[BioC] GEOquery

[Sean Davis]

On Tue, Jul 8, 2008 at 8:26 AM, Svetlana Vinogradova <kintany at gmail.com> wrote:
> If I use
>
> source('http://bioconductor.org/biocLite.R')
> biocLite('GEOquery')
>
> the log is:
>
>  biocLite('GEOquery')
> Running biocinstall version 2.1.11 with R version 2.6.2
> Your version of R requires version 2.1 of BioConductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   argument 'lib' is missing: using
> '/home/student/R/i686-pc-linux-gnu-library/2.6'
> also installing the dependency 'RCurl'
>
> trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_0.9-3.tar.gz'
> Content type 'application/x-gzip' length 150822 bytes (147 Kb)
> opened URL
> ==================================================
> downloaded 147 Kb
>
> trying URL
> 'http://bioconductor.org/packages/2.1/bioc/src/contrib/GEOquery_2.2.1.tar.gz'
> Content type 'application/x-gzip' length 132037 bytes (128 Kb)
> opened URL
> ==================================================
> downloaded 128 Kb
>
> * Installing *source* package 'RCurl' ...
> checking for curl-config... no
> Cannot find curl-config

Do you have the curl libraries installed on your machine?  If not, you
will need to do that.  Be sure to install the devel package for curl
as well.

Sean

> ERROR: configuration failed for package 'RCurl'
> ** Removing '/home/student/R/i686-pc-linux-gnu-library/2.6/RCurl'
> * 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
>   GEODataTable-class                text    html    latex
>   GPL-class                         text    html    latex
>   GSE-class                         text    html    latex
>   GSM-class                         text    html    latex
>   dataTable                         text    html    latex
>   getGEO                            text    html    latex   example
>   getGEOfile                        text    html    latex   example
>   gunzip                            text    html    latex
>   parseGEO                          text    html    latex
> ** building package indices ...
> * DONE (GEOquery)
>
> The downloaded packages are in
>         /tmp/RtmpFbS6fV/downloaded_packages
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   installation of package 'RCurl' had non-zero exit status
>
>
> Here is information about the session:
>
> R version 2.6.2 (2008-02-08)
> i686-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] limma_2.12.0   Biobase_1.16.3
>
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-17
>>
>
>
> Thanks much,
> Svetlana
>
> 2008/7/8 Sean Davis <sdavis2 at mail.nih.gov>:
>>
>> 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:
>>
>> source('http://bioconductor.org/biocLite.R')
>> biocLite('GEOquery')
>>
>> 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?
>>
>> Sean
>
>