[BioC] Download problems from GEO

[James F. Reid]

Hi Hendrik,

it looks like a problem at GEO, for the moment the files at the GEO site 
are pointing to:
ftp://ftp-private.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatrix/GSE508/
instead of the default
ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatrix/GSE508/
Maybe they are doing some maintenance of some kind. I would be patient 
and try later.

J.

On 10/07/12 12:36, Hendrik [guest] wrote:
>
> Anyone else experiencing problems downloading data through the function getGEO? Is it a problem of GEO or the package?
>
>> gse <- getGEO("GSE508")
> Error in function (type, msg, asError = TRUE)  :
>    Server denied you to change to the given directory
>> traceback()
> 7: fun(structure(list(message = msg, call = sys.call()), class = c(typeName,
>         "GenericCurlError", "error", "condition")))
> 6: function (type, msg, asError = TRUE)
>     {
>         if (!is.character(type)) {
>             i = match(type, CURLcodeValues)
>             typeName = if (is.na(i))
>                 character()
>             else names(CURLcodeValues)[i]
>         }
>         typeName = gsub("^CURLE_", "", typeName)
>         fun = (if (asError)
>             stop
>         else warning)
>         fun(structure(list(message = msg, call = sys.call()), class = c(typeName,
>             "GenericCurlError", "error", "condition")))
>     }(9L, "Server denied you to change to the given directory", TRUE)
> 5: .Call("R_curl_easy_perform", curl, .opts, isProtected, .encoding,
>         PACKAGE = "RCurl")
> 4: curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
> 3: getURL(sprintf("ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatrix/%s/",
>         GEO))
> 2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL)
> 1: getGEO("GSE508")
>>
>
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                       LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.23.5    Biobase_2.16.0     BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1.1 tools_2.15.0   XML_3.9-4.1
>
>
> --
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>
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