hello, i've got a problem when i want ti create a package to use with the
oligo package for nimblegen microarray analysis

this the session info

> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu

locale:
 [1] LC_CTYPE=fr_FR.utf8          LC_NUMERIC=C
 [3] LC_TIME=fr_FR.utf8           LC_COLLATE=fr_FR.utf8
 [5] LC_MONETARY=fr_FR.utf8       LC_MESSAGES=fr_FR.utf8
 [7] LC_PAPER=fr_FR.utf8          LC_NAME=fr_FR.utf8
 [9] LC_ADDRESS=fr_FR.utf8        LC_TELEPHONE=fr_FR.utf8
[11] LC_MEASUREMENT=fr_FR.utf8    LC_IDENTIFICATION=fr_FR.utf8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] pdInfoBuilder_1.12.0 oligo_1.12.2         oligoClasses_1.10.0
 [4] affxparser_1.20.0    RSQLite_0.9-2        DBI_0.2-5
 [7] JGR_1.7-2            iplots_1.1-3         JavaGD_0.5-2
[10] rJava_0.8-6          Biobase_2.8.0

loaded via a namespace (and not attached):
[1] affyio_1.16.0         Biostrings_2.16.9     IRanges_1.6.17
[4] preprocessCore_1.10.0 splines_2.11.1        tools_2.11.1
> traceback
function (x = NULL, max.lines = getOption("deparse.max.lines"))
{
    if (is.null(x) && (exists(".Traceback", envir = baseenv())))
        x <- get(".Traceback", envir = baseenv())
    n <- length(x)
    if (n == 0L)
        cat(gettext("No traceback available"), "\n")
    else {
        for (i in 1L:n) {
            label <- paste(n - i + 1L, ": ", sep = "")
            m <- length(x[[i]])
            if (!is.null(srcref <- attr(x[[i]], "srcref"))) {
                srcfile <- attr(srcref, "srcfile")
                x[[i]][m] <- paste(x[[i]][m], " at ",
basename(srcfile$filename),
                  "#", srcref[1L], sep = "")
            }
            if (m > 1)
                label <- c(label, rep(substr("          ", 1L,
                  nchar(label, type = "w")), m - 1L))
            if (is.numeric(max.lines) && max.lines > 0L && max.lines <
                m) {
                cat(paste(label[1L:max.lines], x[[i]][1L:max.lines],
                  sep = ""), sep = "\n")
                cat(label[max.lines + 1L], " ...\n")
            }
            else cat(paste(label, x[[i]], sep = ""), sep = "\n")
        }
    }
    invisible()
}
<environment: namespace:base>

and the tracebck

> traceback()
7: stop("'by' must specify valid column(s)")
6: fix.by(by.x, x)
5: merge.data.frame(ndfdata, xysdata, by.x = c("X", "Y"), by.y = c("X",
       "Y"))
4: merge(ndfdata, xysdata, by.x = c("X", "Y"), by.y = c("X", "Y"))
3: parseNgsPair(object@ndfFile, object@xysFile, verbose = !quiet)
2: makePdInfoPackage(seed, destDir = ".")
1: makePdInfoPackage(seed, destDir = ".")

and this is my script :

> library(pdInfoBuilder)
> baseDir <- "/home/michael/Documents/test_2007"
> (ndf <- list.files(baseDir, pattern = ".ndf",full.names = TRUE))
[1] "/home/michael/Documents/test_2007/new2.ndf"
> (xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1])
[1] "/home/michael/Documents/test_2007/nobless1.xys"
> seed <- new("NgsExpressionPDInfoPkgSeed",
+ ndfFile = ndf, xysFile = xys,
+ author = "Momo Allo",
+ email = "mozemaster@gmail.com",
+ biocViews = "AnnotationData",
+ genomebuild = "LGDP",
+ organism = "Rice", species = "Oryza Sativa",
+ url = "http://www.biostat.jhsph.edu/~bcarvalh")
> makePdInfoPackage(seed, destDir = ".")
================================================================================
Building annotation package for Nimblegen Expression Array
NDF: new2.ndf
XYS: nobless1.xys
================================================================================
Parsing file: new2.ndf... OK
Parsing file: nobless1.xys... OK
Merging NDF and XYS files... Erreur dans fix.by(by.x, x) : 'by' must specify
valid column(s)


so i don't understand why i've got this error, so if anybody could help me
where is the main problem ?

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