[BioC] GEOquery

Cei Abreu-Goodger cei at sanger.ac.uk
Fri Jul 11 17:30:41 CEST 2008

Hi Sean,

I'm trying to help Harpreet to get the GEOquery library working properly 
over here. Thanks to what you pointed out, we are able to track the 
problem down to curl using our http proxy, which for ftp transfers is 
not required. We still have one problem, that I can't figure how to turn 
off the "ftp.use.epsv" option in RCurl. So, on a linux terminal, I can use:

curl --disable-epsv 
-r--r--r--   1 ftp      anonymous   930471 Apr 13 05:32 

(without the --disable-epsv it times out unless I set the ftp_proxy, but 
then I get the HTML index instead of the file listing)

inside R, I imagine I have to turn the "ftp.use.epsv" option off, and 
I've tried doing something like this:

myCurl <- getCurlOptionsConstants()
myCurl[["ftp.use.epsv"]] <- 0

but it keeps timing out...

I also tried:


but that doesn't seem to have any effect on what 
getCurlOptionsConstants() returns, it just creates a CURLOptions object, 
which I can't figure out how to use.

Do you have any suggestions, or should I search for help directly with 
the RCurl developers?

Many thanks,

> So, this appears to be the problem.  It looks like your proxy is
> intercepting the ftp directory listing and converting it to HTML.  I
> do not know how to solve this problem, as it appears to be a proxy
> configuration issue at your institution.  However, I can't say for
> sure.  The output of the getURL() command should look like:
>> getURL("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4201/")
> [1] "-r--r--r--   1 ftp      anonymous   930471 Apr 13 05:32
> GSE4201_series_matrix.txt.gz\n"
> Notice how yours is much longer and is HTML, not plain text.
> Sean

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