[BioC] GEOquery installation problem

[James W. MacDonald]

zhihua zhang wrote:
> Hi, 
> 
> I was trying to install GEOquery_1.7.2.tar.gz into my R (version 2.8.1 ). Because I am not root, so I did the following
> 
>> install.packages("~/download/GEOquery_1.7.2.tar.gz", dependencies = TRUE, repos = NULL)
> 
> This is what I got:
> 
> Warning in install.packages("~/download/GEOquery_1.7.2.tar.gz", dependencies = TRUE,  :
>   argument 'lib' is missing: using '/home/izg/R/x86_64-redhat-linux-gnu-library/2.8'
> * Installing *source* package 'GEOquery' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> 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'
> Execution halted
> ERROR: lazy loading failed for package 'GEOquery'
> ** Removing '/home/izg/R/x86_64-redhat-linux-gnu-library/2.8/GEOquery'
> Warning message:
> In install.packages("~/download/GEOquery_1.7.2.tar.gz", dependencies = TRUE,  :
>   installation of package '/home/izg/download/GEOquery_1.7.2.tar.gz' had non-zero exit status
> 
> I searched in this mailist and found no answer, neither dose in google,
> What am I gonna do then?

I would recommend installing the package the correct way, as the version 
you seem to have downloaded is AFAIK not the correct version for your 
version of R.

source("http://www.bioconductor.org/biocLite.R")
biocLite("GEOquery")

Pointing to a downloaded file and saying dependencies = TRUE, repos = 
NULL is not going to do what you seem to think it will. You can only get 
the correct dependencies if you point to a CRAN type repository, which 
is what biocLite() will do for you.

Best,

Jim



> 
> Thanks
> 
> Zhihua.
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826