Hi, On a fresh install of R on mac os x 10.6.4 (snow leopard) RSQLite did not install while running biocLite() $ R R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0
[...] Loading required package: utils BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). [Previously saved workspace restored] > biocLite("RSQLite") Using R version 2.11.1, biocinstall version 2.6.7. Installing Bioconductor version 2.6 packages: [1] "RSQLite" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using '/Users/druau/R/x86_64-apple-darwin10.4.0-library/2.11' trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.9-1.tar.gz' Content type 'application/x-gzip' length 1402602 bytes (1.3 Mb) opened URL ================================================== downloaded 1.3 Mb * installing *source* package ‘RSQLite’ ... checking for gcc... /opt/local/bin/gcc-mp-4.4 -std=gnu99 checking for C compiler default output file name... rm: a.out.dSYM: is a directory a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /opt/local/bin/gcc-mp-4.4 -std=gnu99 accepts -g... yes checking for /opt/local/bin/gcc-mp-4.4 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... /opt/local/bin/gcc-mp-4.4 -std=gnu99 -E checking for gcc... (cached) /opt/local/bin/gcc-mp-4.4 -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether /opt/local/bin/gcc-mp-4.4 -std=gnu99 accepts -g... (cached) yes checking for /opt/local/bin/gcc-mp-4.4 -std=gnu99 option to accept ISO C89... (cached) none needed configure: creating ./config.status config.status: creating src/Makevars ** libs /opt/local/bin/gcc-mp-4.4 -std=gnu99 -I/opt/local/lib/R/include -I/usr/local/mysql/include -DTHREADSAFE=0 -I/opt/local/include -fPIC -pipe -O2 -m64 -c RS-DBI.c -o RS-DBI.o /opt/local/bin/gcc-mp-4.4 -std=gnu99 -I/opt/local/lib/R/include -I/usr/local/mysql/include -DTHREADSAFE=0 -I/opt/local/include -fPIC -pipe -O2 -m64 -c RS-SQLite.c -o RS-SQLite.o /opt/local/bin/gcc-mp-4.4 -std=gnu99 -I/opt/local/lib/R/include -I/usr/local/mysql/include -DTHREADSAFE=0 -I/opt/local/include -fPIC -pipe -O2 -m64 -c param_binding.c -o param_binding.o /opt/local/bin/gcc-mp-4.4 -std=gnu99 -I/opt/local/lib/R/include -I/usr/local/mysql/include -DTHREADSAFE=0 -I/opt/local/include -fPIC -pipe -O2 -m64 -c sqlite-all.c -o sqlite-all.o sqlite-all.c:1:35: warning: extra tokens at end of #ifdef directive mkdir -p ../inst/include cp sqlite/sqlite3.h ../inst/include cp sqlite/sqlite3ext.h ../inst/include /opt/local/bin/gcc-mp-4.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/lib -o RSQLite.so RS-DBI.o RS-SQLite.o param_binding.o sqlite-all.o -L/usr/local/mysql/lib -lmysqlclient -L/opt/local/lib/R/lib -lR installing to /Users/druau/R/x86_64-apple-darwin10.4.0-library/2.11/RSQLite/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded 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’ The downloaded packages are in ‘/private/var/folders/e9/e9-5zLVqFgGBR2S8qU74+U+++TM/-Tmp-/RtmpBgST91/downloaded_packages’ Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'RSQLite' had non-zero exit status ############# ############# 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 RSQLite.so file is not in libs/RSQLite.so but in libs/x86_64/RSQLite.so > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin10.4.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/C attached base packages: [1] stats graphics grDevices datasets utils methods base loaded via a namespace (and not attached): [1] tools_2.11.1 Thanks, David ______________________________________________ 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.
