Runtime linker ignores RPATH in executable on solaris - linker

Question

I'm trying to compile samtools on a Solaris server where I do not have root. Samtools depends on zlib. The system zlib on this machine is not compiled with large file support, so compiling samtools against this version has the expected effect: samtools only handle small files. I need it to be able to handle large files. Luckily, there is a version of zlib compiled by the admin in /usr/local/apps/zlib-1.2.5/ with large file support. I can compile against this by adding -R /usr/local/apps/zlib-1.2.5/lib to CFLAGS, but this seems not to work. The symptoms are as follows:
When I try to run samtools, it crashes with this error:
ld.so.1: samtools: fatal: relocation error: file samtools: symbol gzopen64: referenced symbol not found
If I add /usr/local/apps/zlib-1.2.5/ to LD_LIBRARY_PATH, then samtools works fine.
Analyzing samtools with ldd and readelf yields the following:
$ ldd -r samtools
libnsl.so.1 => /usr/lib/libnsl.so.1
libsocket.so.1 => /usr/lib/libsocket.so.1
libresolv.so.2 => /usr/lib/libresolv.so.2
libm.so.2 => /usr/lib/libm.so.2
libcurses.so.1 => /usr/lib/libcurses.so.1
libz.so => /usr/lib/libz.so
libc.so.1 => /usr/lib/libc.so.1
libmp.so.2 => /usr/lib/libmp.so.2
libmd.so.1 => /usr/lib/libmd.so.1
libscf.so.1 => /usr/lib/libscf.so.1
libdoor.so.1 => /usr/lib/libdoor.so.1
libuutil.so.1 => /usr/lib/libuutil.so.1
libgen.so.1 => /usr/lib/libgen.so.1
symbol not found: gzopen64 (samtools)
$ ldd -s samtools
...(snip)...
find object=libz.so; required by samtools
search path=/usr/lib:/usr/openwin/lib:/usr/dt/lib:/usr/local/lib (LD_LIBRARY_PATH)
trying path=/usr/lib/libz.so
libz.so => /usr/lib/libz.so
...(snip)...
$ readelf -d samtools | grep RPATH
0x0000000f (RPATH) Library rpath: [/usr/local/apps/zlib-1.2.5/lib:/usr/local/apps/gcc-4.5.1/lib]
So /usr/local/apps/zlib-1.2.5/lib is clearly in the binary's RPATH, which I understand is supposed to be searched at runtime for shared libraries. However, ldd -s shows that this directory is never searched. Adding this path to LD_LIBRARY_PATH and re-running the ldd commands has the expected effect: the directory is searched and the correct version of libz is found.
So how can I force samtools to search in /usr/local/apps/zlib-1.2.5/lib at runtime without using LD_LIBRARY_PATH?
Edit: The documentation here would seem to indicate that the -R option is the correct thing to do. But it doesn't work.

Answer 1

I'm by no means a Solaris expert, but this line:
find object=libz.so; required by samtools
search path=/usr/lib:/usr/openwin/lib:/usr/dt/lib:/usr/local/lib (LD_LIBRARY_PATH)
seems to indicate to me that LD_LIBRARY_PATH is already set, and the /usr/lib path in it is taking precedence over any runtime linker paths. Can you unset LD_LIBRARY_PATH if it is in fact present and see if that resolves it?