RSQLite install R x86_64 fail
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/