[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: âBiocGenericsâ
The following object(s) are masked from âpackage:statsâ:
xtabs
The following object(s) are masked from âpackage: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
> 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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