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: [email protected]
Reporter: [email protected]
Flags: maintainer-feedback?([email protected])
Assignee: [email protected]
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.
