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internal compiler error: Segmentation fault when building scipy #163

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Sola85 opened this issue Jan 17, 2025 · 3 comments
Open
1 task done

internal compiler error: Segmentation fault when building scipy #163

Sola85 opened this issue Jan 17, 2025 · 3 comments
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@Sola85
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Sola85 commented Jan 17, 2025

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

I probably cannot contribute much to solving this issue. The main reason for reporting this bug is because the error message tells me to.

When trying to build scipy using conda following these instructions https://docs.scipy.org/doc/scipy/building/index.html, i get the following error:

Meson build setup OK
💻  ninja -C
.../scipy/build
-j12
ninja: Entering directory `.../scipy/build'
[614/1460] Compiling C++ object scipy/optimize/_h...subprojects_highs_src_mip_HighsImplications.cpp.o
FAILED: scipy/optimize/_highspy/libhighs.a.p/.._.._.._subprojects_highs_src_mip_HighsImplications.cpp.o
.../micromamba/envs/scipy-dev/bin/x86_64-conda-linux-gnu-c++ -Iscipy/optimize/_highspy/libhighs.a.p -Iscipy/optimize/_highspy -I../scipy/optimize/_highspy -I../subprojects/highs/extern -I../subprojects/highs/extern/pdqsort -I../subprojects/highs/extern/filereaderlp -Isubprojects/highs/src -I../subprojects/highs/src -fvisibility=hidden -fvisibility-inlines-hidden -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -O2 -g -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem .../micromamba/envs/scipy-dev/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem .../micromamba/envs/scipy-dev/include -fPIC -pthread -Wno-comment -Wno-invalid-offsetof -Wno-maybe-uninitialized -Wno-reorder -Wno-unused-but-set-variable -Wno-unused-variable -Wno-use-after-free -MD -MQ scipy/optimize/_highspy/libhighs.a.p/.._.._.._subprojects_highs_src_mip_HighsImplications.cpp.o -MF scipy/optimize/_highspy/libhighs.a.p/.._.._.._subprojects_highs_src_mip_HighsImplications.cpp.o.d -o scipy/optimize/_highspy/libhighs.a.p/.._.._.._subprojects_highs_src_mip_HighsImplications.cpp.o -c ../subprojects/highs/src/mip/HighsImplications.cpp
../subprojects/highs/src/mip/HighsImplications.cpp:787:1: internal compiler error: Segmentation fault
  787 | }
      | ^
0x7f0be70b851f ???
        ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
0x7f0be72137fd ???
        ../sysdeps/x86_64/multiarch/strlen-avx2.S:74
0x7f0be709fd8f __libc_start_call_main
        ../sysdeps/nptl/libc_start_call_main.h:58
0x7f0be709fe3f __libc_start_main_impl
        ../csu/libc-start.c:392
Please submit a full bug report, with preprocessed source (by using -freport-bug).
Please include the complete backtrace with any bug report.
See <https://github.com/conda-forge/ctng-compilers-feedstock/issues/new/choose> for instructions.
[616/1460] Compiling C++ object scipy/optimize/_h....._subprojects_highs_src_mip_HighsNodeQueue.cpp.o
FAILED: scipy/optimize/_highspy/libhighs.a.p/.._.._.._subprojects_highs_src_mip_HighsNodeQueue.cpp.o
.../micromamba/envs/scipy-dev/bin/x86_64-conda-linux-gnu-c++ -Iscipy/optimize/_highspy/libhighs.a.p -Iscipy/optimize/_highspy -I../scipy/optimize/_highspy -I../subprojects/highs/extern -I../subprojects/highs/extern/pdqsort -I../subprojects/highs/extern/filereaderlp -Isubprojects/highs/src -I../subprojects/highs/src -fvisibility=hidden -fvisibility-inlines-hidden -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -O2 -g -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem .../micromamba/envs/scipy-dev/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem .../micromamba/envs/scipy-dev/include -fPIC -pthread -Wno-comment -Wno-invalid-offsetof -Wno-maybe-uninitialized -Wno-reorder -Wno-unused-but-set-variable -Wno-unused-variable -Wno-use-after-free -MD -MQ scipy/optimize/_highspy/libhighs.a.p/.._.._.._subprojects_highs_src_mip_HighsNodeQueue.cpp.o -MF scipy/optimize/_highspy/libhighs.a.p/.._.._.._subprojects_highs_src_mip_HighsNodeQueue.cpp.o.d -o scipy/optimize/_highspy/libhighs.a.p/.._.._.._subprojects_highs_src_mip_HighsNodeQueue.cpp.o -c ../subprojects/highs/src/mip/HighsNodeQueue.cpp
In file included from .../micromamba/envs/scipy-dev/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c++/bits/stl_uninitialized.h:63,
                 from .../micromamba/envs/scipy-dev/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c++/memory:69,
                 from ../subprojects/highs/src/mip/HighsNodeQueue.h:17,
                 from ../subprojects/highs/src/mip/HighsNodeQueue.cpp:11:
.../micromamba/envs/scipy-dev/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c++/bits/stl_algobase.h: In instantiation of '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _OI = __gnu_cxx::__normal_iterator<int*, vector<int> >]':
.../micromamba/envs/scipy-dev/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c++/bits/stl_algobase.h:633:7:   required from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const int*, vector<int> >; _OI = __gnu_cxx::__normal_iterator<int*, vector<int> >]'
.../micromamba/envs/scipy-dev/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c++/bits/vector.tcc:250:31:   required from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator<int>]'
../subprojects/highs/src/mip/HighsDomain.h:376:26:   required from here
.../micromamba/envs/scipy-dev/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c++/bits/stl_algobase.h:544:5: internal compiler error: Segmentation fault
  544 |     }
      |     ^
0x7fe3b6d0351f ???
        ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
0x7fe3b6cead8f __libc_start_call_main
        ../sysdeps/nptl/libc_start_call_main.h:58
0x7fe3b6ceae3f __libc_start_main_impl
        ../csu/libc-start.c:392
Please submit a full bug report, with preprocessed source (by using -freport-bug).
Please include the complete backtrace with any bug report.
See <https://github.com/conda-forge/ctng-compilers-feedstock/issues/new/choose> for instructions.
[625/1460] Compiling C++ object scipy/optimize/_h...rojects_highs_src_mip_HighsPrimalHeuristics.cpp.o
ninja: build stopped: subcommand failed.
Build failed!

I would guess that this is related to #154

Installed packages

_libgcc_mutex                  0.1             conda_forge          conda-forge
  _openmp_mutex                  4.5             2_gnu                conda-forge
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  fonts-conda-ecosystem          1               0                    conda-forge
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  importlib-metadata             8.5.0           pyha770c72_1         conda-forge
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  kernel-headers_linux-64        3.10.0          he073ed8_18          conda-forge
  keyutils                       1.6.1           h166bdaf_0           conda-forge
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  libdrm                         2.4.124         hb9d3cd8_0           conda-forge
  libedit                        3.1.20240808    pl5321h7949ede_0     conda-forge
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  lzo                            2.10            hd590300_1001        conda-forge
  markdown-it-py                 3.0.0           pyhd8ed1ab_1         conda-forge
  markupsafe                     3.0.2           py312h178313f_1      conda-forge
  matplotlib                     3.10.0          py312h7900ff3_0      conda-forge
  matplotlib-base                3.10.0          py312hd3ec401_0      conda-forge
  matplotlib-inline              0.1.7           pyhd8ed1ab_1         conda-forge
  mdit-py-plugins                0.4.2           pyhd8ed1ab_1         conda-forge
  mdurl                          0.1.2           pyhd8ed1ab_1         conda-forge
  menuinst                       2.2.0           py312h7900ff3_0      conda-forge
  meson                          1.6.1           pyhd8ed1ab_0         conda-forge
  meson-python                   0.17.1          pyh70fd9c4_1         conda-forge
  mistune                        3.1.0           pyhd8ed1ab_0         conda-forge
  more-itertools                 10.6.0          pyhd8ed1ab_0         conda-forge
  mpc                            1.3.1           h24ddda3_1           conda-forge
  mpfr                           4.2.1           h90cbb55_3           conda-forge
  mpmath                         1.3.0           pyhd8ed1ab_1         conda-forge
  munkres                        1.1.4           pyh9f0ad1d_0         conda-forge
  mypy                           1.14.1          py312h66e93f0_0      conda-forge
  mypy_extensions                1.0.0           pyha770c72_1         conda-forge
  mysql-common                   9.0.1           h266115a_4           conda-forge
  mysql-libs                     9.0.1           he0572af_4           conda-forge
  myst-nb                        1.1.2           pyhd8ed1ab_1         conda-forge
  myst-parser                    4.0.0           pyhd8ed1ab_1         conda-forge
  nbclient                       0.10.2          pyhd8ed1ab_0         conda-forge
  nbconvert-core                 7.16.5          pyhd8ed1ab_1         conda-forge
  nbformat                       5.10.4          pyhd8ed1ab_1         conda-forge
  ncurses                        6.5             h2d0b736_2           conda-forge
  nest-asyncio                   1.6.0           pyhd8ed1ab_1         conda-forge
  ninja                          1.12.1          h297d8ca_0           conda-forge
  nlohmann_json                  3.11.3          he02047a_1           conda-forge
  numpy                          2.2.1           py312h7e784f5_0      conda-forge
  numpydoc                       1.8.0           pyhd8ed1ab_1         conda-forge
  openblas                       0.3.28          pthreads_h6ec200e_1  conda-forge
  openjpeg                       2.5.3           h5fbd93e_0           conda-forge
  openldap                       2.6.9           he970967_0           conda-forge
  openssl                        3.4.0           h7b32b05_1           conda-forge
  overrides                      7.7.0           pyhd8ed1ab_1         conda-forge
  packaging                      24.2            pyhd8ed1ab_2         conda-forge
  pandocfilters                  1.5.0           pyhd8ed1ab_0         conda-forge
  parso                          0.8.4           pyhd8ed1ab_1         conda-forge
  patch                          2.7.6           h7f98852_1002        conda-forge
  patchelf                       0.17.2          h58526e2_0           conda-forge
  pcre2                          10.44           hba22ea6_2           conda-forge
  pexpect                        4.9.0           pyhd8ed1ab_1         conda-forge
  pickleshare                    0.7.5           pyhd8ed1ab_1004      conda-forge
  pillow                         11.1.0          py312h80c1187_0      conda-forge
  pip                            24.3.1          pyh8b19718_2         conda-forge
  pixman                         0.44.2          h29eaf8c_0           conda-forge
  pkg-config                     0.29.2          h4bc722e_1009        conda-forge
  pkginfo                        1.12.0          pyhd8ed1ab_1         conda-forge
  pkgutil-resolve-name           1.3.10          pyhd8ed1ab_2         conda-forge
  platformdirs                   4.3.6           pyhd8ed1ab_1         conda-forge
  pluggy                         1.5.0           pyhd8ed1ab_1         conda-forge
  ply                            3.11            pyhd8ed1ab_3         conda-forge
  pooch                          1.8.2           pyhd8ed1ab_1         conda-forge
  prometheus_client              0.21.1          pyhd8ed1ab_0         conda-forge
  prompt-toolkit                 3.0.48          pyha770c72_1         conda-forge
  psutil                         6.1.1           py312h66e93f0_0      conda-forge
  pthread-stubs                  0.4             hb9d3cd8_1002        conda-forge
  ptyprocess                     0.7.0           pyhd8ed1ab_1         conda-forge
  pure_eval                      0.2.3           pyhd8ed1ab_1         conda-forge
  py-lief                        0.14.1          py312h2ec8cdc_2      conda-forge
  pybind11                       2.13.6          pyh1ec8472_2         conda-forge
  pybind11-abi                   4               hd8ed1ab_3           conda-forge
  pybind11-global                2.13.6          pyh415d2e4_2         conda-forge
  pycodestyle                    2.12.1          pyhd8ed1ab_1         conda-forge
  pycosat                        0.6.6           py312h66e93f0_2      conda-forge
  pycparser                      2.22            pyh29332c3_1         conda-forge
  pydata-sphinx-theme            0.16.1          pyhd8ed1ab_0         conda-forge
  pydevtool                      0.3.0           pyhd8ed1ab_0         conda-forge
  pygments                       2.19.1          pyhd8ed1ab_0         conda-forge
  pympler                        1.1             pyhd8ed1ab_1         conda-forge
  pyparsing                      3.2.1           pyhd8ed1ab_0         conda-forge
  pyproject-metadata             0.9.0           pyhd8ed1ab_1         conda-forge
  pyside6                        6.8.1           py312h91f0f75_0      conda-forge
  pysocks                        1.7.1           pyha55dd90_7         conda-forge
  pytest                         8.3.4           pyhd8ed1ab_1         conda-forge
  pytest-cov                     6.0.0           pyhd8ed1ab_1         conda-forge
  pytest-timeout                 2.3.1           pyhd8ed1ab_2         conda-forge
  pytest-xdist                   3.6.1           pyhd8ed1ab_1         conda-forge
  python                         3.12.8          h9e4cc4f_1_cpython   conda-forge
  python-dateutil                2.9.0.post0     pyhff2d567_1         conda-forge
  python-fastjsonschema          2.21.1          pyhd8ed1ab_0         conda-forge
  python-json-logger             2.0.7           pyhd8ed1ab_0         conda-forge
  python-libarchive-c            5.1             py312h7900ff3_1      conda-forge
  python_abi                     3.12            5_cp312              conda-forge
  pythran                        0.17.0          pyh47d16e9_1         conda-forge
  pytz                           2024.2          pyhd8ed1ab_1         conda-forge
  pyyaml                         6.0.2           py312h66e93f0_1      conda-forge
  pyzmq                          26.2.0          py312hbf22597_3      conda-forge
  qhull                          2020.2          h434a139_5           conda-forge
  qt6-main                       6.8.1           h588cce1_2           conda-forge
  readline                       8.2             h8228510_1           conda-forge
  referencing                    0.36.1          pyhd8ed1ab_0         conda-forge
