Dear all,

I was thinking along the same lines as Dan. I've run some code of
rtracklayer and have some more detailed information that might be useful
for debugging, since this indeed seems to be a european problem.

When initializing a new instance of "UCSCSession" (when invoking method
browserSession with signature missing), the following webadres is assigned
by default to its slot “url”: "http://genome.ucsc.edu/cgi-bin/"

To knock on the door of the UCSC server something similar as the following
code is used:

> handle <- getCurlHandle()

> gw <- getURL("http://genome.ucsc.edu/cgi-bin/hgGateway",

+         cookiefile = tempfile(), curl = handle)

Which gives a response of the server. This response is in Europe not what
is expected, leading to the previously described error. Server response:

> gw

"<!DOCTYPE HTML PUBLIC \"-//IETF//DTD HTML
2.0//EN\">\n<html><head>\n<title>302
Found</title>\n</head><body>\n<h1>Found</h1>\n<p>The document has moved <a
href=\"
http://genome-euro.ucsc.edu:80/cgi-bin/hgGateway?redirect=auto&amp;source=genome.ucsc.edu\">here</a>.</p>\n<hr>\n<address>Apache/2.2.3
(CentOS) Server at genome.ucsc.edu Port 80</address>\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

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