Question: Gviz ideogram error
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gravatar for Siddharth Sethi
6.3 years ago by
Siddharth Sethi10 wrote:
Hi, I am getting this error for the ideogram track : Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie Calls: IdeogramTrack ... browserSession -> new -> initialize -> initialize -> .local Execution halted Command : ideogram <- IdeogramTrack(genome = "mm10", chromosome = "chr6" , background.title = "black") The commands runs fine locally, but gives an error on server. I suspect it might be internet connection problem. Does Gviz needs some particular ports to be open to connect to UCSC? Please help. Thanks, Sid This email may have a PROTECTIVE MARKING, for an explanation please see: http://www.mrc.ac.uk/About/Informationandstandards/Documentmarkin g/index.htm [[alternative HTML version deleted]]
ideogram gviz • 1.1k views
ADD COMMENTlink modified 6.3 years ago by Steve Lianoglou12k • written 6.3 years ago by Siddharth Sethi10
Answer: Gviz ideogram error
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gravatar for Steve Lianoglou
6.3 years ago by
Denali
Steve Lianoglou12k wrote:
Hi, On Wed, Aug 7, 2013 at 3:45 AM, Siddharth Sethi <s.sethi at="" har.mrc.ac.uk=""> wrote: > Hi, > > I am getting this error for the ideogram track : > > Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie > Calls: IdeogramTrack ... browserSession -> new -> initialize -> initialize -> .local > Execution halted > > Command : ideogram <- IdeogramTrack(genome = "mm10", chromosome = "chr6" , background.title = "black") > > > The commands runs fine locally, but gives an error on server. I suspect it might be internet connection problem. > Does Gviz needs some particular ports to be open to connect to UCSC? > Please help. First: please provide the output from `sessionInfo()` after you've loaded the Gviz library on the machine that is failing. Second: you can, perhaps, test a general internet access problem by seeing if you can "fetch" the main google.com page, eg: R> library(RCurl) R> g <- getURL("http://www.google.com") Now take a look at g and see if you're talking with The Internet: R> substr(g, 1, 70) [1] "<html itemscope="\" itemscope\""="" itemtype="\" <a="" href="&lt;a href=" http:="" schema.org"="" rel="nofollow">http://schema.org" rel="nofollow">http://schema.org"" -steve="" --="" steve="" lianoglou="" computational="" biologist="" bioinformatics="" and="" computational="" biology="" genentech="" <="" div="">
ADD COMMENTlink written 6.3 years ago by Steve Lianoglou12k
On 08/07/2013 12:41 PM, Steve Lianoglou wrote: > Hi, > > On Wed, Aug 7, 2013 at 3:45 AM, Siddharth Sethi <s.sethi at="" har.mrc.ac.uk=""> wrote: >> Hi, >> >> I am getting this error for the ideogram track : >> >> Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie >> Calls: IdeogramTrack ... browserSession -> new -> initialize -> initialize -> .local >> Execution halted there were problems like this in rtracklayer version 1.20.2 and before (1.21.7 in Bioc devel). So in a current R biocLite() might be helpful. Martin >> >> Command : ideogram <- IdeogramTrack(genome = "mm10", chromosome = "chr6" , background.title = "black") >> >> >> The commands runs fine locally, but gives an error on server. I suspect it might be internet connection problem. >> Does Gviz needs some particular ports to be open to connect to UCSC? >> Please help. > > First: please provide the output from `sessionInfo()` after you've > loaded the Gviz library on the machine that is failing. > > Second: you can, perhaps, test a general internet access problem by > seeing if you can "fetch" the main google.com page, eg: > > R> library(RCurl) > R> g <- getURL("http://www.google.com") > > Now take a look at g and see if you're talking with The Internet: > > R> substr(g, 1, 70) > [1] "<html itemscope="\" itemscope\""="" itemtype="\" <a="" href="&lt;a href=" http:="" schema.org"="" rel="nofollow">http://schema.org" rel="nofollow">http://schema.org""> > -steve > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 6.3 years ago by Martin Morgan ♦♦ 24k
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