[BioC] GEOquery

Sean Davis sdavis2 at mail.nih.gov
Tue Jul 8 14:12:23 CEST 2008

On Tue, Jul 8, 2008 at 6:17 AM, Svetlana Vinogradova <kintany at gmail.com> wrote:
> Dear Sean Davis,
> I'm a student of Moscow State University and I want to use GEOquery to get
> the information from GEO. I use R on ubuntu, so I've downloaded the
> source... Then I'm trying to install the package but got some problems...
>> install.packages("GEOquery_1.7.2.tar.gz", repos=NULL,
>> lib=.libPaths()[[1]])
> * Installing *source* package 'GEOquery' ...
> ** R
> ** inst
> ** help
>  >>> Building/Updating help pages for package 'GEOquery'
>      Formats: text html latex example
>   GDS-class                         text    html    latex
>   GDS2MA                            text    html    latex   example
>   GEOData-class                     text    html    latex
>      missing link(s):  dataTable-class
>   GEODataTable-class                text    html    latex
>   GPL-class                         text    html    latex
>   GSE-class                         text    html    latex
>   GSM-class                         text    html    latex
>   getGEO                            text    html    latex   example
>   getGEOfile                        text    html    latex   example
>   parseGEO                          text    html    latex
> ** building package indices ...
> * DONE (GEOquery)
> Could you help me to solve it?

Hello, Svetlana.  Thanks for the interest in GEOquery.  The output
above looks OK--I do not see any errors....

However, the better way to install bioconductor packages (and, indeed,
R packages in general) is to use the biocLite() script:


Doing so ensures that the package versions match each other and the
appropriate version of R.  You can refer to the bioconductor website
for more information about installation of bioconductor packages.  If
you have further problems, could you include the output of
sessionInfo() in the email?


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