[BioC] Problems compiling RdbiPgSQL

[Albert Vernon Smith]

For anyone following this, the solution seems to be relatively trivial.

If a symlink for /opt is put in /Developer/SDKs/MacOSX10.4u.sdk , then
RdbiPgSQL compiles fine.  It turns out that the isysroot option
prepends its value to all paths.  This is something which apple has
done, and it is debatable whether this is a bug or a feature.

-albert

On 5/2/07, Seth Falcon <sfalcon at fhcrc.org> wrote:
> "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
>