Hi- When I do that, the compile is still failing to see the proper libcrypt. While the -L/opt/local/lib does get added to the gcc command, it still is trying to look under /Developer/SDKs/MacOSX10.4u.sdk for the library path. == prompt$ export PKG_LIBS="-L/opt/local/lib" prompt$ sudo R CMD INSTALL --configure-args="--with-pgsql-libraries=/opt/local/lib/postgresql82 --with-pgsql-includes=/opt/local/include/postgresql82" RdbiPgSQL_1.10.0.tar.gz * Installing to library '/Library/Frameworks/R.framework/Resources/library' * Installing *source* package 'RdbiPgSQL' ... creating cache ./config.cache updating cache ./config.cache creating ./config.status creating src/Makevars ** libs ** arch - i386 gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include/postgresql82 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=nocona -c PgSQL.c -o PgSQL.o gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include/postgresql82 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=nocona -c PgSQLInit.c -o PgSQLInit.o gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o RdbiPgSQL.so PgSQL.o PgSQLInit.o -L/opt/local/lib -L/opt/local/lib/postgresql82 -lpq -F/Library/Frameworks/R.framework/.. -framework R ld: warning can't open dynamic library: /Developer/SDKs/MacOSX10.4u.sdk/opt/local/lib/libssl.0.9.8.dylib referenced from: /opt/local/lib/postgresql82/libpq.dylib (checking for undefined symbols may be affected) (No such file or directory, errno = 2) ld: warning can't open dynamic library: /Developer/SDKs/MacOSX10.4u.sdk/opt/local/lib/libcrypto.0.9.8.dylib referenced from: /opt/local/lib/postgresql82/libpq.dylib (checking for undefined symbols may be affected) (No such file or directory, errno = 2) ld: Undefined symbols: _SSL_pending referenced from libpq expected to be defined in /opt/local/lib/libssl.0.9.8.dylib ... == Any other suggestion? Particularly how to work around the -sysroot call? -albert On 4/30/07, Seth Falcon <sfalcon at="" fhcrc.org=""> wrote: > "Albert Vernon Smith" <avsmith at="" gmail.com=""> writes: > > > Hi- > > > > I'm trying to compile RdbiPgSQL 1.10 from source on Mac OS X with R > > 2.5. My postgres binaries come from macports, and I can do: > > > > == > > R CMD INSTALL --configure-args="--with-pgsql- libraries=/opt/local/lib/postgresql82 > > --with-pgsql-includes=/opt/local/include/postgresql82" > > == > > > > And the libpq, etc is seen fine. However, postgres needs to link > > against libcrypto which also comes from macports and is in > > "/opt/local/lib". Getting an error like: > > > > == > > ld: warning can't open dynamic library: > > /Developer/SDKs/MacOSX10.4u.sdk/opt/local/lib/libssl.0.9.8.dylib > > referenced from: /opt/local/lib/postgresql82/libpq.dylib (checking for > > undefined symbols may be affected) (No such file or directory, errno = > > 2) > > ld: warning can't open dynamic library: > > /Developer/SDKs/MacOSX10.4u.sdk/opt/local/lib/libcrypto.0.9.8.dylib > > referenced from: /opt/local/lib/postgresql82/libpq.dylib (checking for > > undefined symbols may be affected) (No such file or directory, errno = > > 2) > > == > > > > (It really should be looking just under "/opt/local/lib" during the compile.) > > > > How can I get this to compile properly? I've tried passing variables > > via LDFLAGS, LIBS, and PKG_LIBS, and I've not found the right magic > > dust to get things to work properly. > > I would try the following: > > - Set and export environment variable PKG_LIBS to contain the library > path for libssl: > > export PKG_LIBS="-L /opt/local/lib" > > - Now try R CMD INSTALL with the same --configure-args as before. > > + seth > > -- > Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center > http://bioconductor.org >

"Albert Vernon Smith" <avsmith at="" gmail.com=""> writes: > Hi- > > When I do that, the compile is still failing to see the proper > libcrypt. While the -L/opt/local/lib does get added to the gcc > command, it still is trying to look under > /Developer/SDKs/MacOSX10.4u.sdk for the library path. > > == > prompt$ export PKG_LIBS="-L/opt/local/lib" > prompt$ sudo R CMD INSTALL > --configure-args="--with-pgsql-libraries=/opt/local/lib/postgresql82 > --with-pgsql-includes=/opt/local/include/postgresql82" > RdbiPgSQL_1.10.0.tar.gz > * Installing to library '/Library/Frameworks/R.framework/Resources/library' > * Installing *source* package 'RdbiPgSQL' ... > creating cache ./config.cache > updating cache ./config.cache > creating ./config.status > creating src/Makevars > ** libs > ** arch - i386 > gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk > -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/i386 > -I/opt/local/include/postgresql82 -msse3 -D__NO_MATH_INLINES -fPIC > -g -O2 -std=gnu99 -march=nocona -c PgSQL.c -o PgSQL.o > gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk > -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/i386 > -I/opt/local/include/postgresql82 -msse3 -D__NO_MATH_INLINES -fPIC > -g -O2 -std=gnu99 -march=nocona -c PgSQLInit.c -o PgSQLInit.o > gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk > -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup > -single_module -multiply_defined suppress -L/usr/local/lib -o > RdbiPgSQL.so PgSQL.o PgSQLInit.o -L/opt/local/lib > -L/opt/local/lib/postgresql82 -lpq > -F/Library/Frameworks/R.framework/.. -framework R > ld: warning can't open dynamic library: > /Developer/SDKs/MacOSX10.4u.sdk/opt/local/lib/libssl.0.9.8.dylib > referenced from: /opt/local/lib/postgresql82/libpq.dylib (checking for > undefined symbols may be affected) (No such file or directory, errno = > 2) > ld: warning can't open dynamic library: > /Developer/SDKs/MacOSX10.4u.sdk/opt/local/lib/libcrypto.0.9.8.dylib > referenced from: /opt/local/lib/postgresql82/libpq.dylib (checking for > undefined symbols may be affected) (No such file or directory, errno = > 2) > ld: Undefined symbols: > _SSL_pending referenced from libpq expected to be defined in > /opt/local/lib/libssl.0.9.8.dylib > ... > == > > Any other suggestion? Particularly how to work around the -sysroot > call? Perhaps try the R-sig-mac list? Perhaps unpack teh RdbiPgSQL source package and take a look at the configure.in script. Perhaps you can hard code something to work? When you install another package that has C code, do you get similar link args? I don't on my MacBook. Perhaps you have some other configuration issue going on that is attaching the SDK root? + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org