On Thu, Dec 2, 2010 at 2:03 PM, Guillaume Mouron <guillaume.mouron@gmail.com
> wrote:

> Hi,
>
> My problem might have to do with one previously sent today by Koray Kaya,
> but I was not yet member of the mailing list at that moment, so I don't
> know
> how to answer to that message, sorry for that.
>
> I also have a problem downloading GSE data. GSM and GDS downloads work.
>
> Here is the error I get :
> > test <- getGEO('GSE13481',destdir='./
> test-geoquery')
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
> :
>  line 1 did not have 6 elements
>
>
Hi, Guillaume.  Could you upgrade to the latest versions of R and GEOquery
and see if that works for you?  I am not able to reproduce the error with
the current version of GEOquery.

Thanks,
Sean



> The problem is not a proxy problem, as I already fixed this (by switching
> to
> wget for downloading with options("download.file.method"="wget"), and with
> the ftp_proxy correctly set in the environment variables (meaning defined
> as
> ftp_proxy="http://proxyname:proxyport), if that can help).
>
> When I try this :
> > download.file('
>
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE13481/GSE13481_family.soft.gz
> ',"test.soft.gz")
>
> The download of the GSE file works correctly.
>
> So the problem seems to be somewhere else ...
>
> Content of my sessioninfo() :
> > sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-redhat-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.13.5 Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.5-0 XML_3.2-0
>
>
> Thanks,
> Guillaume Mouron
>
> PS: I've already send an email but I was not subscribed yet, and I can't
> cancel it anymore, but it is not published yet though, sorry for the
> duplicate.
>
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>
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