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 digit) are out of date, although this function is in rtracklayer; maybe 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