Re: rpath error in cython libraries

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

On 7/28/23 14:09, Greg Troxel wrote:
> > 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.
>
> But what does *that* library depend on, and are all those paths available?

I don't think it's a "second level" issue.  The following error simply
shows that libcsamtools cannot find libchtslib, which seems to be in a
location specified by -L, but I'll have to do some hacking to verify this.

ERROR: lib/python3.10/site-packages/pysam/libcsamtools.so: missing
library: libchtslib.so

To answer your earlier question about objdump -x, the necessary rpath
under python*/site-packages clearly is not being added:

objdump -x [snip]/libcsamtools.so

  NEEDED               libpthread.so.1
  RPATH                /home/bacon/Pkgsrc/pkg/lib
  INIT                 0x000000000000f5e0

This explains the runtime errors.

So I know what the problem is now and just need to devise fixes for the
stage-qa issue and get [snip]/python*/site-packages/pysam into rpath.

Thanks to everyone who provided feedback...