py-scipy fails to build (as replace)

To: pkgsrc-users%netbsd.org@localhost
Subject: py-scipy fails to build (as replace)
From: Greg Troxel <gdt%lexort.com@localhost>
Date: Sun, 15 Jun 2025 09:34:46 -0400
netbsd-10 amd64, pkgsrc head, everything else that is installed (except
firefox and thunderbird) up to date.

The problem seems to be about numpy.pxd.  I have py312-numpy-2.2.6,
built on June 13, and starting python3.12 and "import numpy" works fine.

Seeming irregular in build output:

  numpy-config found: NO
  Run-time dependency numpy found: NO (tried pkgconfig and config-tool)

and I have numpy-config-3.12, not numpy-config.  I have no numpy
pkgconfig file in the normal place but I do have

  -rw-r--r--  1 root  wheel  191 Jun 13 11:46 /usr/pkg/lib/python3.12/site-packages/numpy/_core/lib/pkgconfig/numpy.pc

This shows up in the .buildlink tree, but I don't see how the scipy
build will find it, because it's not where pkgconfig files are supposed
to be.

My last successful build of scipy is

  -rw-r--r--  1 root  wheel   409315 May 24 20:21 py312-scipy-1.15.3

which sort of points to the suitesparse option, but the diff looks 100%
ok, the usual add a bl3 line if the option is enabled.  I can't believe
it is the problem.









----------------------------------------
=> Bootstrap dependency digest>=20211023: found digest-20220214
=> Checksum BLAKE2s OK for scipy-1.15.3.tar.gz
=> Checksum SHA512 OK for scipy-1.15.3.tar.gz
work -> /tmp/work/math/py-scipy/work
===> Installing dependencies for py312-scipy-1.15.3
==========================================================================
The supported build options for py312-scipy are:

	suitesparse

You can select which build options to use by setting PKG_DEFAULT_OPTIONS
or the following variable.  Its current value is shown:

	PKG_OPTIONS.scipy (not defined)

==========================================================================
==========================================================================
The following variables will affect the build process of this package,
py312-scipy-1.15.3.  Their current value is shown below:

        * PKGSRC_BLAS_TYPES = netlib openblas openblas_pthread openblas_openmp
        * PYTHON_VERSION_DEFAULT = 312

Based on these variables, the following variables have been set:

        * BLAS_INCLUDES = -I/usr/pkg/include/netlib
        * BLAS_LIBS = -lblas
        * BLAS_PC = blas
        * BLAS_TYPE = netlib
        * CBLAS_LIBS = -lcblas -lblas
        * CBLAS_PC = cblas
        * LAPACKE_LIBS = -llapacke -llapack -lblas
        * LAPACKE_PC = lapacke
        * LAPACK_LIBS = -llapack -lblas
        * LAPACK_PC = lapack
        * PYPACKAGE = python312

