[R] RSQLite install R x86_64 fail

[David Ruau]

Hi Seth,

Thanks for the answer.
I have install R using macport (since many years now). It compile R from source using gcc 4.4 by default. But I don't think this is the problem because I manage to install many other package that do not need RSQLite.
The configure options for the macport port are at:
http://trac.macports.org/browser/trunk/dports/math/R/Portfile

I have Xcode 3.2.3 downloaded yesterday.

The thing is that it compile correctly but the RSQLite.so is not at the place specified.
Instead of being at
~/R/x86_64-apple-darwin10.4.0-library/2.11/RSQLite/libs/
it is in a subfolder
~/R/x86_64-apple-darwin10.4.0-library/2.11/RSQLite/libs/x86_64/

I could create a symbolic link only if biocLite would not erase the folder at the end of the failed install.

David

On Jul 11, 2010, at 4:09 PM, Seth Falcon wrote:

> Hi David,
> 
> 
> On Sun, Jul 11, 2010 at 12:27 PM, David Ruau <druau at stanford.edu> wrote:
>> On a fresh install of R on mac os x 10.6.4 (snow leopard) RSQLite
>> did not install while running biocLite()
> 
> How did you install R?
> 
>> $ R
>> biocLite("RSQLite")
>> Using R version 2.11.1, biocinstall version 2.6.7.
>> Installing Bioconductor version 2.6 packages:
>> [1] "RSQLite"
>> Please wait...
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>  unable to load shared library '/Users/druau/R/x86_64-apple-darwin10.4.0-library/2.11/RSQLite/libs/RSQLite.so':
>>  dlopen(/Users/druau/R/x86_64-apple-darwin10.4.0-library/2.11/RSQLite/libs/RSQLite.so, 6): Symbol not found: _sqlite3_backup_finish
>>  Referenced from: /Users/druau/R/x86_64-apple-darwin10.4.0-library/2.11/RSQLite/libs/RSQLite.so
>>  Expected in: flat namespace
>>  in /Users/druau/R/x86_64-apple-darwin10.4.0-library/2.11/RSQLite/libs/RSQLite.so
>> ERROR: loading failed
>> * removing ‘/Users/druau/R/x86_64-apple-darwin10.4.0-library/2.11/RSQLite’
>> * restoring previous ‘/Users/druau/R/x86_64-apple-darwin10.4.0-library/2.11/RSQLite’
>> 
> 
> What version of XCode do you have?  I have 3.2.1 and can build RSQLite
> from source from an R that I have compiled from source.  If you have
> an earlier version, please try upgrading and repeating the install.
> 
>> The binary install work with install.packages("RSQLite", type='mac.binary') or 'mac.binary.leopard' but the package does not load properly.
>>> library('RSQLite')
>> Error: package 'RSQLite' was built for universal-apple-darwin9.8.0
> 
> The mac binary package is intended to work with the R binary installer
> for OS X.  So if you want to use it, you need to install R that way.
> 
> Hope that helps some.
> 
> + seth
> 
> 
> 
> -- 
> Seth Falcon | @sfalcon | http://userprimary.net/