This seems to be a European issue; working on a fix now.

Michael


On Sun, Jul 7, 2013 at 6:40 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> On Sun, Jul 7, 2013 at 5:37 AM, Maintainer <maintainer@bioconductor.org>
> wrote:
> >
> > Dear All,
> > after I have updated my R and Bioconductor, the makeTranscriptDbFromUCSC
> function from GenomicFeatures package does not work anymore as it gives the
> following error: "Error in .local(.Object, ...) : Failed to obtain 'hguid'
> cookie". I'm using Mac version 10.6.8, the software is updated. Here is the
> R code that led to an error:
> >
> >>library(GenomicFeatures)
> >>supportedUCSCtables() ### the tables are listed
> >>getChromInfoFromUCSC("mm9", goldenPath_url = "
> http://hgdownload.cse.ucsc.edu/goldenPath") ### the chromosomes and their
> lengths are listed
> >> txdb  = makeTranscriptDbFromUCSC(genome="mm9", tablename="refGene")
> > Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
> >
> > Does anyone know the solution to this problem? I would be really
> grateful for your help.
>
> Archived posts suggest the problem is either a local network/proxy
> configuration issue, or it may have something to do with the new
> European mirror.
>
> You might try the following (this involves direct slot access and is
> probably not the approved method, but someone can pipe in with a
> better way).
>
> library(rtracklayer)
> session <- browserSession("UCSC")
> url <- session@url
> session@url <- "http://genome.ucsc.edu/cgi-bin/"
>
> Then retry the line that failed before.
>
> Dan
>
> >
> >
> >
> >  -- output of sessionInfo():
> >
> > R version 3.0.1 (2013-05-16)
> > Platform: x86_64-apple-darwin10.8.0 (64-bit)
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods
>   base
> >
> > other attached packages:
> > [1] GenomicFeatures_1.12.2 AnnotationDbi_1.22.6   Biobase_2.20.1
> > [4] GenomicRanges_1.12.4   IRanges_1.18.1         BiocGenerics_0.6.0
> >
> > loaded via a namespace (and not attached):
> >  [1] biomaRt_2.16.0     Biostrings_2.28.0  bitops_1.0-5
> BSgenome_1.28.0
> >  [5] DBI_0.2-7          RCurl_1.95-4.1     Rsamtools_1.12.3
> RSQLite_0.11.4
> >  [9] rtracklayer_1.20.2 stats4_3.0.1       tools_3.0.1
>  XML_3.95-0.2
> > [13] zlibbioc_1.6.0
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
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