You may want to abort the process now with CTRL-C and change the value
of variables in the first group before continuing.  Be sure to run
`/usr/bin/make clean' after the changes.
==========================================================================
=> Tool dependency py312-cython>=3.0.8: found py312-cython-3.1.2
=> Tool dependency meson>=1.5.0: found meson-1.8.2
=> Tool dependency py312-meson_python>=0.15.0: found py312-meson_python-0.18.0
=> Tool dependency py312-wheel-[0-9]*: found py312-wheel-0.45.1nb1
=> Tool dependency py312-pythran>=0.14.0: found py312-pythran-0.18.0
=> Tool dependency ccache-[0-9]*: found ccache-4.11.3
=> Tool dependency py312-build>=0: found py312-build-1.2.2.post1nb1
=> Tool dependency py312-installer>=0.7.0nb1: found py312-installer-0.7.0nb3
=> Tool dependency mktools-[0-9]*: found mktools-20250213
=> Tool dependency pkgconf-[0-9]*: found pkgconf-2.4.3nb1
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency py312-pybind11>=2.5.0: found py312-pybind11-2.13.6nb1
=> Build dependency py312-pythran>=0.10.0: found py312-pythran-0.18.0
=> Build dependency python312>=3.12.0: found python312-3.12.11
=> Full dependency cblas>=3.9.1nb1: found cblas-3.12.0
=> Full dependency fftw>=3.3.10nb1: found fftw-3.3.10nb2
=> Full dependency gcc10>=10.3.0nb2: found gcc10-10.5.0nb4
=> Full dependency lapack>=3.9.0nb1: found lapack-3.12.0
=> Full dependency lapacke>=3.9.1nb2: found lapacke-3.12.0
=> Full dependency py312-cython>=0.12.1: found py312-cython-3.1.2
=> Full dependency py312-numpy>=1.23.5: found py312-numpy-2.2.6
===> Checking for vulnerabilities in py312-scipy-1.15.3
===> Overriding tools for py312-scipy-1.15.3
===> Extracting for py312-scipy-1.15.3
===> Patching for py312-scipy-1.15.3
=> Applying pkgsrc patches for py312-scipy-1.15.3
=> Verifying /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_ndimage_src___rank__filter__1d.cpp
=> Applying pkgsrc patch /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_ndimage_src___rank__filter__1d.cpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scipy_ndimage_src___rank__filter__1d.cpp,v 1.1 2025/01/07 15:38:35 jperkin Exp $
|
|Avoid WRAP conflict from sys/termios.h on illumos.
|
|--- scipy/ndimage/src/_rank_filter_1d.cpp.orig	2025-01-07 15:15:58.549682110 +0000
|+++ scipy/ndimage/src/_rank_filter_1d.cpp
--------------------------
Patching file scipy/ndimage/src/_rank_filter_1d.cpp using Plan A...
Hunk #1 succeeded at 18.
done
=> Verifying /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_spatial___ckdtree.pyx
=> Applying pkgsrc patch /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_spatial___ckdtree.pyx
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scipy_spatial___ckdtree.pyx,v 1.4 2023/07/17 19:39:56 tnn Exp $
|
|Fix missing isnan/isinf.
|Build breaks on at least NetBSD-10.99.4-aarch64 without this:
|
|scipy/spatial/_ckdtree.cxx: In function 'PyObject* __pyx_pf_5scipy_7spatial_8_ckdtree_7cKDTree_16count_neighbors(__pyx_obj_5scipy_7spatial_8_ckdtree_cKDTree*, __pyx_obj_5scipy_7spatial_8_ckdtree_cKDTree*, PyObject*, __pyx_t_5numpy_float64_t, PyObject*, int)':
|scipy/spatial/_ckdtree.cxx:13392:19: error: 'isinf' was not declared in this scope; did you mean 'std::isinf'?
|
|--- scipy/spatial/_ckdtree.pyx.orig	1970-01-01 00:00:00.000000000 +0000
|+++ scipy/spatial/_ckdtree.pyx
--------------------------
Patching file scipy/spatial/_ckdtree.pyx using Plan A...
Hunk #1 succeeded at 16.
done
=> Verifying /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_spatial_ckdtree_src_ckdtree__decl.h
=> Applying pkgsrc patch /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_spatial_ckdtree_src_ckdtree__decl.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scipy_spatial_ckdtree_src_ckdtree__decl.h,v 1.4 2024/04/19 19:24:25 adam Exp $
|
|Many errors like this:
|scipy/spatial/ckdtree/src/query_pairs.cxx:110:16: error: argument to '__builtin_prefetch' must be a constant integer
|
|--- scipy/spatial/ckdtree/src/ckdtree_decl.h.orig	2024-04-02 18:31:54.000000000 +0000
|+++ scipy/spatial/ckdtree/src/ckdtree_decl.h
--------------------------
Patching file scipy/spatial/ckdtree/src/ckdtree_decl.h using Plan A...
Hunk #1 succeeded at 9.
done
=> Verifying /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_Faddeeva.hh
