[R] trouble with read.table and colClasses='raw'

[Don MacQueen]

The error message says there is no method for 
converting from 'character' to 'raw'.
Apparently, R is seeing character data in the 
file, and is trying to convert it to raw, since 
you specified raw, and it can't.

See, for example,
>  as('aa','raw')
Error in as("aa", "raw") :
   no method or default for coercing "character" to "raw"

(same error message)

So I would ask, what are your data, really? Why 
are you asking for raw? Have you checked the help 
page for raw to make sure it's what you want?

-Don

At 5:23 PM +0100 2/11/10, Ivan Calandra wrote:
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>Well, it's too complicated for me! Here are what I would do (limited
>since I'm still a newbie)
>
>1) the syntax seems correct, it should work. The problem is somewhere
>else, coming from your own file. Did you try skipping the colClasses
>argument? To see how it looks like... If you can import it that way, try
>str(x) to see what you have. It might help you.
>2) I've never had that much data to import, and for me read.table works
>well.
>
>You might want to wait for the experts!
>
>Ivan
>
>Le 2/11/2010 17:14, Johan Jackson a écrit :
>>  Hi Ivan,
>>
>>  Thanks for the reply. Damn IT! My original post was screwed up. HERE
>>  is what I did:
>>
>>  x <- read.table("data",header=TRUE,colClasses=rep('raw',600000))
>>  #returns error:  no method or default for coercing "character" to "raw"
>>
>>   I've read the ?read.table and the colClasses argument. I'm still unclear:
>>
>>  1) colClasses is a character vector, is that right? That seems to be
>>  what the help says, but I get an error when I do the above.
>>
>>  2) what is the most efficient way to read in huge amounts of data? In
>>  the past I found that scan() and readLines() were slower than read.table.
>>
>>  Thanks,
>>
>>  JJ
>>
>>
>>
>>
>>  On Thu, Feb 11, 2010 at 8:53 AM, Ivan Calandra
>>  <ivan.calandra at uni-hamburg.de <mailto:ivan.calandra at uni-hamburg.de>>
>>  wrote:
>>
>>      Hi!
>>
>>      |"colClasses|       character. A vector of classes to be assumed
>>      for the
>>      columns."
>>      I'm not an R expert and I don't know what your "flat file raw" is, but
>>      the colClasses argument is to define whether the column will be
>>      treated
>>      as containing "factors", "logical", "integer" etc...
>>      For more on read.table, read the manual "R Data Import/Export"
>>      available
>>      on the R-project website.
>>
>>      I don't know if it helps, but I hope it does!
>  >
>  >     Ivan
>  >
>  >     Le 2/11/2010 16:36, Johan Jackson a écrit :
>  >     > Hi all,
>  >     >
>  >     > First off, it is surprising that there are no examples of how to use
>  >     > read.table() under ?read.table !
>>      >
>>      > I am trying to read in a flat file of type 'raw'. It has 1000
>>      rows and 600K
>>      > columns. I have the RAM to accomplish this, but can't get the
>>      data into R
>>      > using read.table:
>>      >
>>      > x<- read.table("data",header=TRUE,colClasses=rep(,600000))
>>      > #returns error:  no method or default for coercing "character"
>>      to "raw"
>>      >
>>      > Then I thought that maybe the colClasses vector needed to
>>      actually *be* the
>>      > mode needed (here's where an example under ?read.table would help):
>>      >
>>      > x<- read.table("data",header=TRUE,colClasses=rep(as.raw(1),600000))
>>      >
>>      > I waited on the latter command for a couple of hours before
>>      killing the
>>      > process. What should the colClasses argument be?
>>      >
>>      > Should I be using another method to read the data into R? Previous
>>      > experience using scan() and readLines() showed that read.table()
>>      was faster,
>>      > at least for those examples, so I've stopped trying to use those
>>      other
>>      > functions.
>>      >
>>      > Thank you,
>>      >
>>      > JJ
>>      >
>>      >       [[alternative HTML version deleted]]
>>      >
>>      > ______________________________________________
>>      > R-help at r-project.org <mailto: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.
>>      >
>>      >
>>
>>             [[alternative HTML version deleted]]
>>
>>
>>      ______________________________________________
>>      R-help at r-project.org <mailto: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.
>>
>>
>
>	[[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.


-- 
--------------------------------------
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062