The other possibility is that you could create the function to convert from character to raw (possibly wrapping as.raw around as.integer) so that read.table knows what to do.
-- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of Greg Snow > Sent: Thursday, February 11, 2010 11:06 AM > To: Johan Jackson; Don MacQueen > Cc: r-help@r-project.org > Subject: Re: [R] trouble with read.table and colClasses='raw' > > The read.table function does not know how to convert the character > representation that it reads into raw variables. Try using 'integer' > for the colClasses to read the data in as integers, then convert those > back to raw (if that is really what you need). > > -- > Gregory (Greg) L. Snow Ph.D. > Statistical Data Center > Intermountain Healthcare > greg.s...@imail.org > 801.408.8111 > > > > -----Original Message----- > > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > > project.org] On Behalf Of Johan Jackson > > Sent: Thursday, February 11, 2010 10:29 AM > > To: Don MacQueen > > Cc: r-help@r-project.org > > Subject: Re: [R] trouble with read.table and colClasses='raw' > > > > Hi Don and all, > > > > I guess we're getting somewhere. Thanks. The file (first three > columns, > > first five rows) looks like this: > > > > X10 X20 X30 > > 00 00 01 > > 00 02 02 > > 00 00 00 > > 00 01 01 > > 00 00 00 > > > > > > I guess R is reading 00 as a character? But here's the weird thing: > > this > > data (a raw matrix in R) was written out by R itself: > > > > write.table(dat,"data",col.names=T,row.names=F,quote=F) > > > > *If* I understand correctly, then this seems like very *bad behavior* > > on R's > > part: you should be able to write out a matrix and read it right back > > into R > > without hassles like this (but everytime I blame R, it turns out to > be > > user > > error, so...), > > > > JJ > > > > > > > > On Thu, Feb 11, 2010 at 9:59 AM, Don MacQueen <m...@llnl.gov> wrote: > > > > > 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: > > > > > >> Content-Type: text/plain > > >> Content-Disposition: inline > > >> Content-Transfer-Encoding: 8bit > > >> Content-length: 3983 > > >> > > >> > > >> 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.calan...@uni-hamburg.de <mailto:ivan.calan...@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@r-project.org <mailto: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. > > >>> > > > >>> > > > >>> > > >>> [[alternative HTML version deleted]] > > >>> > > >>> > > >>> ______________________________________________ > > >>> R-help@r-project.org <mailto: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. > > >>> > > >>> > > >>> > > >> [[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. > > >> > > > > > > > > > -- > > > -------------------------------------- > > > Don MacQueen > > > Environmental Protection Department > > > Lawrence Livermore National Laboratory > > > Livermore, CA, USA > > > 925-423-1062 > > > > > > ______________________________________________ > > > 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. > > > > > > > [[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. ______________________________________________ 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.