=> Applying pkgsrc patch /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_Faddeeva.hh
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scipy_special_Faddeeva.hh,v 1.1 2023/05/08 20:39:18 tnn Exp $
|
|Fix missing isnan/isinf.
|
|--- scipy/special/Faddeeva.hh.orig	1970-01-01 00:00:00.000000000 +0000
|+++ scipy/special/Faddeeva.hh
--------------------------
Patching file scipy/special/Faddeeva.hh using Plan A...
Hunk #1 succeeded at 28.
done
=> Verifying /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_boost__special__functions.h
=> Applying pkgsrc patch /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_boost__special__functions.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scipy_special_boost__special__functions.h,v 1.2 2025/01/05 08:58:47 adam Exp $
|
|Fix build.
|
|--- scipy/special/boost_special_functions.h.orig	2025-01-02 22:53:29.000000000 +0000
|+++ scipy/special/boost_special_functions.h
--------------------------
Patching file scipy/special/boost_special_functions.h using Plan A...
Hunk #1 succeeded at 5.
done
=> Verifying /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_meson.build
=> Applying pkgsrc patch /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_meson.build
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scipy_special_meson.build,v 1.1 2024/07/31 18:15:38 adam Exp $
|
|libsf_error_state is better handled as a static library.
|
|--- scipy/special/meson.build.orig	2024-06-24 18:58:56.000000000 +0000
|+++ scipy/special/meson.build
--------------------------
Patching file scipy/special/meson.build using Plan A...
Hunk #1 succeeded at 33.
done
=> Verifying /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_stirling2.h
=> Applying pkgsrc patch /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_stirling2.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scipy_special_stirling2.h,v 1.4 2025/01/14 18:18:06 gdt Exp $
|
|On NetBSD 10, scipy fails to build with many errors like:
|
|  FAILED: scipy/special/_ufuncs_cxx.so.p/meson-generated__ufuncs_cxx.cpp.o 
|c++ -Iscipy/special/_ufuncs_cxx.so.p -Iscipy/special -I../scipy/special -I../scipy/_lib/boost_math/include -Iscipy/_lib -I../scipy/_lib -I../scipy/_build_utils/src -I../../../../../../../usr/pkg/lib/python3.11/site-packages/numpy/_core/include -I/usr/pkg/include/python3.11 -I/usr/pkg/include -I/usr/include -fvisibility=hidden -fvisibility-inlines-hidden -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -O3 -O2 -D__STDC_FORMAT_MACROS -fPIC -DSP_SPECFUN_ERROR -DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION -DCYTHON_CCOMPLEX=0 -DBOOST_MATH_STANDALONE=1 '-DCYTHON_EXTERN_C=extern "C"' -MD -MQ scipy/special/_ufuncs_cxx.so.p/meson-generated__ufuncs_cxx.cpp.o -MF scipy/special/_ufuncs_cxx.so.p/meson-generated__ufuncs_cxx.cpp.o.d -o scipy/special/_ufuncs_cxx.so.p/meson-generated__ufuncs_cxx.cpp.o -c scipy/special/_ufuncs_cxx.so.p/_ufuncs_cxx.cpp
|In file included from ../scipy/special/stirling2.h:9,
|                 from scipy/special/_ufuncs_cxx_defs.h:112,
|                 from scipy/special/_ufuncs_cxx.so.p/_ufuncs_cxx.cpp:1246:
|../scipy/special/xsf/evalpoly.h:26:29: error: expected unqualified-id before '_Complex'
|   26 | XSF_HOST_DEVICE inline std::complex<double> cevalpoly(const double *coeffs, int degree, std::complex<double> z) {
|      |                             ^~~~~~~
|
|
|C++ documentation implies that one should use <complex>, and therefore
|that <complex.h> is only appropriate in C mode.  Using C++ headers in
|C++ mode resolves the build failure.  Therefore, switch to that
|approach.
|
|Not yet sent upstream.
|
|--- scipy/special/stirling2.h.orig	2025-01-13 23:39:01.039575715 +0000
|+++ scipy/special/stirling2.h
--------------------------
Patching file scipy/special/stirling2.h using Plan A...
Hunk #1 succeeded at 3.
done
=> Verifying /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_wright.hh
=> Applying pkgsrc patch /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_wright.hh
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scipy_special_wright.hh,v 1.1 2023/05/08 20:39:18 tnn Exp $
|
|Fix missing isnan/isinf.
|
|--- scipy/special/wright.hh.orig	1970-01-01 00:00:00.000000000 +0000
|+++ scipy/special/wright.hh
--------------------------
Patching file scipy/special/wright.hh using Plan A...
