[BioC] Problems with MANOR and RSPerl

[James Morris]

Hello,

I have been writing a script to run a MANOR analysis from perl script using 
RSPerl

I have created my arrayCGH object successfully I think but when I try and 
evaluate this simple normalisation I get this error

&R::eval("data(flags); local.spatial.flag$args <- alist(var = "LogRatio", 
by.var = NULL, nk = 5, prop = 0.25, thr = 0.15, beta = 1, family = 
"gaussian"); flag.list <- list(spatial = local.spatial.flag); array.norm <- 
norm.arrayCGH(array, flag.list = flag.list, FUN = median, na.rm = TRUE)")

Error in model.frame(formula, fownames, variables, varnames, extras, 
extranames, :
  invalid variable type

this is R 2.2.1 on Mac OS X Server 10.3.9

any ideas on what could be causing this would be great

Thanks

James Morris