[BioC] GRangesForUCSCGenome seems to be missing in rtracklayer 1.10, GenomicRanges 1.2

[Vincent Carey]

Perhaps you made a spelling error (though not in the email AFAICT)

> GRangesForUCSCGenome
function (genome, chrom = NULL, ranges = NULL, ...)
{
    if (missing(genome) || !IRanges:::isSingleString(genome))
        stop("'genome' must be a single string identifying a genome")
    session <- browserSession("UCSC")
    genome(session) <- genome
    GRangesForGenome(genome, seqlengths(session), chrom = chrom,
        ranges = ranges, ...)
}
<environment: namespace:rtracklayer>
> sessionInfo()
R version 2.12.0 Patched (2010-10-15 r53331)
Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
[1] rtracklayer_1.10.0 RCurl_1.4-3        bitops_1.0-4.1     weaver_1.15.0
[5] codetools_0.2-2    digest_0.4.2

loaded via a namespace (and not attached):
[1] BSgenome_1.18.0     Biobase_2.10.0      Biostrings_2.18.0
[4] GenomicRanges_1.2.0 IRanges_1.7.40      XML_3.2-0


On Sat, Oct 23, 2010 at 12:02 AM, Paul Shannon
<pshannon at systemsbiology.org> wrote:
> The rtracklayer vignette  features the GRangesForUCSCGenome rather prominently (page 3), but I cannot seem to find the function.
>
> I can probably make do with 'GRanges', but my failure to match the vignette leaves me uneasy.
>
> Any advice?    SessionInfo follows.
>
>  - Paul
>
>> sessionInfo ()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] GenomicFeatures_1.1.11             rtracklayer_1.10.0                 RCurl_1.4-2                        bitops_1.0-4.1
>  [5] BSgenome.Hsapiens.UCSC.hg18_1.3.16 BSgenome.Mmusculus.UCSC.mm9_1.3.16 BSgenome_1.17.5                    Biostrings_2.18.0
>  [9] GenomicRanges_1.2.0                IRanges_1.8.0                      org.Pt.eg.db_2.4.1                 org.Hs.eg.db_2.4.6
> [13] org.Mm.eg.db_2.4.1                 RSQLite_0.9-2                      DBI_0.2-5                          AnnotationDbi_1.11.8
> [17] Biobase_2.10.0                     RUnit_0.4.25
>
> loaded via a namespace (and not attached):
> [1] biomaRt_2.6.0 XML_3.1-1
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