[BioC] GEOquery installation problem

[Tobias Petri]

I had a similar problem with GEOQuery and a missing libcurl as non-root
user.
What worked for me was:

(1) install libcurl (not the R-package but the library) locally on your
system. The __only__ version that provided the correct interfaces was
"curl-7.16.4", all others failed (I tried 5 or so ...), especially those
mentioned in the GEOQuery manual. The call should be sth like:

./configure --prefix=$HOME --enable-shared
make && make install

Be sure the curl-directory's lib-subdirectory contains libcurl.so,
libcurl.so4 (and some more) afterwards

(2) modify your ~/.bashrc (zshrc, whatever) by adding the lib to your path:
    export LD_LIBRARY_PATH=/path/to/curl/curl-7.16.4/lib/

(3) export PATH=$PATH:/path/to/curl/curl-7.16.4/bin
(this step may be optional)

(4) start R and use
install.packages('RCurl', lib='$RH/library',
repos='http://ftp5.gwdg.de/pub/misc/cran/')
biocLite('GEOquery', lib='$RH/library')

Works fine for me and should survive new installations since the
libraries are found by now.

Tobias


zhihua zhang schrieb:
>
>
> ----- 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
>
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>
>   


-- 


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   Tobias Petri                               
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