Hi,
Thanks for your answer, I'm gonna try that.
One additional piece of information is that if I set GSEMatrix=F, then the
error does not occur.
I will try to upgrade R to see if it fixed the problem.

Cheers
Guillaume

On Thu, Dec 2, 2010 at 14:12, Sean Davis <sdavis2@mail.nih.gov> wrote:

>
>
> 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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>
>

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