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

[Paul Shannon]

Thanks to you both.  after update.packages () and a fresh start, GRangesForUCSCGenome now works fine.  
 
 - Paul

On Oct 23, 2010, at 7:27 AM, Martin Morgan wrote:

> 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 digit) are out of date, although this function is in rtracklayer; maybe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
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>> 
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 
> -- 
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> 
> Location: M1-B861
> Telephone: 206 667-2793