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

[Martin Morgan]

On 10/23/2010 04:43 AM, Paul Shannon wrote:
> Hi Vince,
> 
> Yes, I suspected that right away.  Long function name, clumsy fingers, ...
> 
> Function name completion (I use ESS) and repeated typing led me to the same result.   
> 
> Just now I cut-and-pasted from your email into my R session
> 
>> GRangesForUCSCGenome
> Error: object 'GRangesForUCSCGenome' not found

Looks like GenomicFeatures, GenomicRanges, (odd-numbered second version
digit) are out of date, although this function is in rtracklayer; maybe
update or reinstall packages (including rtracklayer)?

  http://bioconductor.org/install/index.html#update-bioconductor-packages

Martin

> 
> Puzzled,
> 
>  - Paul
> 
> On Oct 23, 2010, at 4:28 AM, Vincent Carey wrote:
> 
>> 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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> 
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