[BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")

[Simone [guest]]

Hi!

Currently I am trying to use the library "GEOquery" to retrieve meta information (phenodata information) and the data tables of GEO samples (from GEO series without GEO datasets).

I already have got the data (.soft.gz files), so I tried it the following way for example: 

GSE19711 <- getGEO(filename=system.file("mypath/GSE19711_family.soft.gz", package="GEOquery"))

But I get the following error: 

Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : 
  invalid 'nlines' argument
In addition: Warning messages:
1: In file(fname, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former
2: In file(con, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former
3: In file(fname, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former

I tried it on windows and linux and also with the newest version of R and GEOquery. 

On both machines there occurs the same error, also with other GEO accession numbers. 

What is going wrong and what can I do to get the information I need? 

When I use a path to my file which is not existing, I get the same error, but I am quite sure that I set the working directory and path to the GEO file correctly. 

Greets, 
Simone

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=German_Austria.1252  LC_CTYPE=German_Austria.1252    LC_MONETARY=German_Austria.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Austria.1252    

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

other attached packages:
[1] GEOquery_2.23.3     Biobase_2.16.0      BiocGenerics_0.2.0  BiocInstaller_1.4.4

loaded via a namespace (and not attached):
[1] RCurl_1.91-1.1 tools_2.15.0   XML_3.9-4.1 

> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             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_2.21.9 Biobase_2.14.0 

loaded via a namespace (and not attached):
[1] RCurl_1.91-1 tools_2.14.1 XML_3.9-4  

> traceback()
6: read.table(con, sep = "\t", header = FALSE, nrows = nseries)
5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
4: suppressWarnings(read.table(con, sep = "\t", header = FALSE, 
       nrows = nseries))
3: parseGSEMatrix(fname)
2: parseGEO(filename, GSElimits)
1: getGEO(filename = system.file("homo_sapiens/peripheral_whole_blood/GSE19711/GSE19711_family.soft.gz", 
       package = "GEOquery"))

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