I think this has been fixed in devel already. See:

https://stat.ethz.ch/pipermail/bioconductor/2010-October/035985.html

Thanks,
Michael

On Wed, Feb 23, 2011 at 4:06 PM, Janet Young <jayoung@fhcrc.org> wrote:

> Hi again,
>
> (sorry, you're probably tired of hearing from me now).
>
> I have just started to play with ChIPpeakAnno - it looks like it might be
> very useful for me.  However, once I load it I get an error from BSgenome's
> getSeq function.  Here's the error alone (myregions_RD is a RangedData
> object), and below is my full code.
>
> getSeq(Cfamiliaris,myregions_RD)
> Error in x[[name, exact = FALSE]] :
>  missing '[[' method for Sequence class GRanges
>
>
> thanks (yet again),
>
> Janet
>
> -------------------------------------------------------------------
>
> Dr. Janet Young (Trask lab)
>
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N., C3-168,
> P.O. Box 19024, Seattle, WA 98109-1024, USA.
>
> tel: (206) 667 1471 fax: (206) 667 6524
> email: jayoung  ...at...  fhcrc.org
>
> http://www.fhcrc.org/labs/trask/
>
> -------------------------------------------------------------------
>
>
>
>
> R version 2.12.1 (2010-12-16)
> Copyright (C) 2010 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>  Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> > library(IRanges)
>
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
>    cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin,
>    pmin.int, rbind, rep.int, table
>
>
>
> > library(BSgenome.Cfamiliaris.UCSC.canFam2)
> Loading required package: BSgenome
> Loading required package: GenomicRanges
> Loading required package: Biostrings
>
> > myregions_RD <-
> RangedData(IRanges(start=c(100001L,2000001L),end=c(100100L,2000100L)),space=c("chr1","chr2"),strand=c("+","+")
>   )
>
> > getSeq(Cfamiliaris,myregions_RD)
> [1]
> "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
> [2]
> "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
>
> > library(ChIPpeakAnno)
> Loading required package: biomaRt
> Loading required package: multtest
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
>
> Attaching package: 'Biobase'
>
> The following object(s) are masked from 'package:IRanges':
>
>    updateObject
>
> Loading required package: BSgenome.Ecoli.NCBI.20080805
> Loading required package: GO.db
> Loading required package: AnnotationDbi
> Loading required package: DBI
> Loading required package: org.Hs.eg.db
> Loading required package: limma
>
> > getSeq(Cfamiliaris,myregions_RD)
> Error in x[[name, exact = FALSE]] :
>  missing '[[' method for Sequence class GRanges
>
> > sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] ChIPpeakAnno_1.6.0
>  [2] limma_3.6.9
>  [3] org.Hs.eg.db_2.4.6
>  [4] GO.db_2.4.5
>  [5] RSQLite_0.9-4
>  [6] DBI_0.2-5
>  [7] AnnotationDbi_1.12.0
>  [8] BSgenome.Ecoli.NCBI.20080805_1.3.16
>  [9] multtest_2.7.1
> [10] Biobase_2.10.0
> [11] biomaRt_2.6.0
> [12] BSgenome.Cfamiliaris.UCSC.canFam2_1.3.16
> [13] BSgenome_1.18.3
> [14] Biostrings_2.18.2
> [15] GenomicRanges_1.2.3
> [16] IRanges_1.8.9
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-11     RCurl_1.5-0     splines_2.12.1  survival_2.36-5
> [5] XML_3.2-0
>
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