[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')

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?

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

> 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/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.

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.

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

Thanks

Zhihua.





-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