On Sun, Jul 11, 2010 at 4:25 PM, David Ruau <dr...@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 <dr...@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/ ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.