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

[Dario Strbenac]

Thanks. The order of loading the packages solves the problem for now.

---- Original message ----
>Date: Thu, 17 Mar 2011 16:25:08 -0700
>From: Martin Morgan <mtmorgan at fhcrc.org>  
>Subject: Re: [Bioc-sig-seq] ChIPpeakAnno Causes GenomicRanges Package Error  
>To: D.Strbenac at garvan.org.au
>Cc: bioc-sig-sequencing at r-project.org
>
>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
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>
>-- 
>Computational Biology
>Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
>Location: M1-B861
>Telephone: 206 667-2793


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