[BioC] problem with 'FDb.InfiniumMethylation.hg19'

[Moiz Bootwalla]

I believe this is a result of not having the BSgenome.Hsapiens.UCSC.hg19 package installed on your system. Try installing the package, loading it into your R session and then running get450k(). It should solve it. Post back if it still does not work.

HTH,

Moiz


On Oct 23, 2012, at 7:19 AM, Tim Triche, Jr. wrote:

> This is odd.  I'll look into it today.  Thanks for the bug report.
> 
> --t
> 
> 
> On Tue, Oct 23, 2012 at 6:48 AM, Hooiveld, Guido <Guido.Hooiveld at wur.nl>wrote:
> 
>> Hi,
>> I would like to report a problem with the annotation package
>> "FDb.InfiniumMethylation.hg19".
>> When I try to explore the content of it for the 450K array as per the
>> example on the help pages, I get an error.
>> Any suggestions on what is going wrong?
>> 
>> Thanks and regards,
>> Guido
>> 
>> 
>>> library(FDb.InfiniumMethylation.hg19)
>> Loading required package: GenomicFeatures
>> Loading required package: BiocGenerics
>> 
>> Attaching package: 'BiocGenerics'
>> 
>> The following object(s) are masked from 'package:stats':
>> 
>>    xtabs
>> 
>> The following object(s) are masked from 'package:base':
>> 
>>    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
>>    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
>>    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
>>    rownames, sapply, setdiff, table, tapply, union, unique
>> 
>> Loading required package: IRanges
>> Loading required package: GenomicRanges
>> Loading required package: AnnotationDbi
>> Loading required package: Biobase
>> Welcome to Bioconductor
>> 
>>    Vignettes contain introductory material; view with
>>    'browseVignettes()'. To cite Bioconductor, see
>>    'citation("Biobase")', and for packages 'citation("pkgname")'.
>> 
>> Loading required package: Biostrings
>> Loading required package: rtracklayer
>> Warning messages:
>> 1: replacing previous import 'initialize' when loading 'rtracklayer'
>> 2: replacing previous import 'show' when loading 'rtracklayer'
>>> hm450 <- get450k()
>> Error in `seqinfo<-`(`*tmp*`, value = NULL) :
>>  the supplied 'seqinfo' must be a Seqinfo object
>> In addition: Warning message:
>> In if (is.na(genome(GR))) { :
>>  the condition has length > 1 and only the first element will be used
>>> sessionInfo()
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>> 
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.18.0
>> [3] Biostrings_2.26.2                  GenomicFeatures_1.10.0
>> [5] AnnotationDbi_1.20.2               Biobase_2.18.0
>> [7] GenomicRanges_1.10.2               IRanges_1.16.3
>> [9] BiocGenerics_0.4.0                 BiocInstaller_1.8.2
>> 
>> loaded via a namespace (and not attached):
>> [1] biomaRt_2.14.0   bitops_1.0-4.1   BSgenome_1.26.1  DBI_0.2-5
>> [5] parallel_2.15.1  RCurl_1.95-1.1   Rsamtools_1.10.1 RSQLite_0.11.2
>> [9] stats4_2.15.1    tools_2.15.1     XML_3.95-0.1     zlibbioc_1.4.0
>>> 
>> 
>> 
>> ---------------------------------------------------------
>> Guido Hooiveld, PhD
>> Nutrition, Metabolism & Genomics Group
>> Division of Human Nutrition
>> Wageningen University
>> Biotechnion, Bomenweg 2
>> NL-6703 HD Wageningen
>> the Netherlands
>> tel: (+)31 317 485788
>> fax: (+)31 317 483342
>> email:      guido.hooiveld at wur.nl
>> internet:   http://nutrigene.4t.com
>> http://scholar.google.com/citations?user=qFHaMnoAAAAJ
>> http://www.researcherid.com/rid/F-4912-2010
>> 
>> 
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>> 
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> 
> 
> 
> -- 
> *A model is a lie that helps you see the truth.*
> *
> *
> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
> 
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> 
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