[BioC] GEOquery installation problem

[zhihua zhang]

I installed in many ways 
source("http://www.bioconductor.org/biocLite.R")
biocLite("RCurl",lib = '/home/izg/R/x86_64-redhat-linux-gnu-library' )

or 

install.packages("RCurl",lib = '/home/izg/R/x86_64-redhat-linux-gnu-library')

or in command line

~/tmp/curl-7.19.5> make install

all those seems successfully done!:

* DONE (RCurl)
The downloaded packages are in
    /tmp/RtmpYm80DR/downloaded_packages

but, you r right, when I try to load the RCurl,
either:
 >library("RCurl")
Error in library("RCurl") : there is no package called 'RCurl'
or 

>library("RCurl", lib.loc="/home/izg/R/x86_64-redhat-linux-gnu-library/")
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared library '/home/izhang/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/namespace load failed for 'RCurl'

there is nothing in the RCurl folder at all.

Zhihua.




----- Original Message ----
From: Steve Lianoglou <mailinglist.honeypot at gmail.com>
To: zhihua zhang <biozhang2001 at yahoo.com.cn>
Cc: James W. MacDonald <jmacdon at med.umich.edu>; bioconductor at stat.math.ethz.ch
Sent: Monday, August 3, 2009 4:01:26 PM
Subject: Re: [BioC] GEOquery installation problem

Hi,

On Aug 3, 2009, at 3:46 PM, zhihua zhang wrote:

> 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,

It doesn't seem that all is well, because the next biocLite tries to load the RCurlo.so file, and fails:

> 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'
> 
...

> 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

It seems as if it can't open the libcurl library (or maybe the RCurl.so library itself?).

> 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.

What do you mean "copy and install those lib"? How are you installing RCurl?

I'd be quite surprised if failing to install GEOquery would then cause the system to go and remove a successfully installed RCurl library.

Try to install RCurl again by itself. Don't install GEOquery yet. After installing RCurl, try to load it as a library:

R> library(RCurl)

I'm guessing that's going to fail. Yes?

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
  |  Memorial Sloan-Kettering Cancer Center
  |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact