Date: Sun, 05 Apr 2026 04:29:53 +0000 From: bugzilla-noreply@freebsd.org To: python@FreeBSD.org Subject: [Bug 294255] science/py-scipy fails to build after update to 1.17.1 Message-ID: <bug-294255-21822@https.bugs.freebsd.org/bugzilla/>
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=294255 Bug ID: 294255 Summary: science/py-scipy fails to build after update to 1.17.1 Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Only Me Priority: --- Component: Individual Port(s) Assignee: python@FreeBSD.org Reporter: russo@bogodyn.org Flags: maintainer-feedback?(python@FreeBSD.org) Assignee: python@FreeBSD.org Not actually sure if this is caused when scipy was updated in ports ef9180aa84690bd5181cd60be75c891ee7bdb74e or if it's due to the numpy/numpy1 shakeup, but I am unable to build science/py-scipy [see below for the workaround I found while writing this report]. As an aside, I was forced to "pkg delete -f py311-numpy" because it wanted to upgrade to numpy 2, and py-scipy now has an explicit BUILD_DEPENDS on math/py-numpy1 --- which it refused to install after py311-numpy was updated because they conflict. The vast majority of the ports I have that depend on scipy *also* depend on numpy1 this way anyway, so that's fine. But that only helped a little. Now I get a compilation failure. The build error is: [853/1238] Compiling C++ object scipy/...1.so.p/src__fmm_core_write_coo_64.cpp. FAILED: [code=1] scipy/io/_fast_matrix_market/_fmm_core.cpython-311.so.p/src__fmm_core_write_coo_64.cpp.o c++ -Iscipy/io/_fast_matrix_market/_fmm_core.cpython-311.so.p -Iscipy/io/_fast_matrix_market -I../scipy/io/_fast_matrix_market -I../scipy/io/_fast_matrix_market/fast_matrix_market/include -I../../../../../../local/lib/python3.11/site-packages/numpy/core/include -I../scipy/io/_fast_matrix_market/fast_matrix_market/dependencies/fast_float/include -Iscipy/io/_fast_matrix_market/fast_matrix_market/dependencies/ryu -I../scipy/io/_fast_matrix_market/fast_matrix_market/dependencies/ryu -I/include -I/usr/local/include/python3.11 -fvisibility=hidden -fvisibility-inlines-hidden -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -O3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION -DFMM_SCIPY_PRUNE -DFMM_USE_FAST_FLOAT -DFMM_USE_RYU -DFMM_FROM_CHARS_INT_SUPPORTED -DFMM_TO_CHARS_INT_SUPPORTED -MD -MQ scipy/io/_fast_matrix_market/_fmm_core.cpython-311.so.p/src__fmm_core_write_coo_64.cpp.o -MF scipy/io/_fast_matrix_market/_fmm_core.cpython-311.so.p/src__fmm_core_write_coo_64.cpp.o.d -o scipy/io/_fast_matrix_market/_fmm_core.cpython-311.so.p/src__fmm_core_write_coo_64.cpp.o -c ../scipy/io/_fast_matrix_market/src/_fmm_core_write_coo_64.cpp In file included from ../scipy/io/_fast_matrix_market/src/_fmm_core_write_coo_64.cpp:5: ../scipy/io/_fast_matrix_market/src/_fmm_core.hpp:14:10: fatal error: 'pybind11/pybind11.h' file not found 14 | #include <pybind11/pybind11.h> | ^~~~~~~~~~~~~~~~~~~~~ 1 error generated. (the same problem is reported in several files if I build without setting MAKE_JOBS_UNSAFE) Yet my system has pybind11 installed, and /usr/local/include/pybind11/pybind11.h exists. from pkg info: py311-pybind11-3.0.1 Seamless interoperability between C++11 and Python pybind11-3.0.1 Seamless interoperability between C++11 and Python (cmake part) and ls -l /usr/local/include/pybind11/pybind11.h shows: -rw-r--r-- 1 root wheel 160679 Aug 22 2025 /usr/local/include/pybind11/pybind11.h Uname: FreeBSD xxxx.xx 14.3-STABLE FreeBSD 14.3-STABLE stable/14-n273238-c95f96dea30a GENERIC amd64 In /usr/ports, git describe shows: git describe 14.2-eol-19692-gcc704ef2c80e UPDATE: After reading a comment in 281470 about CMake maybe being a problem, I removed the "cmake part" of pybind11, which *removed* pybind11/pybind11.h. After that the py-scipy port compiled and installed without throwing this error about not being able to find the file. So this is an oddity introduced entirely by the presence of the pybind11 package. py-pybind11 is still needed. There's still something fishy about this port, but that's the workaround. -- You are receiving this mail because: You are the assignee for the bug.home | help
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