[BioC] GEOquery installation problem

[Steve Lianoglou]

> ---Right, libcurl was not in my system, the third line command I was  
> trying to install a local copy of libcurl as you said.

Did that work? You just showed:

~/tmp/curl-7.19.5> make install

Since you're not an admin, this couldn't have worked w/o choosing an  
appropriate prefix during the configure step -- what did you use?


> Are you saying that there is no RCurl folder at all in /home/izg/R/ 
> x86_64-redhat-linux-gnu-library, or that there is a folder, but  
> there's nothing inside it?
>
> -- there is a folder call RCurl in /home/izg/R/x86_64-redhat-linux- 
> gnu-library, just not any files in the folder however.

Just out of curiosity -- in your previous emails, you showed some R  
commands to install RCurl, and then say that "all those seems  
successfully done!" And yet there is nothing in those directories ...  
did R not report an error during RCurl install?

> -- do you mean to modify the Makefile of RCurl to link to the  
> locally installed libcurl?

No, I don't think you have to modify any Makefiles, but you'll need to  
tell R where to find your installed libcurl.

When calling install.packages, I believe you can pass this info in  
through the "configure.args" parameter. I'M JUST GUESSING, but maybe  
something like this would work:

install.packages("RCurl", configure.args=c(RCurl='-I/home/izg/local/ 
include -L/home/izg/local/lib -lcurl'))

First thing is first, though, and you have to make sure that libcurl  
is installed correctly, and also know what --prefix you used when  
configuring/installing it.

-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