[BioC] GEOquery installation problem

[zhihua zhang]

----- Original Message ----
From: Steve Lianoglou <mailinglist.honeypot at gmail.com>
To: zhihua zhang <biozhang2001 at yahoo.com.cn>
Cc: bioconductor at stat.math.ethz.ch
Sent: Monday, August 3, 2009 5:25:04 PM
Subject: Re: [BioC] GEOquery installation problem

> ---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?
-- yes, I made it into my home ~/local/

> 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?

-- no, actually, before I try to load RCurl, it's alright.  The Rcurl installation didn't report any error. 


install.packages("RCurl",lib = '/home/izg/R/x86_64-redhat-linux-gnu-library')
it says 
...
** building package indices 
* DONE (RCurl)

The downloaded packages are in
    /tmp/RtmpYm80DR/downloaded_packages

but there is nothing in the folder :~/R/x86_64-redhat-linux-gnu-library/RCurl/libs
and I can not load 

>library("RCurl", lib.loc="/home/izg/R/x86_64-redhat-linux-gnu-library/")
Error in library("RCurl", lib.loc = "/home/izg/R/x86_64-redhat-linux-gnu-library/") : 
  no library trees found in 'lib.loc'



> -- 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.

-- I tried, system even said

configure: error: unrecognized option: -I/home/izhang/local/include/
Try `./configure --help' for more information.
ERROR: configuration failed for package 'RCurl'

Thanks.


-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