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Re: rpath error in cython libraries



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


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