[BioC] GEOquery installation problem

[Steve Lianoglou]

On Aug 3, 2009, at 4:20 PM, zhihua zhang wrote:

> 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')

Are you sure these are working properly? What is the output of these  
commands?

> 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

I can't figure out what the deal is, but it looks like you mixing two  
things together here. The first two commands you listed were for  
installing the R package "RCurl," but by the looks of your "make  
install" command, you are trying to install libcurl 7.19.5 from the  
command line.

Is that right? Is libcurl not already installed in your system?

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

Just as an aside: tell R that you have your own libraries in a special  
directory. I think something like this in your ~/.Rprofile file would  
do the trick:

Sys.setenv(R_LIBS_USER="/home/izg/R/x86_64-redhat-linux-gnu-library")

So you don't have to call library("Something", lib.loc='/home/izg/R/ 
x86_64-redhat-linux-gnu-library') all the time, you can just call  
library("Something")

> 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.


Are you saying that there is no RCurl folder at all in /home/izhang/R/ 
x86_64-redhat-linux-gnu-library, or that there is a folder, but  
there's nothing inside it?

In either of these two events, RCurl is definitely not installing  
successfully at all. From the bits and pieces I can put together from  
the email, I'm guessing it's failing to install because it can't find  
libcurl on your system. It sounds like you're not the admin of your  
machine, so you can either ask your admin to install libcurl system  
wide, or d/l the sources and install libcurl into your home directory  
-- you'd then have to most likely *compile* RCurl from source and have  
it link against the libcurl you've installed locally.

-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