Re: rpath error in cython libraries

[Jason Bacon <jtocino%gmx.com@localhost>]

On 7/28/23 11:46, Greg Troxel wrote:
> Jason Bacon <jtocino%gmx.com@localhost> writes:
>
> > I'm not sure what "$ORIGIN" is here, but output from the FreeBSD port
>
> ORIGIN is a scheme to do something complicated, which I think is to make
> rpath relative to the directory from which the executable was loaded.
> pkgsrc tends to avoid this, at least
Are you saying that pkgsrc does not support $ORIGIN and this needs to be
replaced by the actual path(s)?

> > cc -shared -L. -Wl,-zrelro -Wl,-znow -L/usr/lib -Wl,-R/usr/lib
> > -L/home/bacon/Pkgsrc/pkg/lib -Wl,-R/home/bacon/Pkgsrc/pkg/lib
> > -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -Wl,-znow -L/usr/lib
> > -Wl,-R/usr/lib -L/home/bacon/Pkgsrc/pkg/lib
> > -Wl,-R/home/bacon/Pkgsrc/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib
> > -Wl,-zrelro -Wl,-znow -L/usr/lib -Wl,-R/usr/lib
> > -L/home/bacon/Pkgsrc/pkg/lib -Wl,-R/home/bacon/Pkgsrc/pkg/lib -O2 -fPIC
> > -D_FORTIFY_SOURCE=2 -I/usr/include
> > -I/home/bacon/Pkgsrc/pkg/include/python3.10
> > -I/home/bacon/Pkgsrc/pkg/include -I/usr/include
> > -I/home/bacon/Pkgsrc/pkg/include/python3.10
> > -I/home/bacon/Pkgsrc/pkg/include
> > build/temp.netbsd-9.3-amd64-cpython-310/pysam/libcsamfile.o
> > -L/home/bacon/Pkgsrc/pkgsrc/wip/py-pysam/work/pysam-0.21.0/pysam
> > -L/home/bacon/Pkgsrc/pkg/lib
> > -Lbuild/lib.netbsd-9.3-amd64-cpython-310/pysam
> > -Lbuild/lib.netbsd-9.3-amd64-cpython-310/pysam
> > -Lbuild/lib.netbsd-9.3-amd64-cpython-310/pysam
> > -Lbuild/lib.netbsd-9.3-amd64-cpython-310/pysam
> > -Lbuild/lib.netbsd-9.3-amd64-cpython-310/pysam
> > -Lbuild/lib.netbsd-9.3-amd64-cpython-310/pysam
> > -L/home/bacon/Pkgsrc/pkg/lib -lz -lhts -lchtslib -lcutils -o
> > build/lib.netbsd-9.3-amd64-cpython-310/pysam/libcsamfile.so
> > -Wl,-rpath,$ORIGIN
> > ld: warning: libcsamtools.so, needed by
> > build/lib.netbsd-9.3-amd64-cpython-310/pysam/libcutils.so, not found
>
> So where is libcsamtools.so, and is there a -L for it?   What does
> libcsamtools.so say when you run objdump -x and look for RPATH and NEEDED?

Did you miss the "find" commands at the end of my original message?

find work/ -name libcsamtools.so
work/pysam-0.21.0/build/lib.netbsd-9.3-amd64-cpython-310/pysam/libcsamtools.so

I think CWD should be work/pysam-0.21.0, so I think the

-Lbuild/lib.netbsd-9.3-amd64-cpython-310/pysam

should cover it during stage-qa checks.  Post-install is another issue.
Perhaps replacing $ORIGIN with the final installation path should fix it?

Thanks,

	J