[R] RSQLite install R x86_64 fail

[Seth Falcon]

On Sun, Jul 11, 2010 at 4:25 PM, David Ruau <druau at stanford.edu> wrote:
> 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.

I don't use macports so I'm afraid I can't be of much help.  I suspect
that something isn't getting configured properly for 64bit R in
macports.

When I build R from source on OS X and install RSQLite, I see the
package in .../libs/x86_64 and this works.
Maybe it will be useful to review the advice here:
http://r.research.att.com/building.html

+ seth

>
> 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/
>
>



-- 
Seth Falcon | @sfalcon | http://userprimary.net/