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

[Martin Morgan]

On 03/17/2011 04:00 PM, Dario Strbenac wrote:
> 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

Hi Dario --

I think the error occurs with

   library(GenomicRanges); library(ChIPpeakAnno)

and then your commands, and the workaround is to load ChIPpeakAnno first

   library(ChIPpeakAnno)

I think also this specific issue has been addressed in the development 
branch (or at least it's not reproducible in this way).

Also, your packages below are a bit of mish-mash; check out

   source('http://bioconductor.org/biocLite.R')
   old.packages(repos=biocinstallRepos())

and then maybe

   update.packages(repos=biocinstallRepos())

Martin

>
>> 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
>
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