R help - Apr 2005 - strange behaviour of importFrom directive in name space

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?
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


-- 
Florian Hahne <f.hahne at dkfz-heidelberg.de>

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
> 
>