[Bioc-devel] Importing generic functions from other pkgs and defining methods on them?

[Florian Hahne]

Hi Wolfgang,
do you export your method in the NAMSPACE? There should be an 
exportMethods("logLik"). I had similar problems a while ago. The error 
message indicates that there is no logLik method, so the problem isn't 
the import but rather the export,  I suppose. The environment in R CMD 
check in not the same as when running Sweave interactively, so although 
the latter works with a misconfigured NAMESPACE, R CMD check may fail.
Florian

Wolfgang Huber schrieb:
> Hi,
>
> I post this problem to the list b/c perhaps others have it as well and
> so we only need to solve it once. Something with S4 and Namespaces
> appears to have changed. With the current R-devel, I get from "R CMD
> check tilingArray":
>
>     .... SNIP ...
> * checking package vignettes in 'inst/doc' ... WARNING
> *** Weave Errors ***
> File
> /net/nfs7/vol6/research-huber/users/huber/madman/Rpacks/tilingArray.Rcheck/tilingArray/doc/findsegments.Rnw
> :
> Error :  chunk 8 (label=penLLsim)
> Error in logLik(seg) : no applicable method for "logLik"
>
> When I run Sweave on the vignette interactively, there is no error!
> Also, the package used to pass R CMD check a while ago, and has not
> changed - but of course R has changed. In my NAMESPACE I have:
>
>   importFrom("stats", "confint", "logLik", "residuals")
>
> and in tilingArray/R/methods-segmentation.R
>
> setMethod("logLik", "segmentation",
>   function(object, penalty="none", ...) {
>     ## BLA
>   })
>
> Does anybody have a pointer for where to look at?
>
>  Best wishes
>   Wolfgang
>
>
>
>
>   
>> sessionInfo()
>>     
> R version 2.5.0 Under development (unstable) (2007-03-08 r40820)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
>  [1] "splines"   "grid"      "tools"     "stats"     "graphics"  "grDevices"
>  [7] "utils"     "datasets"  "methods"   "base"
>
> other attached packages:
>  tilingArray       pixmap  geneplotter      lattice     annotate
> genefilter
>     "1.13.3"      "0.4-6"     "1.13.7"    "0.14-16"     "1.13.6"
> "1.13.8"
>     survival          vsn  strucchange     sandwich          zoo
> RColorBrewer
>       "2.31"     "2.0.18"      "1.3-1"      "2.0-1"      "1.2-2"
> "0.2-3"
>         affy       affyio      Biobase     fortunes
>    "1.13.14"      "1.3.3"    "1.13.39"      "1.3-2"
>
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