Hunk #1 succeeded at 2.
done
=> Verifying /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_xsf_amos_amos.h
=> Applying pkgsrc patch /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_xsf_amos_amos.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scipy_special_xsf_amos_amos.h,v 1.2 2025/02/19 09:23:15 adam Exp $
|
|Prefer C++ headers.
|Fix error: 'isinf' was not declared in this scope; did you mean 'std::isinf'?
|
|--- scipy/special/xsf/amos/amos.h.orig	2025-02-16 22:01:46.000000000 +0000
|+++ scipy/special/xsf/amos/amos.h
--------------------------
Patching file scipy/special/xsf/amos/amos.h using Plan A...
Hunk #1 succeeded at 94.
done
=> Verifying /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_xsf_specfun_specfun.h
=> Applying pkgsrc patch /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_special_xsf_specfun_specfun.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scipy_special_xsf_specfun_specfun.h,v 1.1 2025/01/05 08:58:47 adam Exp $
|
|Prefer C++ copysign().
|
|--- scipy/special/xsf/specfun/specfun.h.orig	2024-07-31 10:16:24.693973249 +0000
|+++ scipy/special/xsf/specfun/specfun.h
--------------------------
Patching file scipy/special/xsf/specfun/specfun.h using Plan A...
Hunk #1 succeeded at 2128 (offset 32 lines).
done
=> Verifying /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_stats___unuran_meson.build
=> Applying pkgsrc patch /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy/patches/patch-scipy_stats___unuran_meson.build
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scipy_stats___unuran_meson.build,v 1.1 2023/08/26 19:50:01 tnn Exp $
|
|On NetBSD/powerpc and evbarm, you can't build with _ISOC99_SOURCE defined,
|the include of <ieeefp.h> deep down in the python headers will fail
|with undefined types.
|
|--- scipy/stats/_unuran/meson.build.orig	1970-01-01 00:00:00.000000000 +0000
|+++ scipy/stats/_unuran/meson.build
--------------------------
Patching file scipy/stats/_unuran/meson.build using Plan A...
Hunk #1 succeeded at 208 (offset 4 lines).
done
===> Creating toolchain wrappers for py312-scipy-1.15.3
===> Configuring for py312-scipy-1.15.3
/bin/ln -sf /usr/pkg/bin/pybind11-config-3.12 /tmp/work/math/py-scipy/work/.buildlink/bin/pybind11-config
=> Fixing f2py binary name.
=> Fixing pythran binary name.
=> Checking for portability problems in extracted files
===> Building for py312-scipy-1.15.3
* Building wheel...
+ meson setup /tmp/work/math/py-scipy/work/scipy-1.15.3 /tmp/work/math/py-scipy/work/scipy-1.15.3/.mesonpy-fhs4qo1u -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md -Dblas=blas -Dlapack=lapack --native-file=/tmp/work/math/py-scipy/work/scipy-1.15.3/.mesonpy-fhs4qo1u/meson-python-native-file.ini
The Meson build system
Version: 1.8.2
Source dir: /tmp/work/math/py-scipy/work/scipy-1.15.3
Build dir: /tmp/work/math/py-scipy/work/scipy-1.15.3/.mesonpy-fhs4qo1u
Build type: native build
Project name: scipy
Project version: 1.15.3
C compiler for the host machine: gcc (gcc 10.5.0 "gcc (nb2 20230710) 10.5.0")
C linker for the host machine: gcc ld.bfd 2.34
C++ compiler for the host machine: c++ (gcc 10.5.0 "g++ (nb2 20230710) 10.5.0")
C++ linker for the host machine: c++ ld.bfd 2.34
Cython compiler for the host machine: cython-3.13 (cython 3.1.2)
Host machine cpu family: x86_64
Host machine cpu: x86_64
Program python found: YES (/usr/pkg/bin/python3.12)
Found pkg-config: YES (/tmp/work/math/py-scipy/work/.tools/bin/pkg-config) 2.4.3
Run-time dependency python found: YES 3.12
Program cython-3.13 found: YES (/usr/pkg/bin/cython-3.13)
Compiler for C supports arguments -Wno-unused-but-set-variable: YES 
Compiler for C supports arguments -Wno-unused-function: YES 
Compiler for C supports arguments -Wno-conversion: YES 
Compiler for C supports arguments -Wno-misleading-indentation: YES 
Library m found: YES
Fortran compiler for the host machine: gfortran (gcc 10.5.0 "GNU Fortran (GCC) 10.5.0")
Fortran linker for the host machine: gfortran ld.bfd 2.34
../meson.build:86: WARNING: Consider using the built-in option for language standard version instead of using "-std=legacy".
Compiler for Fortran supports arguments -Wno-conversion: YES 
Checking if "-Wl,--version-script" links: YES 
