[BioC] Trouble with getGEO retrieving dataset

smohapat at vbi.vt.edu smohapat at vbi.vt.edu
Wed May 30 05:33:23 CEST 2007


Thanks for fixing the bug so promptly. I observed something new using
GEOquery 2.0.4. Parsing is fine, but it pauses with a "Browse[1]>". I hit
enter and it moves on. I do not know why it halts, and I was planning to
use the getGEO call as part of a script, not interactive. Is there anyway
we could circumvent this?



> library("GEOquery")

> GDS1082=getGEO("GDS1082")
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1082.soft.gz'
using Synchronous WinInet calls
opened URL
downloaded 294Kb

File stored at:
parsing geodata
parsing subsets
Called from: parseGDSSubsets(txt)
ready to return
> sessionInfo()
R version 2.5.0 (2007-04-23)

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:


>> Hi, Saroj.  You are not doing anything wrong.  GDS1082 is unusual in
>> that it contains no SUBSET tags.  I was unaware that such GDS files
>> existed, so the code didn't deal with this situation.  I have corrected
>>  the problem in the development version of GEOquery which should be
>> available in the next day or so.  I will be changing the release
>> version as well; look for a new version early next week.  Thanks for the
>> bug report.
>> Sean

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