Hi
I am trying to get GSE24080 from GEO using getGeo() function in Geoquery package and get several warnings. 

Can anyone please help me clear out the warnings and get successful download? I am using R version 2.13.1 (2011-07-08) 
on Windows XP. Thanks.--Silav


> Sys.getlocale()
[1] "LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252"


> library(GEOquery)
Loading required package: Biobase
Welcome to Bioconductor
  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.
Setting options('download.file.method.GEOquery'='curl')
Warning message:
'.readRDS' is deprecated.
Use 'readRDS' instead.
See help("Deprecated") 

> gse24080 <- getGEO("GSE24080")
Found 3 file(s)
GSE24080_series_matrix-1.txt.gz
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE24080/GSE24080_series_matrix-1.txt.gz'
ftp data connection made, file length 38807310 bytes
opened URL
downloaded 37.0 Mb

File stored at: 
C:\DOCUME~1\.......
GSE24080_series_matrix-2.txt.gz
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE24080/GSE24080_series_matrix-2.txt.gz'
ftp data connection made, file length 38738618 bytes
opened URL
downloaded 36.9 Mb

Using locally cached version of GPL570 found here:
C:\DOCUME~1\......... 
GSE24080_series_matrix-3.txt.gz
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE24080/GSE24080_series_matrix-3.txt.gz'
ftp data connection made, file length 7721111 bytes
opened URL
downloaded 7.4 Mb

Using locally cached version of GPL570 found here:
C:\DOCUME~1\........ 
There were 15 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
  seek on a gzfile connection returned an internal error
2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
  seek on a gzfile connection returned an internal error
3: In readLines(con, 1) : seek on a gzfile connection returned an internal error
4: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error
5: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error
6: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
  seek on a gzfile connection returned an internal error
7: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
  seek on a gzfile connection returned an internal error
8: In readLines(con, 1) : seek on a gzfile connection returned an internal error
9: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error
10: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error
11: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
  seek on a gzfile connection returned an internal error
12: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
  seek on a gzfile connection returned an internal error
13: In readLines(con, 1) : seek on a gzfile connection returned an internal error
14: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error
15: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error
> 


--Silav
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