[BioC] marrayInput problems following fresh 1.2 install

[Rafael A. Irizarry]

this is a bug (that only affects windows users). the fix should appear 
soon. in the meantime you can use the code below. 
the difference is line 6 (descript <- ...)

read.marrayInfo <- function (fname, info.id = NULL, labels = NULL, 
    notes = fname, 
    sep = "	", skip = 0, quote = "", ...) 
{
    h <- strsplit(readLines(fname, n = skip + 1), split = sep)
    h <- as.list(unlist(h[[length(h)]]))
    names(h) <- gsub("\"", "", unlist(h))
    dat <- read.table(fname, sep = sep, skip = skip + 1, fill = TRUE, 
        quote = quote, ...)
    colnames(dat) <- h
    descript <- new("marrayInfo", maInfo=data.frame(),maNotes = notes)
    if (is.null(info.id)) 
        info.id <- 1:ncol(dat)
    maInfo(descript) <- as.data.frame(dat[, info.id])
    if (length(labels) == nrow(dat)) 
        maLabels(descript) <- as.vector(labels)
    else {
        if (is.null(labels)) 
            labels <- 1
        maLabels(descript) <- as.character(as.vector(dat[, labels]))
    }
    return(descript)
}

-r
On Thu, 19 Jun 2003, Barry 
Henderson wrote:

> Hi
>  
> I just installed R 1.71 and BioC to 1.2.  Under this configuration BioC
> fails to to read in data/sample info.  If I take the same code and try
> it with my previous installation (R 1.62 and BioC v1.1).  I've looked at
> the traceback output but can't make any sense of it.  Any suggestions?
> Has anything changed with marrayInfo, classes or the way R is handling
> paths under windows?  I haven't been able to locate changes in the
> vignetes or help pages.  Code and traceback output below from the new
> installation is below.
>  
> Thanks 
> Barry
>  
> > exp <- "complete"
> > datadir <- paste("C:\\Array Data\\tox\\", exp, sep="")
> > setwd(datadir)
> > 
> > 
> > library(marrayInput)
> > exp.layout <- read.marrayLayout(fname=file.path(datadir, "genes.txt"),
> ngr= 4, ngc = 4, nsr = 12, nsc = 14, skip=0, ctl.col= 6)
> > ctl <- rep("Control", maNspots(exp.layout))
> > ctl[maControls(exp.layout) != "Control"] <- "normal"
> > maControls(exp.layout) <- factor(ctl)
> > 
> > #Load Sample data from samples.txt
> > 
> > exp.samples <- read.marrayInfo(file.path(datadir, "samples.txt"), sep
> = "\t")
> Error in validObject(.Object) : Invalid "marrayInfo" object: Invalid
> object for slot "maInfo" in class "marrayInfo": got class "NULL", should
> be or extend class "data.frame"
> > traceback()
> 6: stop(paste("Invalid \"", Class, "\" object: ", errors, sep = ""))
> 5: validObject(.Object)
> 4: initialize(value, ...)
> 3: initialize(value, ...)
> 2: new("marrayInfo", maNotes = notes)
> 1: read.marrayInfo(file.path(datadir, "samples.txt"), sep = "   ")
> > 
> 
> 
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