[BioC] Problem installing goseq and RCurl

[Martin Morgan]

On 10/31/2012 08:47 AM, Dave Tang wrote:
> On Tue, 30 Oct 2012 22:06:21 +0900, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
>> On Tue, Oct 30, 2012 at 6:03 AM, Dave Tang <davetingpongtang at gmail.com> wrote:
>>> Hi Dan,
>>>
>>>
>>> On Tue, 30 Oct 2012 21:43:35 +0900, Dan Tenenbaum <dtenenba at fhcrc.org>
>>> wrote:
>>>
>>>> What Linux distribution are you running?
>>>> If ubuntu, try:
>>>> sudo apt-get install libcurl4-openssl-dev
>>>> (this is from http://www.omegahat.org/RCurl/FAQ.html)
>>>
>>>
>>> I'm working on a shared server where I don't have admin privileges and it's
>>> running Centos 5.
>>>
>>> I guess I should just get the admin to update curl? Is that the actual
>>> problem?
>>
>> I am not sure what the actual problem is. But in many cases,
>> installing libcurl with the OS's package installer does seem to fix
>> the problem.
>> Dan
>
> I got the admin to install the latest version of curl and the libcurl.so.4
> library file is now in /usr/local/lib but I still get the same error when trying
> to install RCurl on CentOS release 5.8 (Final):

It's the -dev extension on Dan's suggestion that is probably throwing you off -- 
you need to have the header files for the library, in addition to the library 
per se.

Martin

>
> [snipped]
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o RCurl.so base64.o curl.o curlInit.o
> curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -L/usr/local/lib -lcurl
> -lxml2 -lz -lm
> installing to /home/davetang/src/R-2.15.2/library/RCurl/libs
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Creating a generic function for 'close' from package 'base' in package 'RCurl'
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>    unable to load shared object
> '/home/davetang/src/R-2.15.2/library/RCurl/libs/RCurl.so':
>    libcurl.so.4: cannot open shared object file: No such file or directory
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing '/home/davetang/src/R-2.15.2/library/RCurl'
>
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.2
>
> I could install Rcurl and goseq on my own computer running Ubuntu precise by
> installing curl via apt-get.
>
> Cheers,
>
>


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