Francois Lefebvre [guest] | 18 Jan 05:43 2013

cummeRbund masks featureNames and samples from Biobase


Hi, I observed that featureNames()<- from cummeRbund masks its homonym from Biobase and can create errors .

Code and error:
---------------------------------------
library(Biobase)
library(cummeRbund)
example('ExpressionSet')

Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘featureNames’ for signature ‘"ExpressionSet"’
---------------------------------------

Of course, this can be avoided by calling Biobase::featureNames(), or not loading both packages at the
same time or in a different order.

I am not entirely familiar with the details of S4 classes, but couldn't cummeRbund methods be defined in a
way to at least not interfere with the actual "base" package of project? Perhaps there is a bug in the
signature definition?

Or has this something to do with my installation.

Thanks for your time.

François Lefebvre

 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] cummeRbund_2.0.0     Gviz_1.2.1           rtracklayer_1.18.2  
 [4] GenomicRanges_1.10.6 IRanges_1.16.4       fastcluster_1.1.7   
 [7] reshape2_1.2.2       ggplot2_0.9.3        RSQLite_0.11.2      
[10] DBI_0.2-5            Biobase_2.18.0       BiocGenerics_0.4.0  

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.20.3   biomaRt_2.14.0         Biostrings_2.26.2     
 [4] biovizBase_1.6.2       bitops_1.0-4.2         BSgenome_1.26.1       
 [7] cluster_1.14.3         colorspace_1.2-0       dichromat_1.2-4       
[10] digest_0.6.0           GenomicFeatures_1.10.1 gtable_0.1.2          
[13] Hmisc_3.10-1           labeling_0.1           lattice_0.20-13       
[16] MASS_7.3-23            munsell_0.4            parallel_2.15.2       
[19] plyr_1.8               proto_0.3-10           RColorBrewer_1.0-5    
[22] RCurl_1.95-3           Rsamtools_1.10.2       scales_0.2.3          
[25] stats4_2.15.2          stringr_0.6.2          tools_2.15.2          
[28] XML_3.95-0.1           zlibbioc_1.4.0 

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