[BioC] warning in lumi

[Martin Morgan]

On 02/22/2012 07:56 AM, Francesco Mancuso wrote:
> Dear all,
> I am the author of a CRAN package (HumMeth27QCReport) that denpends on
> lumi.
> Every time I call the lumi package I obtain the following warning:
>
> "
>    Functions for exporting methods must have been made generic,
> explicitly or implicitly; not true when loading ‘lumi’ for ‘summary’
> "
>
> Since this error comes not only when I try to build ny package but also
> when I require lumi from normal R command line, I think this is a
> problem in lumi package itself. Am I correct?
> Is there the possibility to solve it?

Hi Francesco -- we are addressing these warnings in a number of Bioc 
packages; this particular problem was fixed in the devel branch last 
night. Martin

r62969 | mtmorgan at fhcrc.org | 2012-02-21 20:37:50 -0800 (Tue, 21 Feb 
2012) | 6 lines

code tidyup

- avoid implicit plot, summary generic  with BiocGenerics
- avoid partial matching
- remove empty documentation sections


>
> Many thanks,
> Francesco
>
>
>   >  sessionInfo()
> R Under development (unstable) (2012-01-30 r58238)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] lumi_2.7.2         nleqslv_1.9.2      methylumi_2.1.13
> Biobase_2.15.3     BiocGenerics_0.1.4
>
> loaded via a namespace (and not attached):
>    [1] affy_1.33.2           affyio_1.23.1         annotate_1.33.1
> AnnotationDbi_1.17.15 BiocInstaller_1.3.7   DBI_0.2-5
> grid_2.15.0           hdrcde_2.15
>    [9] IRanges_1.13.20       KernSmooth_2.23-7     lattice_0.20-0
> MASS_7.3-16           Matrix_1.0-3          mgcv_1.7-13
> nlme_3.1-103          preprocessCore_1.17.1
> [17] RSQLite_0.11.1        tools_2.15.0          xtable_1.6-0
> zlibbioc_1.1.1
>
>
>
>
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793