QA Issue: File FILE in package python3-scipy contains reference to TMPDIR [buildpaths]

[lifeisafractal]

I ran into the following issues where the TMPDIR is leaking into the produced files. My workaround for the mement is to add the following to python3-scipy.bb, which produces useable output, but is masking the issue, not fixing it.

INSANE_SKIP += " \
	buildpaths \
"

I'm comping python3-scipy on master of upstream Yocto. I'm not sure if this is a new QA step added on master that isn't on styhead, or if this is a regression in the build of Scipy in some other way.

It looks like the path is leaking in a two places, both of which are related to Cython.

• In __config__.py files the compiler config output isn't sanitized for the tmpdir paths. I'm not sure the best way to address this.
• In Cython generated code (and the resulting compiled *.so files). Again, I'm not sure exacly why this leakage is happening, nor the best way to address it.

Adding the cython bbclass seems to address most, but still not all of the issues. It looks like most of that bblcass is about sanitzing these paths from the Cython output. I'm not sure why 5 or so of the errors persist.

QA Error log output without cython.bbclass [click to expand]

ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/__config__.py in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/interpolate/_ppoly.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/interpolate/interpnd.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/interpolate/_bspl.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/interpolate/_rgi_cython.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/linalg/_solve_toeplitz.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/linalg/_decomp_lu_cython.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/linalg/_matfuncs_sqrtm_triu.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/linalg/_cythonized_array_utils.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/signal/_sosfilt.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/signal/_peak_finding_utils.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/signal/_upfirdn_apply.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/__pycache__/__config__.cpython-313.pyc in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/special/_comb.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/special/cython_special.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/special/_specfun.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/special/_ellip_harm_2.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/special/_test_internal.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/cluster/_optimal_leaf_ordering.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/cluster/_hierarchy.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/cluster/_vq.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/optimize/_bglu_dense.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/optimize/_moduleTNC.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/optimize/_highs/_highs_wrapper.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/optimize/_trlib/_trlib.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/optimize/_lsq/givens_elimination.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/fftpack/convolve.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/ndimage/_ni_label.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/ndimage/_cytest.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/stats/_qmc_cy.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/stats/_sobol.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/stats/_ansari_swilk_statistics.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/stats/_stats.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/stats/_biasedurn.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/stats/_levy_stable/levyst.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/stats/_unuran/unuran_wrapper.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/stats/_rcont/rcont.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/io/matlab/_streams.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/io/matlab/_mio_utils.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/io/matlab/_mio5_utils.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/spatial/_ckdtree.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/spatial/_voronoi.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/spatial/_hausdorff.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/spatial/_qhull.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/spatial/transform/_rotation.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/_lib/_test_deprecation_call.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/_lib/messagestream.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/_lib/_ccallback_c.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/sparse/csgraph/_traversal.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/sparse/csgraph/_min_spanning_tree.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/sparse/csgraph/_tools.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/sparse/csgraph/_matching.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/sparse/csgraph/_shortest_path.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/sparse/csgraph/_flow.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/sparse/csgraph/_reordering.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/interpolate/_bspl.cpython-313-aarch64-linux-gnu.so.p/_bspl.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/interpolate/_ppoly.cpython-313-aarch64-linux-gnu.so.p/_ppoly.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/interpolate/interpnd.cpython-313-aarch64-linux-gnu.so.p/interpnd.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/interpolate/_rgi_cython.cpython-313-aarch64-linux-gnu.so.p/_rgi_cython.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/linalg/_solve_toeplitz.cpython-313-aarch64-linux-gnu.so.p/_solve_toeplitz.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/linalg/_cythonized_array_utils.cpython-313-aarch64-linux-gnu.so.p/_cythonized_array_utils.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/linalg/_matfuncs_sqrtm_triu.cpython-313-aarch64-linux-gnu.so.p/_matfuncs_sqrtm_triu.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/linalg/_decomp_lu_cython.cpython-313-aarch64-linux-gnu.so.p/_decomp_lu_cython.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/signal/_sosfilt.cpython-313-aarch64-linux-gnu.so.p/_sosfilt.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/signal/_peak_finding_utils.cpython-313-aarch64-linux-gnu.so.p/_peak_finding_utils.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/signal/_upfirdn_apply.cpython-313-aarch64-linux-gnu.so.p/_upfirdn_apply.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/special/_comb.cpython-313-aarch64-linux-gnu.so.p/_comb.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/special/_test_internal.cpython-313-aarch64-linux-gnu.so.p/_test_internal.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/special/_specfun.cpython-313-aarch64-linux-gnu.so.p/_specfun.cpp in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/special/_ellip_harm_2.cpython-313-aarch64-linux-gnu.so.p/_ellip_harm_2.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/special/cython_special.cpython-313-aarch64-linux-gnu.so.p/cython_special.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/cluster/_optimal_leaf_ordering.cpython-313-aarch64-linux-gnu.so.p/_optimal_leaf_ordering.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/cluster/_vq.cpython-313-aarch64-linux-gnu.so.p/_vq.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/cluster/_hierarchy.cpython-313-aarch64-linux-gnu.so.p/_hierarchy.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/optimize/_moduleTNC.cpython-313-aarch64-linux-gnu.so.p/_moduleTNC.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/optimize/_highs/_highs_wrapper.cpython-313-aarch64-linux-gnu.so.p/_highs_wrapper.cpp in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/optimize/_trlib/_trlib.cpython-313-aarch64-linux-gnu.so.p/_trlib.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/optimize/_bglu_dense.cpython-313-aarch64-linux-gnu.so.p/_bglu_dense.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/optimize/_lsq/givens_elimination.cpython-313-aarch64-linux-gnu.so.p/givens_elimination.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/fftpack/convolve.cpython-313-aarch64-linux-gnu.so.p/convolve.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/ndimage/_ni_label.cpython-313-aarch64-linux-gnu.so.p/_ni_label.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/ndimage/_cytest.cpython-313-aarch64-linux-gnu.so.p/_cytest.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/stats/_qmc_cy.cpython-313-aarch64-linux-gnu.so.p/_qmc_cy.cpp in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/stats/_ansari_swilk_statistics.cpython-313-aarch64-linux-gnu.so.p/_ansari_swilk_statistics.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/stats/_stats.cpython-313-aarch64-linux-gnu.so.p/_stats.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/stats/_biasedurn.cpython-313-aarch64-linux-gnu.so.p/_biasedurn.cpp in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/stats/_sobol.cpython-313-aarch64-linux-gnu.so.p/_sobol.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/stats/_levy_stable/levyst.cpython-313-aarch64-linux-gnu.so.p/levyst.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/stats/_unuran/unuran_wrapper.cpython-313-aarch64-linux-gnu.so.p/unuran_wrapper.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/stats/_rcont/rcont.cpython-313-aarch64-linux-gnu.so.p/rcont.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/io/matlab/_mio_utils.cpython-313-aarch64-linux-gnu.so.p/_mio_utils.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/io/matlab/_mio5_utils.cpython-313-aarch64-linux-gnu.so.p/_mio5_utils.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/io/matlab/_streams.cpython-313-aarch64-linux-gnu.so.p/_streams.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/spatial/_hausdorff.cpython-313-aarch64-linux-gnu.so.p/_hausdorff.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/spatial/transform/_rotation.cpython-313-aarch64-linux-gnu.so.p/_rotation.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/spatial/_ckdtree.cpython-313-aarch64-linux-gnu.so.p/_ckdtree.cpp in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/spatial/_voronoi.cpython-313-aarch64-linux-gnu.so.p/_voronoi.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/spatial/_qhull.cpython-313-aarch64-linux-gnu.so.p/_qhull.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/_lib/messagestream.cpython-313-aarch64-linux-gnu.so.p/messagestream.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/_lib/_test_deprecation_call.cpython-313-aarch64-linux-gnu.so.p/_test_deprecation_call.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/_lib/_ccallback_c.cpython-313-aarch64-linux-gnu.so.p/_ccallback_c.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/sparse/csgraph/_matching.cpython-313-aarch64-linux-gnu.so.p/_matching.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/sparse/csgraph/_shortest_path.cpython-313-aarch64-linux-gnu.so.p/_shortest_path.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/sparse/csgraph/_flow.cpython-313-aarch64-linux-gnu.so.p/_flow.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/sparse/csgraph/_tools.cpython-313-aarch64-linux-gnu.so.p/_tools.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/sparse/csgraph/_min_spanning_tree.cpython-313-aarch64-linux-gnu.so.p/_min_spanning_tree.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/sparse/csgraph/_traversal.cpython-313-aarch64-linux-gnu.so.p/_traversal.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/sparse/csgraph/_reordering.cpython-313-aarch64-linux-gnu.so.p/_reordering.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]

QA Error log output with cython.bbclass [click to expand]

ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/src/debug/python3-scipy/1.14.1/scipy/cluster/_hierarchy.cpython-313-aarch64-linux-gnu.so.p/_hierarchy.c in package python3-scipy-src contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/__config__.py in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/__pycache__/__config__.cpython-313.pyc in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: QA Issue: File /usr/lib/python3.13/site-packages/scipy/cluster/_hierarchy.cpython-313-aarch64-linux-gnu.so in package python3-scipy contains reference to TMPDIR [buildpaths]
ERROR: python3-scipy-1.14.1-r0 do_package_qa: Fatal QA errors were found, failing task.
ERROR: Logfile of failure stored in: /build/tmp/work/cortexa76-aether-linux/python3-scipy/1.14.1/temp/log.do_package_qa.48343
ERROR: Task (/build/../work/layers/meta-aether-scipy/recipes-devtools/python/python3-scipy_1.14.1.bb:do_package_qa) failed with exit code '1'

[zboszor]

I should really start testing Yocto master builds, but I can only do it in January.

The TMPDIR report for .so files may be RPATH related.

The pyc files are compiled on-demand, so the recipe may just remove them.

[zboszor]

I have updated the scipy recipe to 1.15.1.

With this version, buildpaths issues only occurred in __config__.py which is fixed even without inherit cython with the current Yocto master.

Please try it.

[lifeisafractal]

I bumped all my upstream layers to the tip of main/master and grabbed your recipes into my custom layer. I ran into this error when trying to build scipy:

| cc1plus: error: include location "/usr/include/python3.13" is unsafe for cross-compilation [-Werror=poison-system-directories]

It looks like the system build environment is leaking into the cross build or somehow bitbake isn't setting up the proper cross compile paths for Python.

FWIW here is the state of all my upstream layers:

meta-networking      
meta-oe              
meta-perl            
meta-python          = "master:27ab1bbc95b27a72a6a8a750a7fd3e98526e2050"
meta-qt5             = "master:957e71a90a73946acb414680f4e22a6089b606f1"
meta-raspberrypi     = "master:880d36b7c2be9cf7fa7cb287d8eefe3a27d7ede9"
meta-rauc            = "master:4f2cbd5a95c6b6ab7f0423675c222b05fcf89b1a"
meta                 
meta-poky            
meta-yocto-bsp       = "master:59db27de565fb33f9e4326e76ebd6fa3935557b9"

I can keep on the older version just fine with my workaround, but it is curious that this seemingly new error is happening.

[zboszor]

I have since upgraded scipy to 1.15.2. Can you please try it using walnascar instead of main/master?

FWIW, neither 1.15.1 nor the new version gave me this unsafe for cross-compilation error.

[lifeisafractal]

I will give it a look, but I've since run into a deeper issue around building SciPy against the tip of Poky. When updating the recipe for scipy and also going to the tip of Poky, scipy broke. It looked to be a latent issue that was exposed by this commit in Poky. In short, the filter for system path poising failed if the path didn't exist, which in my case with my build version of Ubuntu having different python version from the target, did not. That commit unmasked this error.

The root of the problem is that somewhere under the hood, meson is giving the system python include path rather than the cross compile. I haven't been able to figure out how to get messon to stop using the host system include path.

I'm pretty sure this issue has been there for a white and has just recently been uncovered, and that all SciPy builds will break when moving past this commit. With no central maintainer of SciPy for Yocto, I'm not really sure where to log this issue (I'm pretty sure this repo is the most active place currently).