[BioC] Bioconductor GEOquery package error

[Sean Davis]

On Mon, May 3, 2010 at 2:55 PM, Sean Davis <seandavi at gmail.com> wrote:
> On Sat, May 1, 2010 at 8:56 AM, Rahul Sharma <rahularjun86 at gmail.com> wrote:
>> Hello Sir/Madam
>>
>> I am Rahul Sharma, Research fellow from New Delhi India, i need to do some
>> analysis on the GDS1825 dataset, i am using the GEOquery package of
>> Bioconductor, following error occurs when i try to fetch the
>> link.....internet connection is there on my system dnt know why it is not
>> connecting to the ftp..
>>
>> ======================================================================
>>
>>> library(GEOquery)
>> Loading required package: Biobase
>>
>> Welcome to Bioconductor
>>
>>  Vignettes contain introductory material. To view, type
>>  'openVignette()'. To cite Bioconductor, see
>>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>>
>> Loading required package: RCurl
>> Loading required package: bitops
>>> gpl <- getGEO('GDS1825',destdir=".")
>> Error in download.file(myurl, destfile, mode = mode, quiet = TRUE) :
>>  cannot open URL '
>> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1825.soft.gz'
>
> Hi, Rahul.
>
> This has nothing to do with GEOquery.  The ftp site is broken at NCBI
> GEO; I'm checking with them about the details.

It appears they were rebuilding the ftp site, as the files are slowly
being repopulated.  The above code works here, at least.

Sean