[BioC] GEOquery Error

[Sean Davis]

On Thu, Feb 2, 2012 at 12:38 PM, ying chen <ying_chen at live.com> wrote:
>
>
>
> Hi,
>
> I want to use GEOquery package to get the raw files of a lot GEO datasets at once ( > files <- sapply(mydata$GSE_ID, getGEOSuppFiles) ), but I got the following error message when I did a simple test run. Any suggestion?
>

Hi, Ying.

This is not a GEOquery issue.  The directory housing the data is not
on the FTP site.  NCBI GEO periodically rebuilds stuff on the site.
That might be occurring now.  I'd suggest emailing NCBI GEO directly
if you are in a hurry.  Alternatively, wait an hour or two to see if
the problem is resolved.

Sean


>> library(GEOquery)
> Loading required package: Biobase
> Welcome to Bioconductor
>  Vignettes contain introductory material. To view, type
>  'browseVignettes()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation("pkgname")'.
> Setting options('download.file.method.GEOquery'='curl')
>> files <- getGEOSuppFiles("GSE23720")
> [1] "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE23720/"
> Error in function (type, msg, asError = TRUE)  :
>  Server denied you to change to the given directory
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
> 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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 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_2.20.8 Biobase_2.14.0
> loaded via a namespace (and not attached):
> [1] RCurl_1.9-5 XML_3.9-4
>>
>
>
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