[Bioc-devel] GEOquery function getGEO broken?

[Steve Lianoglou]

Hi,

On Fri, Sep 16, 2011 at 4:48 AM, Andreas Heider
<aheider at trm.uni-leipzig.de> wrote:
> Ok, so I tried the following:
>
> *source("http://www.bioconductor.org/biocLite.R")
> biocLite("GEOquery")
> *
> Lade nötiges Paket: 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')
> Warnmeldung:
> '.readRDS' ist veraltet.
> Benutzen Sie stattdessen 'readRDS'
> Siehe help("Deprecated")
>
> *library(GEOquery)
> gds858<- getGEO('GDS858')  #GSEMatrix=TRUE is default
> *
> File stored at:
> C:\DOKUME~1\admin\LOKALE~1\
> Temp\RtmpAyyjO2/GDS858.soft.gz
> Es gab 50 oder mehr Warnungen (Anzeige der ersten 50 mit warnings())
>
> 50 or more warnings? Why?
> It was a clean install of R 2.13. on Windows.

Warnings aren't errors, so ... it looked like this actually worked.

If you really want to know why, though, you can run `warnings()` after
the command completes to see the last 50 of them.

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact