py-pysam: Add cython dep and TODO for rpath errors

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Jul 27 20:47:10 2023 -0500
Changeset:	fc8b76a4964ea7117707062db922d7349bd2e42c

Modified Files:
	py-pysam/Makefile
Added Files:
	py-pysam/TODO

Log Message:
py-pysam: Add cython dep and TODO for rpath errors

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=fc8b76a4964ea7117707062db922d7349bd2e42c

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 py-pysam/Makefile | 1 +
 py-pysam/TODO     | 6 ++++++
 2 files changed, 7 insertions(+)

diffs:
diff --git a/py-pysam/Makefile b/py-pysam/Makefile
index 3628b1225c..cd281703da 100644
--- a/py-pysam/Makefile
+++ b/py-pysam/Makefile
@@ -25,6 +25,7 @@ post-install:
 
 .include "../../lang/python/egg.mk"
 .include "../../biology/htslib/buildlink3.mk"
+.include "../../devel/py-cython/tool.mk"
 # CentOS doesn't have zlib in the base, so uncomment if needed.
 # .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/py-pysam/TODO b/py-pysam/TODO
new file mode 100644
index 0000000000..2f72563035
--- /dev/null
+++ b/py-pysam/TODO
@@ -0,0 +1,6 @@
+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 (try using -rpath or -rpath-link)
+ld: warning: libcbcftools.so, needed by build/lib.netbsd-9.3-amd64-cpython-310/pysam/libcutils.so, not found (try using -rpath or -rpath-link)
+
+# => Checking for missing run-time search paths in py310-pysam-0.21.0
+# ERROR: lib/python3.10/site-packages/pysam/libcalignedsegment.so: missing library: libchtslib.so