[BioC] Unable to download esets through GEOquery

T.Kartheeswaran [guest] guest at bioconductor.org
Wed Oct 17 11:06:00 CEST 2012


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: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    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
> 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()


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