I need to build a custom cdf for Affy Rat Gene ST 1.0 chipset and am
attempting to follow Jim's helpful suggestions which can be found at
http://article.gmane.org/gmane.science.biology.informatics.conductor/18963/match=oligo+st
I get the error '"AffyGenePDInfoPkgSeed" is not a defined class'. My script,
debugging info and sessionInfo is below. Any help is much appreciated.

Mark

> require(oligo)
Loading required package: oligo
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: preprocessCore
Loading required package: AnnotationDbi
Loading required package: affxparser
Loading required package: oligoClasses
oligo Package - Series 1.5.x
> setwd("~/R.functions/Annotation_builds/Rat_ST_1.0_lib_files")
> pgfFile <- "RaGene-1_0-st-v1.r3.pgf"
> clfFile <- "MoGene-1_0-st-v1.r3.clf"
> transFile <- "RaGene-1_0-st-v1.na26.rn4.transcript.csv"
> probeFile <- "RaGene-1_0-st-v1.probe.tab"
> pkg <- new("AffyGenePDInfoPkgSeed", author = "authorname", email =
+ "mwkimpel@gmail.com", version = "0.0.1", genomebuild = "July,2008",
+ biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile,
+ transFile = transFile, probeFile = probeFile)
Error in getClass(Class, where = topenv(parent.frame())) :
  "AffyGenePDInfoPkgSeed" is not a defined class

Enter a frame number, or 0 to exit

1: new("AffyGenePDInfoPkgSeed", author = "authorname", email =
"mwkimpel@gmail
2: getClass(Class, where = topenv(parent.frame()))

Selection: 2
Called from: eval(expr, envir, enclos)
Browse[1]> ls()
[1] "Class" "value" "where"
Browse[1]> Class
[1] "AffyGenePDInfoPkgSeed"
Browse[1]> value
NULL
Browse[1]> where
where 1: eval(expr, envir, enclos)
where 2: eval(quote(browser()), envir = sys.frame(which))
where 3: function ()
{
    if (.isMethodsDispatchOn()) {
        tState <- tracingState(FALSE)
        on.exit(tracingState(tState))
    }
    calls <- sys.calls()
    from <- 0
    n <- length(calls)
    if (identical(sys.function(n), recover))
        n <- n - 1
    for (i in rev(seq_len(n))) {
        calli <- calls[[i]]
        fname <- calli[[1]]
        if (!is.na(match(deparse(fname)[1], c("methods::.doTrace",
            ".doTrace")))) {
            from <- i - 1
            break
        }
    }
    if (from == 0)
        for (i in rev(seq_len(n))) {
            calli <- calls[[i]]
            fname <- calli[[1]]
            if (!is.name(fname) || is.na(match(as.character(fname),
                c("recover", "stop", "Stop")))) {
                from <- i
                break
            }
        }
    if (from > 0) {
        if (!interactive()) {
            try(dump.frames())
            cat(gettext("recover called non-interactively; frames dumped,
use debugger() to view\n"))
            return(NULL)
        }
        else if (identical(getOption("show.error.messages"),
            FALSE))
            return(NULL)
        calls <- limitedLabels(calls[1:from])
        repeat {
            which <- menu(calls, title = "\nEnter a frame number, or 0 to
exit  ")
            if (which > 0)
                eval(quote(browser()), envir = sys.frame(which))
            else break
        }
    }
    else cat(gettext("No suitable frames for recover()\n"))
}()
where 4: stop(gettextf("\"%s\" is not a defined class", Class), domain = NA)
where 5: getClass(Class, where = topenv(parent.frame()))
where 6: new("AffyGenePDInfoPkgSeed", author = "authorname", email = "
mwkimpel@gmail.com",
    version = "0.0.1", genomebuild = "July,2008", biocViews =
"AnnotationData",
    pgfFile = pgfFile, clfFile = clfFile, transFile = transFile,
    probeFile = probeFile)

Browse[1]> c

Enter a frame number, or 0 to exit

1: new("AffyGenePDInfoPkgSeed", author = "authorname", email =
"mwkimpel@gmail
2: getClass(Class, where = topenv(parent.frame()))

Selection: 0
> sessionInfo()
R version 2.8.0 Under development (unstable) (2008-08-30 r46465)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] oligo_1.5.9          oligoClasses_1.3.6   affxparser_1.13.8
[4] AnnotationDbi_1.3.12 preprocessCore_1.3.4 RSQLite_0.7-0
[7] DBI_0.2-4            Biobase_2.1.7        graph_1.19.6

loaded via a namespace (and not attached):
[1] cluster_1.11.11
------------------------------------------------------------
Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219  Home
Skype:  mkimpel

"The real problem is not whether machines think but whether men do." -- B.
F. Skinner
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