This is really an R-devel question, and I've moved it there.

Florian Hahne wrote:
Dear listers,
After activating the name space for my bioconductor package (prada) I
successfully ran R CMD check. However when loading the package in R and
running the examples the imported function brewer.pal from package
RColorBrewer is not found. I can directly call brewer.pal from the
RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not
imported into my prada name space. When I attach RColorBrewer, the
example runs fine. For several other function from different packages
the import works without problems.
I'm quite puzzled how this import can work with R CMD check but not when
attaching the package in a "regular" R session. And if the importFrom
directive was corrupted, shouldn't there be an error message?
This is not realy a problem, since I can load RColorBrewer by putting it
into the dependent field in my DESCRIPTION file as I did before, but
none the less I wanted to mention this strange behaviour. Could it be a
bug?

Could you be more specific about the bug? Which example fails? Is it run by the R CMD check tests?


Generally, I wouldn't expect "importFrom" to be sufficient to make an example using the import work, either during Rcmd CHECK or in the console. It makes the import available from within your package, but examples are run in the global environment.

Duncan Murdoch

Regards, Florian

Here is my NAMESPACE file:
export("analysePlate", "as.all",
       "barploterrbar", "combineFrames",
       "csApply", "ddCt",
       "densCols", "eListWrite",
       "fitNorm2", "getPradaPar",
       "histStack", "plotNorm2",
       "plotPlate", "readCytoSet",
       "readFCS", "readSDM",
       "removeCensored", "setPradaPars",
       "smoothScatter", "thresholds")


importFrom("KernSmooth", "bkde2D")
importFrom("RColorBrewer", "brewer.pal")
importFrom("utils", "getFromNamespace", "assignInNamespace")
importFrom("MASS", "cov.rob") S3method("$", "cytoFrame")
exportClasses("cytoFrame", "cytoSet")
exportMethods("colnames", "colnames<-",
"description", "description<-",
"exprs", "exprs<-",
"length", "[", "[[", "[[<-",
"pData", "phenoData", "phenoData<-",
"show")


System:
R 2.1.0 on Suse9.2 Linux box



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