Program tools/generate_f2pymod.py found: YES (/usr/pkg/bin/python3.12 /tmp/work/math/py-scipy/work/scipy-1.15.3/tools/generate_f2pymod.py)
Program scipy/_build_utils/tempita.py found: YES (/usr/pkg/bin/python3.12 /tmp/work/math/py-scipy/work/scipy-1.15.3/scipy/_build_utils/tempita.py)
Program pythran-3.12 found: YES 0.18.0 0.18.0 (/usr/pkg/bin/pythran-3.12)
Found CMake: /usr/pkg/bin/cmake (3.31.7)
Run-time dependency xsimd found: NO (tried pkgconfig and cmake)
Run-time dependency threads found: YES
numpy-config found: NO
Run-time dependency numpy found: NO (tried pkgconfig and config-tool)
Library npymath found: YES
pybind11-config found: YES (/tmp/work/math/py-scipy/work/.buildlink/bin/pybind11-config) 2.13.6
Run-time dependency pybind11 found: YES 2.13.6
Checking if "thread_local" compiles: NO 
Checking if "_Thread_local" compiles: YES 
Checking if "__thread" compiles: YES 
Configuring scipy_config.h using configuration
Program f2py-3.12 found: YES (/usr/pkg/bin/f2py-3.12)
Run-time dependency blas found: YES 3.12.0
Run-time dependency cblas found: YES 3.12.0
Run-time dependency lapack found: YES 3.12.0
Compiler for C supports arguments -Wno-maybe-uninitialized: YES 
Compiler for C supports arguments -Wno-discarded-qualifiers: YES 
Compiler for C supports arguments -Wno-empty-body: YES 
Compiler for C supports arguments -Wno-implicit-function-declaration: YES 
Compiler for C supports arguments -Wno-parentheses: YES 
Compiler for C supports arguments -Wno-switch: YES 
Compiler for C supports arguments -Wno-unused-label: YES 
Compiler for C supports arguments -Wno-unused-result: YES 
Compiler for C supports arguments -Wno-unused-variable: YES 
Compiler for C supports arguments -Wno-unused-but-set-variable: YES (cached)
Compiler for C++ supports arguments -Wno-bitwise-instead-of-logical: NO 
Compiler for C++ supports arguments -Wno-cpp: YES 
Compiler for C++ supports arguments -Wno-class-memaccess: YES 
Compiler for C++ supports arguments -Wno-deprecated-declarations: YES 
Compiler for C++ supports arguments -Wno-deprecated-builtins: NO 
Compiler for C++ supports arguments -Wno-format-truncation: YES 
Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES 
Compiler for C++ supports arguments -Wno-sign-compare: YES 
Compiler for C++ supports arguments -Wno-switch: YES 
Compiler for C++ supports arguments -Wno-terminate: YES 
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES 
Compiler for C++ supports arguments -Wno-unused-function: YES 
Compiler for C++ supports arguments -Wno-unused-local-typedefs: YES 
Compiler for C++ supports arguments -Wno-unused-variable: YES 
Compiler for C++ supports arguments -Wno-int-in-bool-context: YES 
Compiler for Fortran supports arguments -Wno-argument-mismatch: YES 
Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
Compiler for Fortran supports arguments -Wno-intrinsic-shadow: YES 
Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES 
Compiler for Fortran supports arguments -Wno-surprising: YES 
Compiler for Fortran supports arguments -Wno-uninitialized: YES 
Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES 
Compiler for Fortran supports arguments -Wno-unused-label: YES 
Compiler for Fortran supports arguments -Wno-unused-variable: YES 
Compiler for Fortran supports arguments -Wno-tabs: YES 
Compiler for Fortran supports arguments -Wno-argument-mismatch: YES (cached)
Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-label: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-variable: YES (cached)
Compiler for Fortran supports arguments -Wno-tabs: YES (cached)
Checking if "Check atomic builtins without -latomic" links: YES 
Configuring __config__.py using configuration
Checking for function "open_memstream" : YES 
Configuring messagestream_config.h using configuration
Program _generate_pyx.py found: YES (/usr/pkg/bin/python3.12 /tmp/work/math/py-scipy/work/scipy-1.15.3/scipy/special/_generate_pyx.py)
Program _generate_pyx.py found: YES (/usr/pkg/bin/python3.12 /tmp/work/math/py-scipy/work/scipy-1.15.3/scipy/linalg/_generate_pyx.py)
Program ../_generate_sparsetools.py found: YES (/usr/pkg/bin/python3.12 /tmp/work/math/py-scipy/work/scipy-1.15.3/scipy/sparse/sparsetools/../_generate_sparsetools.py)
Checking for size of "void*" : 8 
Compiler for Fortran supports arguments -w: YES 
Checking for size of "void*" : 8 

