[BioC] GEOquery installation problem

[zhihua zhang]

Thanks James,

I tried (since I don't have root)

source("http://www.bioconductor.org/biocLite.R")
biocLite("GEOquery",lib = '/home/izg/R/x86_64-redhat-linux-gnu-library' )

it was failed by short of package RCurl, so I installed RCurl in '/home/izg/R/x86_64-redhat-linux-gnu-library' as well, 

then try again:

biocLite("GEOquery", lib = '/home/izg/R/x86_64-redhat-linux-gnu-library' )

Running biocinstall version 2.3.13 with R version 2.8.1 
Your version of R requires version 2.3 of Bioconductor.
also installing the dependency 'RCurl'

trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_0.98-1.tar.gz'
Content type 'application/x-gzip' length 486610 bytes (475 Kb)
opened URL
==================================================
downloaded 475 Kb

trying URL 'http://bioconductor.org/packages/2.3/bioc/src/contrib/GEOquery_2.6.0.tar.gz'
Content type 'application/x-gzip' length 136228 bytes (133 Kb)
opened URL
==================================================
downloaded 133 Kb

* Installing *source* package 'RCurl' ...
...
...
...
...
** building package indices ...
* DONE (RCurl)
* Installing *source* package 'GEOquery' ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor
Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: RCurl
Loading required package: bitops
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared library '/home/izg/R/x86_64-redhat-linux-gnu-library/RCurl/libs/RCurl.so':
  libcurl.so.4: cannot open shared object file: No such file or directory
Error: package 'RCurl' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'GEOquery'
** Removing '/home/izg/R/x86_64-redhat-linux-gnu-library/GEOquery'

The downloaded packages are in
    /tmp/Rtmphp1tUO/downloaded_packages
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
installation of package 'GEOquery' had non-zero exit status


Then I goto '/home/izg/R/x86_64-redhat-linux-gnu-library/RCurl/libs/' and found there is nothing here, all library has been deleted somehow. even if I copy/install those lib again,
it always happened like this.   I tried to change the mode of this libraries as read-only, it's still been deleted anyhow.

Thanks.

Zhihua.








----- Original Message ----
From: James W. MacDonald <jmacdon at med.umich.edu>

Cc: bioconductor at stat.math.ethz.ch
Sent: Monday, August 3, 2009 12:30:40 PM
Subject: Re: [BioC] GEOquery installation problem



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
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1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826