[BioC] Problems compiling RdbiPgSQL

[Seth Falcon]

"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