[BioC] Problems compiling RdbiPgSQL

[Seth Falcon]

"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