Question: Download problems from GEO
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7.2 years ago by
Guest User12k
Guest User12k 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/SeriesMatri x/%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 -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 7.2 years ago by James F. Reid120 • written 7.2 years ago by Guest User12k
Answer: Download problems from GEO
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gravatar for James F. Reid
7.2 years ago by
James F. Reid120
James F. Reid120 wrote:
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/SeriesMat rix/%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 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 7.2 years ago by James F. Reid120
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