On Wed, Oct 17, 2012 at 5:06 AM, T.Kartheeswaran [guest] <
guest@bioconductor.org> wrote:

>
> How can i download the eset available on ncbi through this command
> gset <- getGEO("GSE1542", GSEMatrix =TRUE)
>
>
>
>
>  -- output of sessionInfo():
>
> >library(GEOquery)
> Loading required package: Biobase
> Loading required package: BiocGenerics
>
> Attaching package: â€˜BiocGenericsâ€™
>
> The following object(s) are masked from â€˜package:statsâ€™:
>
>     xtabs
>
> The following object(s) are masked from â€˜package:baseâ€™:
>
>     anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
>     get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
>     pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
>     rownames, sapply, setdiff, table, tapply, union, unique
>
> Welcome to Bioconductor
>
>     Vignettes contain introductory material; view with
>     'browseVignettes()'. To cite Bioconductor, see
>     'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Setting options('download.file.method.GEOquery'='auto')>gset <-
> getGEO("GSE1542", GSEMatrix =TRUE)
> Error in function (type, msg, asError = TRUE)  :
>   Could not resolve host: ftp.ncbi.nlm.nih.gov; No data record of
> requested type
>

Obvious question, but are you connected to the internet?  If so, are you
behind a firewall?  If you are behind a firewall, do you need to set up a
proxy?

Sean



> > 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")))
>    }(6L, "Could not resolve host: ftp.ncbi.nlm.nih.gov; No data record of
> requested type",
>        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("GSE1542", GSEMatrix = TRUE)
> >
> sessionInfo()
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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