[Bioc-sig-seq] ChIPpeakAnno Causes GenomicRanges Package Error

[Dario Strbenac]

Can anyone see what's going wrong here ? From the documentation, it should work. Oh, and importantly, it only has an error if I have the ChIPpeakAnno package loaded. In a fresh session without ChIPpeakAnno loaded, it works as I expect.

library(GenomicRanges)
Pks <- GRanges("chr1", IRanges(c(500, 600), width = 100))
elementMetadata(Pks) <- DataFrame(ordID = 1:length(Pks))

I get :
Error in x[[name, exact = FALSE]] : 
  missing '[[' method for Sequence class GRanges

> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Australia.1252 
[2] LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

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

other attached packages:
 [1] ChIPpeakAnno_1.6.0                 
 [2] limma_3.4.5                        
 [3] org.Hs.eg.db_2.4.1                 
 [4] GO.db_2.4.1                        
 [5] RSQLite_0.9-0                      
 [6] DBI_0.2-5                          
 [7] AnnotationDbi_1.12.0               
 [8] BSgenome.Ecoli.NCBI.20080805_1.3.16
 [9] BSgenome_1.18.0                    
[10] Biostrings_2.18.0                  
[11] multtest_2.4.0                     
[12] Biobase_2.8.0                      
[13] biomaRt_2.4.0                      
[14] GenomicRanges_1.2.3                
[15] IRanges_1.8.9                      

loaded via a namespace (and not attached):
[1] MASS_7.3-11     RCurl_1.3-1     splines_2.12.2  survival_2.36-5
[5] tools_2.12.2    XML_2.8-1

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia