We're trying to set up a new FreeBSD 13.4 server, and have run into some issues installing the Python packages we need. We saw a similar issue with NumPy, but were able to work around it by installing an older version. The server started at FreeBSD 13.0 and was immediately upgraded to 13.4. The Python version we are running is 3.10.14, we are trying to install Pandas version 2.2.3 and pip is at 24.2.
We have tried installing Pandas with the following command:
Equivalent commands have succeeded for the other packages we need, so we expected this to work as well, but are seeing the following error:
Looking around, it seems that this issue with these missing files may be related to various build tools, but as far as I am aware we have them installed. We have tried installing older versions, which worked when we faced a similar issue installing NumPy, but have had no luck. I'm quite new to this kind of thing so if there are any details you may need that I've missed, please let me know. Any further pointers would be greatly appreciated!
We have tried installing Pandas with the following command:
Code:
sudo python3.10 -m pip install pandasEquivalent commands have succeeded for the other packages we need, so we expected this to work as well, but are seeing the following error:
Code:
Collecting pandas
Using cached pandas-2.2.3.tar.gz (4.4 MB)
Installing build dependencies ... error
error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> [335 lines of output]
Collecting meson-python==0.13.1
Using cached meson_python-0.13.1-py3-none-any.whl.metadata (4.1 kB)
Collecting meson==1.2.1
Using cached meson-1.2.1-py3-none-any.whl.metadata (1.7 kB)
Collecting wheel
Using cached wheel-0.44.0-py3-none-any.whl.metadata (2.3 kB)
Collecting Cython~=3.0.5
Using cached Cython-3.0.11-py2.py3-none-any.whl.metadata (3.2 kB)
Collecting numpy>=2.0
Using cached numpy-2.1.1.tar.gz (18.9 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [304 lines of output]
+ /usr/local/bin/python3.10 /tmp/pip-install-bltn0aj3/numpy_a1fdca0786c14938b2788c097daf84a8/vendored-meson/meson/meson.py setup /tmp/pip-install-bltn0aj3/numpy_a1fdca0786c14938b2788c097daf84a8 /tmp/pip-install-bltn0aj3/numpy_a1fdca0786c14938b2788c097daf84a8/.mesonpy-e9_twr0h -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/tmp/pip-install-bltn0aj3/numpy_a1fdca0786c14938b2788c097daf84a8/.mesonpy-e9_twr0h/meson-python-native-file.ini
The Meson build system
Version: 1.4.99
Source dir: /tmp/pip-install-bltn0aj3/numpy_a1fdca0786c14938b2788c097daf84a8
Build dir: /tmp/pip-install-bltn0aj3/numpy_a1fdca0786c14938b2788c097daf84a8/.mesonpy-e9_twr0h
Build type: native build
Project name: NumPy
Project version: 2.1.1
C compiler for the host machine: cc (clang 18.1.6 "FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)")
C linker for the host machine: cc ld.lld 18.1.6
C++ compiler for the host machine: c++ (clang 18.1.6 "FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)")
C++ linker for the host machine: c++ ld.lld 18.1.6
Cython compiler for the host machine: cython (cython 3.0.11)
Host machine cpu family: x86_64
Host machine cpu: x86_64
Program python found: YES (/usr/local/bin/python3.10)
Found pkg-config: YES (/usr/local/bin/pkg-config) 2.2.0
Run-time dependency python found: YES 3.10
Has header "Python.h" with dependency python-3.10: YES
Compiler for C supports arguments -fno-strict-aliasing: YES
Compiler for C supports arguments -ftrapping-math: YES
Test features "SSE SSE2 SSE3" : Supported
Test features "SSSE3" : Supported
Test features "SSE41" : Supported
Test features "POPCNT" : Supported
Test features "SSE42" : Supported
Test features "AVX" : Supported
Test features "F16C" : Supported
Test features "FMA3" : Supported
Test features "AVX2" : Supported
Test features "AVX512F" : Supported
Test features "AVX512CD" : Supported
Test features "AVX512_KNL" : Supported
Test features "AVX512_KNM" : Unsupported due to Arguments "-msse, -msse2, -msse3, -mssse3, -msse4.1, -mpopcnt, -msse4.2, -mavx, -mf16c, -mfma, -mavx2, -maes, -mpclmul, -mbmi, -mbmi2, -mno-mmx, -mavx512f, -mavx512cd, -mavx512er, -mavx512pf, -mavx5124fmaps, -mavx5124vnniw, -mavx512vpopcntdq" are not supported
Test features "AVX512_SKX" : Supported
Test features "AVX512_CLX" : Supported
Test features "AVX512_CNL" : Supported
Test features "AVX512_ICL" : Supported
Test features "AVX512_SPR" : Unsupported due to Compiler fails against the test code of "AVX512_SPR"
Configuring npy_cpu_dispatch_config.h using configuration
Message:
CPU Optimization Options
baseline:
Requested : min
Enabled : SSE SSE2 SSE3
dispatch:
Requested : max -xop -fma4
Enabled : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2 AVX512F AVX512CD AVX512_KNL AVX512_SKX AVX512_CLX AVX512_CNL AVX512_ICL
Library m found: YES
Run-time dependency scipy-openblas found: NO (tried pkgconfig)
Run-time dependency mkl found: NO (tried pkgconfig and system)
Run-time dependency mkl found: NO (tried pkgconfig and system)
Run-time dependency openblas found: YES 0.3.27
Message: BLAS symbol suffix:
Run-time dependency mkl found: NO (tried pkgconfig and system)
Run-time dependency openblas found: YES 0.3.27
Checking if "Check atomic builtins without -latomic" : links: NO
Library atomic found: NO
Program _build_utils/process_src_template.py found: YES (/usr/local/bin/python3.10 /tmp/pip-install-bltn0aj3/numpy_a1fdca0786c14938b2788c097daf84a8/numpy/_build_utils/process_src_template.py)
Program _build_utils/tempita.py found: YES (/usr/local/bin/python3.10 /tmp/pip-install-bltn0aj3/numpy_a1fdca0786c14938b2788c097daf84a8/numpy/_build_utils/tempita.py)
Configuring __config__.py using configuration
Checking for size of "short" : 2
Checking for size of "int" : 4
Checking for size of "long" : 8
Checking for size of "long long" : 8
Checking for size of "float" : 4
Checking for size of "double" : 8
Checking for size of "long double" : 16
Checking for size of "size_t" : 8
Checking for size of "size_t" : 8 (cached)
Checking for size of "wchar_t" : 4
Checking for size of "off_t" : 8
Checking for size of "Py_intptr_t" with dependency python-3.10: 8
Checking for size of "PY_LONG_LONG" with dependency python-3.10: 8
Has header "complex.h" : YES
Checking for type "complex float" : YES
Checking for size of "complex float" : 8
Checking for type "complex double" : YES
Checking for size of "complex double" : 16
Checking for type "complex long double" : YES
Checking for size of "complex long double" : 32
Checking for function "sin" with dependency -lm: YES
Checking for function "cos" with dependency -lm: YES
Checking for function "tan" with dependency -lm: YES
Checking for function "sinh" with dependency -lm: YES
Checking for function "cosh" with dependency -lm: YES
Checking for function "tanh" with dependency -lm: YES
Checking for function "fabs" with dependency -lm: YES
Checking for function "floor" with dependency -lm: YES
Checking for function "ceil" with dependency -lm: YES
Checking for function "sqrt" with dependency -lm: YES
Checking for function "log10" with dependency -lm: YES
Checking for function "log" with dependency -lm: YES
Checking for function "exp" with dependency -lm: YES
Checking for function "asin" with dependency -lm: YES
Checking for function "acos" with dependency -lm: YES
Checking for function "atan" with dependency -lm: YES
Checking for function "fmod" with dependency -lm: YES
Checking for function "modf" with dependency -lm: YES
Checking for function "frexp" with dependency -lm: YES
Checking for function "ldexp" with dependency -lm: YES
Checking for function "expm1" with dependency -lm: YES
Checking for function "log1p" with dependency -lm: YES
Checking for function "acosh" with dependency -lm: YES
Checking for function "asinh" with dependency -lm: YES
Checking for function "atanh" with dependency -lm: YES
Checking for function "rint" with dependency -lm: YES
Checking for function "trunc" with dependency -lm: YES
Checking for function "exp2" with dependency -lm: YES
Checking for function "copysign" with dependency -lm: YES
Checking for function "nextafter" with dependency -lm: YES
Checking for function "cbrt" with dependency -lm: YES
Checking for function "log2" with dependency -lm: YES
Checking for function "pow" with dependency -lm: YES
Checking for function "hypot" with dependency -lm: YES
Checking for function "atan2" with dependency -lm: YES
Checking for function "csin" with dependency -lm: YES
Checking for function "csinh" with dependency -lm: YES
Checking for function "ccos" with dependency -lm: YES
Checking for function "ccosh" with dependency -lm: YES
Checking for function "ctan" with dependency -lm: YES
Checking for function "ctanh" with dependency -lm: YES
Checking for function "creal" with dependency -lm: YES
Checking for function "cimag" with dependency -lm: YES
Checking for function "conj" with dependency -lm: YES
Checking for function "strtoll" : YES
Checking for function "strtoull" : YES
Checking for function "cabs" with dependency -lm: YES
Checking for function "cabsf" with dependency -lm: YES
Checking for function "cabsl" with dependency -lm: YES
Checking for function "cacos" with dependency -lm: YES
Checking for function "cacosf" with dependency -lm: YES
Checking for function "cacosl" with dependency -lm: YES
Checking for function "cacosh" with dependency -lm: YES
Checking for function "cacoshf" with dependency -lm: YES
Checking for function "cacoshl" with dependency -lm: YES
Checking for function "carg" with dependency -lm: YES
Checking for function "cargf" with dependency -lm: YES
Checking for function "cargl" with dependency -lm: YES
Checking for function "casin" with dependency -lm: YES
Checking for function "casinf" with dependency -lm: YES
Checking for function "casinl" with dependency -lm: YES
Checking for function "casinh" with dependency -lm: YES
Checking for function "casinhf" with dependency -lm: YES
Checking for function "casinhl" with dependency -lm: YES
Checking for function "catan" with dependency -lm: YES
Checking for function "catanf" with dependency -lm: YES
Checking for function "catanl" with dependency -lm: YES
Checking for function "catanh" with dependency -lm: YES
Checking for function "catanhf" with dependency -lm: YES
Checking for function "catanhl" with dependency -lm: YES
Checking for function "cexp" with dependency -lm: YES
Checking for function "cexpf" with dependency -lm: YES
Checking for function "cexpl" with dependency -lm: YES
Checking for function "clog" with dependency -lm: YES
Checking for function "clogf" with dependency -lm: YES
Checking for function "clogl" with dependency -lm: YES
Checking for function "cpow" with dependency -lm: YES
Checking for function "cpowf" with dependency -lm: YES
Checking for function "cpowl" with dependency -lm: YES
Checking for function "csqrt" with dependency -lm: YES
Checking for function "csqrtf" with dependency -lm: YES
Checking for function "csqrtl" with dependency -lm: YES
Checking for function "csin" with dependency -lm: YES (cached)
Checking for function "csinf" with dependency -lm: YES
Checking for function "csinl" with dependency -lm: NO
Checking for function "csinh" with dependency -lm: YES (cached)
Checking for function "csinhf" with dependency -lm: YES
Checking for function "csinhl" with dependency -lm: NO
Checking for function "ccos" with dependency -lm: YES (cached)
Checking for function "ccosf" with dependency -lm: YES
Checking for function "ccosl" with dependency -lm: NO
Checking for function "ccosh" with dependency -lm: YES (cached)
Checking for function "ccoshf" with dependency -lm: YES
Checking for function "ccoshl" with dependency -lm: NO
Checking for function "ctan" with dependency -lm: YES (cached)
Checking for function "ctanf" with dependency -lm: YES
Checking for function "ctanl" with dependency -lm: NO
Checking for function "ctanh" with dependency -lm: YES (cached)
Checking for function "ctanhf" with dependency -lm: YES
Checking for function "ctanhl" with dependency -lm: NO
Checking for function "isfinite" with dependency -lm: YES
Header "Python.h" has symbol "isfinite" with dependency python-3.10: YES
Checking for function "isinf" with dependency -lm: YES
Header "Python.h" has symbol "isinf" with dependency python-3.10: YES
Checking for function "isnan" with dependency -lm: YES
Header "Python.h" has symbol "isnan" with dependency python-3.10: YES
Checking for function "signbit" with dependency -lm: YES
Header "Python.h" has symbol "signbit" with dependency python-3.10: YES
Checking if "thread_local" compiles: NO
Checking if "_Thread_local" compiles: YES
Checking if "__thread" compiles: YES
Checking if "__declspec(thread)" compiles: NO
Checking for function "fallocate" : NO
Header "Python.h" has symbol "HAVE_FTELLO" with dependency python-3.10: YES
Header "Python.h" has symbol "HAVE_FSEEKO" with dependency python-3.10: YES
Checking for function "backtrace" : NO
Checking for function "madvise" : YES
Has header "features.h" : NO
Has header "xlocale.h" : YES
Has header "dlfcn.h" : YES
Has header "execinfo.h" : YES
Has header "libunwind.h" : YES
Has header "sys/mman.h" : YES
Checking for function "strtold_l" : YES
Compiler for C supports arguments -O3: YES
Has header "endian.h" : YES
Has header "sys/endian.h" : YES
Compiler for C supports function attribute visibility:hidden: YES
Configuring config.h using configuration
Configuring _numpyconfig.h using configuration
Configuring npymath.ini using configuration
Configuring mlib.ini using configuration
Configuring numpy.pc using configuration
Generating multi-targets for "_umath_tests.dispatch.h"
Enabled targets: AVX2, SSE41, baseline
Generating multi-targets for "argfunc.dispatch.h"
Enabled targets: AVX512_SKX, AVX2, SSE42, baseline
Generating multi-targets for "x86_simd_argsort.dispatch.h"
Enabled targets: AVX512_SKX, AVX2
Generating multi-targets for "x86_simd_qsort.dispatch.h"
Enabled targets: AVX512_SKX, AVX2
Generating multi-targets for "x86_simd_qsort_16bit.dispatch.h"
Enabled targets: AVX512_ICL
Generating multi-targets for "highway_qsort.dispatch.h"
Enabled targets:
Generating multi-targets for "highway_qsort_16bit.dispatch.h"
Enabled targets:
Generating multi-targets for "loops_arithm_fp.dispatch.h"
Enabled targets: AVX2, baseline
Generating multi-targets for "loops_arithmetic.dispatch.h"
Enabled targets: AVX512_SKX, AVX512F, AVX2, SSE41, baseline
Generating multi-targets for "loops_comparison.dispatch.h"
Enabled targets: AVX512_SKX, AVX512F, AVX2, SSE42, baseline
Generating multi-targets for "loops_exponent_log.dispatch.h"
Enabled targets: AVX512_SKX, AVX512F, AVX2, baseline
Generating multi-targets for "loops_hyperbolic.dispatch.h"
Enabled targets: AVX512_SKX, AVX2, baseline
Generating multi-targets for "loops_logical.dispatch.h"
Enabled targets: AVX512_SKX, AVX2, baseline
Generating multi-targets for "loops_minmax.dispatch.h"
Enabled targets: AVX512_SKX, AVX2, baseline
Generating multi-targets for "loops_modulo.dispatch.h"
Enabled targets: baseline
Generating multi-targets for "loops_trigonometric.dispatch.h"
Enabled targets: AVX512_SKX, AVX2, baseline
Generating multi-targets for "loops_umath_fp.dispatch.h"
Enabled targets: AVX512_SKX, baseline
Generating multi-targets for "loops_unary.dispatch.h"
Enabled targets: AVX512_SKX, AVX2, baseline
Generating multi-targets for "loops_unary_fp.dispatch.h"
Enabled targets: SSE41, baseline
Generating multi-targets for "loops_unary_fp_le.dispatch.h"
Enabled targets: SSE41, baseline
Generating multi-targets for "loops_unary_complex.dispatch.h"
Enabled targets: AVX512F, AVX2, baseline
Generating multi-targets for "loops_autovec.dispatch.h"
Enabled targets: AVX2, baseline
Generating multi-targets for "_simd.dispatch.h"
Enabled targets: SSE42, AVX2, FMA3, AVX512F, AVX512_SKX, baseline
Build targets in project: 103
NumPy 2.1.1
User defined options
Native files: /tmp/pip-install-bltn0aj3/numpy_a1fdca0786c14938b2788c097daf84a8/.mesonpy-e9_twr0h/meson-python-native-file.ini
buildtype : release
b_ndebug : if-release
b_vscrt : md
Found ninja-1.11.1 at /usr/local/bin/ninja
+ /usr/local/bin/ninja
[1/512] Copying file numpy/__init__.py
[2/512] Copying file numpy/__init__.pxd
[3/512] Copying file numpy/__init__.cython-30.pxd
[4/512] Generating numpy/_core/npy_math_internal.h with a custom command
[5/512] Generating 'numpy/_core/libnpymath.a.p/ieee754.c'
[6/512] Generating 'numpy/_core/libnpymath.a.p/npy_math_complex.c'
[7/512] Compiling C object numpy/_core/libnpymath.a.p/meson-generated_ieee754.c.o
[8/512] Compiling C++ object numpy/_core/libhighway.a.p/src_highway_hwy_abort.cc.o
FAILED: numpy/_core/libhighway.a.p/src_highway_hwy_abort.cc.o
c++ -Inumpy/_core/libhighway.a.p -Inumpy/_core -I../numpy/_core -I../numpy/_core/src/highway -I/tmp/pip-install-bltn0aj3/numpy_a1fdca0786c14938b2788c097daf84a8/.mesonpy-e9_twr0h/meson_cpu -fvisibility=hidden -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -O3 -ftrapping-math -DNPY_HAVE_CLANG_FPSTRICT -msse -msse2 -msse3 -DNPY_HAVE_SSE2 -DNPY_HAVE_SSE -DNPY_HAVE_SSE3 -fPIC -DTOOLCHAIN_MISS_ASM_HWCAP_H -MD -MQ numpy/_core/libhighway.a.p/src_highway_hwy_abort.cc.o -MF numpy/_core/libhighway.a.p/src_highway_hwy_abort.cc.o.d -o numpy/_core/libhighway.a.p/src_highway_hwy_abort.cc.o -c ../numpy/_core/src/highway/hwy/abort.cc
In file included from ../numpy/_core/src/highway/hwy/abort.cc:12:
In file included from /usr/include/c++/v1/string:573:
In file included from /usr/include/c++/v1/__algorithm/remove.h:12:
/usr/include/c++/v1/__algorithm/find.h:23:10: fatal error: '__string/constexpr_c_functions.h' file not found
23 | #include <__string/constexpr_c_functions.h>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
[9/512] Compiling C object numpy/_core/libnpymath.a.p/meson-generated_npy_math_complex.c.o
[10/512] Compiling C++ object numpy/_core/libnpymath.a.p/src_npymath_halffloat.cpp.o
FAILED: numpy/_core/libnpymath.a.p/src_npymath_halffloat.cpp.o
c++ -Inumpy/_core/libnpymath.a.p -Inumpy/_core -I../numpy/_core -Inumpy/_core/include -I../numpy/_core/include -I../numpy/_core/src/npymath -I../numpy/_core/src/common -I/usr/local/include/python3.10 -I/tmp/pip-install-bltn0aj3/numpy_a1fdca0786c14938b2788c097daf84a8/.mesonpy-e9_twr0h/meson_cpu -fvisibility=hidden -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -O3 -ftrapping-math -DNPY_HAVE_CLANG_FPSTRICT -msse -msse2 -msse3 -DNPY_HAVE_SSE2 -DNPY_HAVE_SSE -DNPY_HAVE_SSE3 -fPIC -MD -MQ numpy/_core/libnpymath.a.p/src_npymath_halffloat.cpp.o -MF numpy/_core/libnpymath.a.p/src_npymath_halffloat.cpp.o.d -o numpy/_core/libnpymath.a.p/src_npymath_halffloat.cpp.o -c ../numpy/_core/src/npymath/halffloat.cpp
In file included from ../numpy/_core/src/npymath/halffloat.cpp:12:
In file included from ../numpy/_core/src/common/common.hpp:9:
In file included from ../numpy/_core/src/common/npstd.hpp:9:
In file included from /usr/include/c++/v1/string:573:
In file included from /usr/include/c++/v1/__algorithm/remove.h:12:
/usr/include/c++/v1/__algorithm/find.h:23:10: fatal error: '__string/constexpr_c_functions.h' file not found
23 | #include <__string/constexpr_c_functions.h>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
ninja: build stopped: subcommand failed.
[end of output]Looking around, it seems that this issue with these missing files may be related to various build tools, but as far as I am aware we have them installed. We have tried installing older versions, which worked when we faced a similar issue installing NumPy, but have had no luck. I'm quite new to this kind of thing so if there are any details you may need that I've missed, please let me know. Any further pointers would be greatly appreciated!
