[BioC] [devteam-bioc] Failed to obtain \'hguid\' cookie for UCSC browser session

[Dan Tenenbaum]

On Sun, Jul 7, 2013 at 5:37 AM, Maintainer <maintainer at 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 at url
session at 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
>
> --
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>
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