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Last seen 9.6 years ago
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.
-- 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.
Found
\nThe document has moved here.
\n\nApache/2.2.3 (CentOS) Server at genome.ucsc.edu Port 80\n</body></html>\n" Which basically tells me to try a different web-server (a similar warning as we get when we would visit UCSC through the browser in Europe) : http://genome-euro.ucsc.edu/cgi-bin/hgGateway. Following Dans suggestion: > browserSession("UCSC",url="http://genome-euro.ucsc.edu/cgi-bin/") Does not really help us as the response of the server: > gw <- getURL("http://genome-euro.ucsc.edu/cgi-bin/hgGateway", + cookiefile = tempfile(), curl = handle) is quite lengthy and informative, though unfortunately it does not contain the stuff were looking for. Neither a hguid or the word Cookie is present. It does tell about hgsids, which are also required for a successful browser session, so I guess I'm on the right place. I can send you the total output if you want. I didnt paste it in here, because of the length of the response. My guess would be that due to a new European law, sites are not allowed to store cookies locally at users anymore, unless the user explicitly agrees. Hence this is not offered anymore by the European mirror of UCSC. I hope this helps in debugging. Cheerz, Erik [[alternative HTML version deleted]]
Found
\nThe document has moved href=\" > http://genome-euro.ucsc.edu:80/cgi-bin/hgGateway?redirect=auto&s ource=genome.ucsc.edu\">here.
\n\nApache/2.2.3 > (CentOS) Server at genome.ucsc.edu Port 80\n</body></html>\n" > > Which basically tells me to try a different web-server (a similar warning > as we get when we would visit UCSC through the browser in Europe) : > http://genome-euro.ucsc.edu/cgi-bin/hgGateway. Following Dan?s suggestion: > > > browserSession("UCSC",url="http://genome-euro.ucsc.edu/cgi-bin/") > > Does not really help us as the response of the server: > > > gw <- getURL("http://genome-euro.ucsc.edu/cgi-bin/hgGateway", > > + cookiefile = tempfile(), curl = handle) > > is quite lengthy and informative, though unfortunately it does not contain > the stuff we?re looking for. Neither a hguid or the word ?Cookie? is > present. It does tell about hgsid?s, which are also required for a > successful browser session, so I guess I'm on the right place. I can send > you the total output if you want. I didn?t paste it in here, because of the > length of the response. > > My guess would be that due to a new European law, sites are not allowed to > store cookies locally at users anymore, unless the user explicitly agrees. > Hence this is not offered anymore by the European mirror of UCSC. > > I hope this helps in debugging. > > Cheerz, > > Erik > > [[alternative HTML version deleted]] >