[Bioc-devel] GEOquery function getGEO broken?

[Valerie Obenchain]

Here is thread where Sean acknowledges the warnings and a plan to fix. 
Bottom line, they can be safely ignored.

https://stat.ethz.ch/pipermail/bioconductor/2011-September/041150.html

Valerie


On 09/16/2011 02:19 AM, Steve Lianoglou wrote:
> 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
>