[BioC] GEOquery::parseGEO throws error reading file

[Gad Abraham]

Hi,

I'm using GEOquery 2.4.1 to read an NCBI GEO file 
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4284/GSE4284_series_matrix.txt.gz 
  but parseGEO throws an error. The switch argument evaluates to "0", 
which doesn't match alternative, so it tries to match on the last empty 
argument and fails. I don't know if this is related to the warnings; the 
file contains text such as manufacturer\xa1\xafs which may not parse 
correctly.

Below is the output.

Thanks for any advice,
Gad

 > g <- getGEO(filename="GSE4284_series_matrix.txt")
Error in switch(as.character(first.entity[1]), sample = { :
   argument is missing, with no default
In addition: Warning messages:
1: In grep("^\\^(DATASET|SAMPLE|SERIES|PLATFORM|ANNOTATION)", line,  :
   input string 1 is invalid in this locale
2: In grep("^\\^(DATASET|SAMPLE|SERIES|PLATFORM|ANNOTATION)", line,  :
   input string 1 is invalid in this locale
 > debugger()
Message:  Error in switch(as.character(first.entity[1]), sample = { :
   argument is missing, with no default
Available environments had calls:
1: getGEO(filename = "GSE4284_series_matrix.t
2: parseGEO(con, GSElimits)
3: switch(as.character(first.entity[1]), sample = {

Enter an environment number, or 0 to exit  Selection: 2
Browsing in the environment with call:
    parseGEO(con, GSElimits)
Called from: debugger.look(ind)
Browse[1]> as.character(first.entity[1])
[1] "0"

 > sessionInfo()
R version 2.7.1 (2008-06-23)
i486-pc-linux-gnu

locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] GEOquery_2.4.1 RCurl_0.9-3    Biobase_2.0.1

-- 
Gad Abraham
Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: gabraham at csse.unimelb.edu.au
web: http://www.csse.unimelb.edu.au/~gabraham