yes, that should be

if(all(is.na(genome(GR)))

In the code.  I'll repackage & reupload it in the next couple of days.

Thanks!

--t


On Tue, Oct 23, 2012 at 12:34 PM, Hooiveld, Guido <Guido.Hooiveld@wur.nl>wrote:

>  Hi,****
>
> To report back: installing ‘the BSgenome.Hsapiens.UCSC.hg19’ indeed made
> the error disappear. There was no need to explicitly load this library,
> calling just the function get450K() also loaded it. However, FYI, the
> warning still is present:****
>
> ** **
>
> > hm450 <- get450k()****
>
> Warning message:****
>
> In if (is.na(genome(GR))) { :****
>
>   the condition has length > 1 and only the first element will be used****
>
> >** **
>
> ** **
>
> Regards,****
>
> Guido****
>
> ** **
>
> *From:* Tim Triche, Jr. [mailto:tim.triche@gmail.com]
> *Sent:* Tuesday, October 23, 2012 18:37
> *To:* Moiz Bootwalla
> *Cc:* Hooiveld, Guido; bioconductor (bioconductor@stat.math.ethz.ch)
> *Subject:* Re: [BioC] problem with 'FDb.InfiniumMethylation.hg19'****
>
> ** **
>
> Hmmm... well, there's something to add to the Depends: line in the
> description, then.  ****
>
> And the hg18 version for the hg18 FDb.  ****
>
> I think it's time to merge the two...****
>
> ** **
>
> Thanks for catching that Moiz.****
>
> ** **
>
> --t****
>
> ** **
>
> ** **
>
> On Tue, Oct 23, 2012 at 8:01 AM, Moiz Bootwalla <msbootwalla@gmail.com>
> wrote:****
>
> 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@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@wur.nl
> >> internet:   http://nutrigene.4t.com
> >> http://scholar.google.com/citations?user=qFHaMnoAAAAJ
> >> http://www.researcherid.com/rid/F-4912-2010
> >>
> >>
> >>        [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >
> >
> > --****
>
> > *A model is a lie that helps you see the truth.*
> > *
> > *
> > Howard Skipper<
> http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>****
>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor****
>
>
>
> ****
>
> ** **
>
> --
> *A model is a lie that helps you see the truth.*****
>
> ** **
>
> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
> ****
>
> ** **
>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

	[[alternative HTML version deleted]]

