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.