everything-I.txt", header=T,
sep=" ",
>> dec=".",
> na.strings=NA, strip.white=T)
>> attach(vc1)
> Error in attach(vc1) : variable names are limited to 256 bytes
>
> Is there a way to get around this, and make R accept the given  
> variable names? Or will I have to shorten them?
1. Don't use `attach`. Here's a good starting point to help you  
develop your R coding style, I'm sending you straight to the section  
about using "attach" :-)

http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html#attach

2. what do you get when you run "names(vc1)"?

> Also, when I try to read in a much larger file with 430 columns, I  
> get the error:
>
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,  
> na.strings, :
> line 397 did not have 431 elements
>
> Is it that R isn't dealing too well with Excel-converted-to-text  
> files? Is it a function of file size?
It's not a function of file size, but rather due to the fact that line  
397 does not have as many data entries as the other lines .. maybe  
this is a function of how excel is exporting the data?
> I have double-checked the 430 column file and all data seems to be  
> in place.
How did you check the column to verify that? In Excel?

I'm not an excel guru, so I don't know how it handles data export when  
certain cells are missing in a row -- each row should have as many  
demarcated data points as any other. So if its a CSV, there should be  
just as many ","'s in line 397 as there are in the preceding
lines.

HTH,
-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

On Mon, Sep 21, 2009 at 3:04 PM, A Singh <Aditi.Singh at bristol.ac.uk>
wrote:
> Dear R users,
>
> I am trying to read in a file with 105 columns, and when trying to attach
> it, get an error as follows:
>
>> vc1<-read.table("P:\\R\\Everything-I.txt", header=T,
sep=" ", dec=".",
>
> na.strings=NA, strip.white=T)
>>
>> attach(vc1)
>
> Error in attach(vc1) : variable names are limited to 256 bytes
>
> Is there a way to get around this, and make R accept the given variable
> names? Or will I have to shorten them?
Don't use attach?

Hadley

-- 
http://had.co.nz/