Executing subproject highs 

highs| Project name: highs
highs| Project version: 1.8.0
highs| C compiler for the host machine: gcc (gcc 10.5.0 "gcc (nb2 20230710) 10.5.0")
highs| C linker for the host machine: gcc ld.bfd 2.34
highs| C++ compiler for the host machine: c++ (gcc 10.5.0 "g++ (nb2 20230710) 10.5.0")
highs| C++ linker for the host machine: c++ ld.bfd 2.34
highs| Compiler for C++ supports arguments -Wno-invalid-offsetof: YES
highs| Compiler for C++ supports arguments -Wno-maybe-uninitialized: YES
highs| Compiler for C++ supports arguments -Wno-reorder: YES
highs| Compiler for C++ supports arguments -Wno-reorder-ctor: NO
highs| Compiler for C++ supports arguments -Wno-sometimes-uninitialized: NO
highs| Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES (cached)
highs| Compiler for C++ supports arguments -Wno-unused-variable: YES (cached)
highs| Compiler for C++ supports arguments -Wno-use-after-free: NO
highs| Compiler for C++ supports arguments -Wno-comment: YES
highs| Compiler for C supports arguments -Wno-comment: YES
highs| Compiler for C supports arguments -Wno-invalid-offsetof: NO
highs| Compiler for C supports arguments -Wno-maybe-uninitialized: YES (cached)
highs| Compiler for C supports arguments -Wno-sometimes-uninitialized: NO
highs| Compiler for C supports arguments -Wno-unused-label: YES (cached)
highs| Compiler for C supports arguments -Wno-use-after-free: NO
highs| Compiler for C supports arguments -Wno-unused-but-set-variable: YES (cached)
highs| Compiler for C supports arguments -Wno-unused-variable: YES (cached)
highs| Compiler for C supports arguments -Wno-use-after-free: NO (cached)
highs| Compiler for C++ supports arguments -mpopcnt: YES
highs| Dependency threads found: YES unknown (cached)
highs| Checking if "Check atomic builtins without -latomic" links: YES (cached)
highs| Dependency zlib skipped: feature use_zlib disabled
highs| Checking if "mm_pause check" compiles: YES
highs| Checking if "builtin_clz check" compiles: YES
highs| Configuring HConfig.h.meson.interim using configuration
highs| Build targets in project: 145
highs| Subproject highs finished.

Build targets in project: 195

scipy 1.15.3

  Subprojects
    highs       : YES

  User defined options
    Native files: /tmp/work/math/py-scipy/work/scipy-1.15.3/.mesonpy-fhs4qo1u/meson-python-native-file.ini
    b_ndebug    : if-release
    b_vscrt     : md
    blas        : blas
    buildtype   : release
    lapack      : lapack

