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Clash of lib64 symlink and R extensions in wrappers
as I wrote earlier, I'm setting a lib64 → lib symlink in the pkgsrc
prefix to ensure libs there are found before other random locations in
the system becuase of the search order of gcc, which prefers any lib64
before any lib, to summarize.
Now I get linker failure of R extensions because the pkgsrc wrappers
link in only the lib location but R also picked up the lib64 name and
tries to link to $prefix/lib64/R/libR.so instead of
$prefix/lib/R/libR.so . The build of the extensions is handled by R in
the do-install target of math/R/Makefile.extension .
I wonder how I should approach this. Is it more promising to
a) Hack R (and any other package for which it may occur) to ignore any
lib64 (symlink) it finds, or
b) Hack the wrappers to also link in the symlink, which would fix all
packages with such trouble, but manifests the presence of the doubled
paths with and without lib64 in RPATH/RUNPATH.
Suggestions? Of course I'd like to have a sane search behaviour for
gcc, but I won't be able to change distro compilers like on CentOS.
So I guess best would be wrapper behaviour that handles the lib64
symlink explicitly and mangles -Wl,-R arguments to only include the
real directory …
Dr. Thomas Orgis
HPC @ Universität Hamburg
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