[BioC] Problems compiling RdbiPgSQL

[Albert Vernon Smith]

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
>