Found ninja-1.12.1 at /usr/pkg/bin/ninja
Generating targets:   0%|          | 0/195 eta ?Generating targets:  48%|████▊     | 93/195 eta 00:00Generating targets:  89%|████████▉ | 174/195 eta 00:00                                                      
Writing build.ninja:   0%|          | 0/1643 eta ?                                                  + /usr/pkg/bin/ninja -j1
[1/1489] Scanning target lib__spropack for modules
[2/1489] Generating from 'spropack.pyf'
[3/1489] Scanning target lib__dpropack for modules
[4/1489] Generating from 'dpropack.pyf'
[5/1489] Scanning target lib__cpropack for modules
[6/1489] Generating from 'cpropack.pyf'
[7/1489] Scanning target lib__zpropack for modules
[8/1489] Generating from 'zpropack.pyf'
[9/1489] Scanning target arpack_lib for modules
[10/1489] Generating scipy/sparse/linalg/_eigen/arpack/arpack_module with a custom command
[11/1489] Generating from 'mvn.pyf'
[12/1489] Generating from 'test_fortran.pyf'
[13/1489] Generating from 'cobyla/cobyla.pyf'
[14/1489] Generating from 'slsqp/slsqp.pyf'
[15/1489] Copying file scipy/optimize/cython_optimize/__init__.py
[16/1489] Scanning target mach_lib for modules
[17/1489] Scanning target lsoda_lib for modules
[18/1489] Scanning target vode_lib for modules
[19/1489] Scanning target dop_lib for modules
[20/1489] Generating from 'vode.pyf'
[21/1489] Generating from 'lsoda.pyf'
[22/1489] Generating from 'dop.pyf'
[23/1489] Generating from 'tests/test_odeint_banded.pyf'
[24/1489] Scanning target fitpack_lib for modules
[25/1489] Generating from 'src/dfitpack.pyf'
[26/1489] Scanning target odrpack for modules
[27/1489] Copying file scipy/__init__.py
[28/1489] Copying file scipy/_lib/__init__.py
[29/1489] Copying file scipy/_lib/_ccallback_c.pxd
[30/1489] Copying file scipy/_lib/ccallback.pxd
[31/1489] Copying file scipy/_lib/messagestream.pxd
[32/1489] Copying file scipy/special/__init__.py
[33/1489] Copying file scipy/special/_agm.pxd
[34/1489] Copying file scipy/special/_boxcox.pxd
[35/1489] Copying file scipy/special/_cdflib_wrappers.pxd
[36/1489] Copying file scipy/special/_complexstuff.pxd
[37/1489] Copying file scipy/special/_convex_analysis.pxd
[38/1489] Copying file scipy/special/_cunity.pxd
[39/1489] Copying file scipy/special/_ellip_harm.pxd
[40/1489] Copying file scipy/special/_ellip_harm_2.pxd
[41/1489] Copying file scipy/special/_ellipk.pxd
[42/1489] Copying file scipy/special/_factorial.pxd
[43/1489] Copying file scipy/special/_hyp0f1.pxd
[44/1489] Copying file scipy/special/_hypergeometric.pxd
[45/1489] Copying file scipy/special/_legacy.pxd
[46/1489] Copying file scipy/special/_ndtri_exp.pxd
[47/1489] Copying file scipy/special/_sici.pxd
[48/1489] Copying file scipy/special/_spence.pxd
[49/1489] Copying file scipy/special/_xlogy.pxd
[50/1489] Copying file scipy/special/orthogonal_eval.pxd
[51/1489] Copying file scipy/special/sf_error.pxd
[52/1489] Copying file scipy/special/_ufuncs_extra_code.pxi
[53/1489] Copying file scipy/special/_ufuncs_extra_code_common.pxi
[54/1489] Generating scipy/special/cython_special with a custom command
[55/1489] Copying file scipy/special/cython_special.pxd
[56/1489] Copying file scipy/special/__init__.pxd
[57/1489] Copying file scipy/linalg/__init__.py
[58/1489] Copying file scipy/linalg/_cythonized_array_utils.pxd
[59/1489] Copying file scipy/linalg/__init__.pxd
[60/1489] Generating scipy/linalg/cython_linalg with a custom command
[61/1489] Generating scipy/linalg/_decomp_update with a custom command
[62/1489] Generating scipy/sparse/_csparsetools_pyx with a custom command
[63/1489] Copying file scipy/sparse/csgraph/parameters.pxi
[64/1489] Generating dynamic dependency information for target lib__spropack
[65/1489] Scanning target _spropack for modules
[66/1489] Generating dynamic dependency information for target lib__dpropack
