[BioC] Download problem with GEOquery::getGEO()

[axel.klenk at actelion.com]

Dear Bioconductors,

I'm having trouble downloading GSE31014 (or any other study that I tried) 
from GEO:

> library("GEOquery")
Setting options('download.file.method.GEOquery'='curl')
> options(download.file.method.GEOquery ="wget")
> gse <- getGEO(GEO = "GSE31014")
Error in function (type, msg, asError = TRUE)  : 
  Server denied you to change to the given directory

Searching the archive reveals that two years ago a similar problem has 
been 
temporary (?) and attributed to server changes at NCBI/GEO. 

https://stat.ethz.ch/pipermail/bioconductor/2010-March/032095.html

Is there a known solution or workaround, or can anyone reproduce the error 
to
confirm the problem is on the server side?

Thanks in advance,

 - axel


> 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(GEO = "GSE31014")



> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C 
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8 
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8 
 [7] LC_PAPER=C                 LC_NAME=C 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C 
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C 

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base 

other attached packages:
 [1] GEOquery_2.23.5      limma_3.12.1         gtools_2.7.0 
 [4] sfsmisc_1.0-20       geneplotter_1.34.0   lattice_0.20-6 
 [7] annotate_1.34.1      AnnotationDbi_1.18.1 Biobase_2.16.0 
[10] BiocGenerics_0.2.0   MASS_7.3-18 

loaded via a namespace (and not attached):
 [1] compiler_2.15.1    DBI_0.2-5          grid_2.15.1 IRanges_1.14.4 
 [5] RColorBrewer_1.0-5 RCurl_1.91-1       RSQLite_0.11.1 stats4_2.15.1  
 [9] tools_2.15.1       XML_3.9-4          xtable_1.7-0 
> 



Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland



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