I tried retrieving a data from NCBI GEO using Rstudio.
The download was complete as the following was shown.
> gset <- getGEO("GSE30565", GSEMatrix =TRUE, destdir= "C:/Documents and Settings/Administrator/My Documents/Downloads", AnnotGPL=FALSE)
Found 1 file(s)
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30565/matrix/GSE30565_series_matrix.txt.gz'
downloaded 792 KB
File stored at:
C:/Documents and Settings/Administrator/My Documents/Downloads/GPL13884.soft
But what worries me is the warning line following this :
In read.table(file = file, header = header, sep = sep, quote = quote, :
not all columns named in 'colClasses' exist
I am sure that my Rstudio is uptodate including the packages:
R version 3.3.1 (2016-06-21)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows XP (build 2600) Service Pack 3
 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
attached base packages:
 parallel stats graphics grDevices utils datasets methods base
other attached packages:
 GEOquery_2.38.4 Biobase_2.32.0 BiocGenerics_0.18.0
loaded via a namespace (and not attached):
 httr_1.2.1 R6_2.1.3 tools_3.3.1 RCurl_1.95-4.8 bitops_1.0-6
Kindly check if there is a bug in the package or tell me what i should do to sort this warning.