[67/1489] Scanning target _dpropack for modules
[68/1489] Generating dynamic dependency information for target lib__cpropack
[69/1489] Scanning target _cpropack for modules
[70/1489] Generating dynamic dependency information for target lib__zpropack
[71/1489] Scanning target _zpropack for modules
[72/1489] Generating dynamic dependency information for target arpack_lib
[73/1489] Scanning target _arpack for modules
[74/1489] Copying file scipy/stats/__init__.py
[75/1489] Copying file scipy/stats/_stats.pxd
[76/1489] Copying file scipy/stats/_biasedurn.pxd
[77/1489] Scanning target _mvn for modules
[78/1489] Copying file scipy/stats/_unuran/__init__.py
[79/1489] Copying file scipy/stats/_unuran/unuran.pxd
[80/1489] Scanning target _test_fortran for modules
[81/1489] Scanning target _cobyla for modules
[82/1489] Scanning target _slsqp for modules
[83/1489] Copying file scipy/optimize/__init__.py
[84/1489] Copying file scipy/optimize/cython_optimize.pxd
[85/1489] Copying file scipy/optimize/__init__.pxd
[86/1489] Copying file scipy/optimize/cython_optimize/c_zeros.pxd
[87/1489] Copying file scipy/optimize/cython_optimize/_zeros.pxd
[88/1489] Generating scipy/optimize/cython_optimize/_zeros_pyx with a custom command
[89/1489] Generating subprojects/highs/src/HConfig.h with a custom command
[90/1489] Copying file scipy/spatial/_qhull.pxd
[91/1489] Copying file scipy/spatial/setlist.pxd
[92/1489] Generating dynamic dependency information for target mach_lib
[93/1489] Generating dynamic dependency information for target lsoda_lib
[94/1489] Generating dynamic dependency information for target vode_lib
[95/1489] Generating dynamic dependency information for target dop_lib
[96/1489] Scanning target _vode for modules
[97/1489] Scanning target _lsoda for modules
[98/1489] Scanning target _dop for modules
[99/1489] Scanning target _test_odeint_banded for modules
[100/1489] Generating dynamic dependency information for target fitpack_lib
[101/1489] Scanning target _dfitpack for modules
[102/1489] Generating dynamic dependency information for target odrpack
[103/1489] Compiling C object scipy/lib_fortranobject.a.p/b9ac16bc79f90eddc3990ddcd009012a3e39f2d4_site-packages_numpy_f2py_src_fortranobject.c.o
[104/1489] Compiling C object scipy/libdummy_g77_abi_wrappers.a.p/_build_utils_src_wrap_dummy_g77_abi.c.o
[105/1489] Generating 'scipy/_lib/_ccallback_c.so.p/_ccallback_c.c'
[106/1489] Generating 'scipy/_lib/_test_deprecation_call.so.p/_test_deprecation_call.c'
[107/1489] Generating 'scipy/_lib/_test_deprecation_def.so.p/_test_deprecation_def.c'
[108/1489] Generating 'scipy/_lib/messagestream.so.p/messagestream.c'
[109/1489] Compiling C object scipy/special/libsf_error_state.a.p/sf_error_state.c.o
[110/1489] Compiling C object scipy/special/libcdflib.a.p/cdflib.c.o
[111/1489] Generating 'scipy/special/_specfun.so.p/_specfun.cpp'
FAILED: scipy/special/_specfun.so.p/_specfun.cpp 
/usr/pkg/bin/cython-3.13 --cplus -3 --fast-fail --output-file scipy/special/_specfun.so.p/_specfun.cpp --include-dir . ../scipy/special/_specfun.pyx -Xfreethreading_compatible=True

Error compiling Cython file:
------------------------------------------------------------
...
from libcpp.complex cimport complex as ccomplex

cimport numpy as cnp
        ^
------------------------------------------------------------

/tmp/work/math/py-scipy/work/scipy-1.15.3/scipy/special/_specfun.pyx:3:8: 'numpy.pxd' not found
ninja: build stopped: subcommand failed.

ERROR Backend subprocess exited when trying to invoke build_wheel
*** Error code 1

Stop.
make[1]: stopped in /n0/gdt/pkgsrc-current/pkgsrc/math/py-scipy
*** Error code 1

Stop.
make: stopped in /usr/pkgsrc/math/py-scipy
Follow-Ups:
- Re: py-scipy fails to build (as replace)
  - From: Greg Troxel
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