[BioC] Unable to use GEOquery (SOLVED)

[Juan C Oliveros Collazos]

Sean,

I did what you said and now GEOquery is running properly.

I think biocLite also installs a number of additional packages needed 
for GEOquery to work.

Thanks a lot!

Best,

Juan Carlos




Sean Davis wrote:
> On Thu, Apr 17, 2008 at 6:21 AM, Juan C Oliveros Collazos
> <oliveros at cnb.csic.es> wrote:
>> Hi all,
>>
>>  I just downloadad and installed the package "GEOquery" from bioconductor
>>  web site. The installation carried-out with no errors.
> 
> Hi, Juan.  You might want to try again.  First, remove the package
> with remove.packages('GEOquery').  Then, type:
> 
> source('http://bioconductor.org/biocLite.R')
> biocLite('GEOquery')
> 
> Does this fix the problem?
> 
> Sean
> 
> 
>>  However, when I try to load the library: "library(GEOquery)", I get the
>>  following error:
>>
>>  -------------------------------------------------------------------------
>>   > library(GEOquery);
>>  Error in makeClassRepresentation(Class, properties, superClasses,
>>  prototype,  :
>>    element 2 is empty;
>>     the part of the args list of 'list' being evaluated was:
>>     (header = list(), )
>>  Error : unable to load R code in package 'GEOquery'
>>  Error: package/namespace load failed for 'GEOquery'
>>  ------------------------------------------------------------------------
>>
>>
>>  This is the sessionInfo() output:
>>  ------------------------------------------------------------------------
>>   > sessionInfo();
>>  R version 2.6.0 (2007-10-03)
>>  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] Biobase_1.16.1 limma_2.12.0
>>
>>  loaded via a namespace (and not attached):
>>  [1] rcompgen_0.1-15
>>  ----------------------------------------------------------------------
>>
>>  Looking at this output, It seems that the package is not installed.
>>  However, when i do "installed.packages()" GEOquery appears in the list!
>>
>>  I can not figure-out where the error is...
>>
>>  Any help?
>>
>>  Thanks in advance!
>>
>>  Best,
>>
>>  Juan Carlos
>>
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>>
> 

-- 
Juan Carlos Oliveros
BioinfoGP, CNB-CSIC

** NEW EMAIL ADDRESS: oliveros at cnb.csic.es **