  reproc                         14.2.5.post0    hb9d3cd8_0           conda-forge
  reproc-cpp                     14.2.5.post0    h5888daf_0           conda-forge
  requests                       2.32.3          pyhd8ed1ab_1         conda-forge
  rfc3339-validator              0.1.4           pyhd8ed1ab_1         conda-forge
  rfc3986-validator              0.1.1           pyh9f0ad1d_0         conda-forge
  rich                           13.9.4          pyhd8ed1ab_1         conda-forge
  rich-click                     1.8.5           pyhd8ed1ab_0         conda-forge
  ripgrep                        14.1.1          h8fae777_0           conda-forge
  rpds-py                        0.22.3          py312h12e396e_0      conda-forge
  ruamel.yaml                    0.18.10         py312h66e93f0_0      conda-forge
  ruamel.yaml.clib               0.2.8           py312h66e93f0_1      conda-forge
  ruff                           0.9.1           py312h2156523_0      conda-forge
  send2trash                     1.8.3           pyh0d859eb_1         conda-forge
  setuptools                     67.1.0          pyhd8ed1ab_0         conda-forge
  simdjson                       3.11.6          h84d6215_0           conda-forge
  six                            1.17.0          pyhd8ed1ab_0         conda-forge
  sniffio                        1.3.1           pyhd8ed1ab_1         conda-forge
  snowballstemmer                2.2.0           pyhd8ed1ab_0         conda-forge
  sortedcontainers               2.4.0           pyhd8ed1ab_0         conda-forge
  soupsieve                      2.5             pyhd8ed1ab_1         conda-forge
  spdlog                         1.15.0          h10c9db5_0           conda-forge
  sphinx                         7.4.7           pyhd8ed1ab_0         conda-forge
  sphinx-copybutton              0.5.2           pyhd8ed1ab_1         conda-forge
  sphinx-design                  0.6.1           pyhd8ed1ab_2         conda-forge
  sphinxcontrib-applehelp        2.0.0           pyhd8ed1ab_1         conda-forge
  sphinxcontrib-devhelp          2.0.0           pyhd8ed1ab_1         conda-forge
  sphinxcontrib-htmlhelp         2.1.0           pyhd8ed1ab_1         conda-forge
  sphinxcontrib-jsmath           1.0.1           pyhd8ed1ab_1         conda-forge
  sphinxcontrib-qthelp           2.0.0           pyhd8ed1ab_1         conda-forge
  sphinxcontrib-serializinghtml  1.1.10          pyhd8ed1ab_1         conda-forge
  sqlalchemy                     2.0.37          py312h66e93f0_0      conda-forge
  stack_data                     0.6.3           pyhd8ed1ab_1         conda-forge
  sysroot_linux-64               2.17            h0157908_18          conda-forge
  tabulate                       0.9.0           pyhd8ed1ab_2         conda-forge
  terminado                      0.18.1          pyh0d859eb_0         conda-forge
  threadpoolctl                  3.5.0           pyhc1e730c_0         conda-forge
  tinycss2                       1.4.0           pyhd8ed1ab_0         conda-forge
  tk                             8.6.13          noxft_h4845f30_101   conda-forge
  tokenize-rt                    6.1.0           pyhd8ed1ab_1         conda-forge
  toml                           0.10.2          pyhd8ed1ab_1         conda-forge
  tomli                          2.2.1           pyhd8ed1ab_1         conda-forge
  tornado                        6.4.2           py312h66e93f0_0      conda-forge
  tqdm                           4.67.1          pyhd8ed1ab_1         conda-forge
  traitlets                      5.14.3          pyhd8ed1ab_1         conda-forge
  truststore                     0.10.0          pyhd8ed1ab_0         conda-forge
  types-psutil                   6.1.0.20241221  pyhd8ed1ab_0         conda-forge
  types-python-dateutil          2.9.0.20241206  pyhd8ed1ab_0         conda-forge
  typing-extensions              4.12.2          hd8ed1ab_1           conda-forge
  typing_extensions              4.12.2          pyha770c72_1         conda-forge
  typing_utils                   0.1.0           pyhd8ed1ab_1         conda-forge
  tzdata                         2025a           h78e105d_0           conda-forge
  unicodedata2                   16.0.0          py312h66e93f0_0      conda-forge
  uri-template                   1.3.0           pyhd8ed1ab_1         conda-forge
  urllib3                        2.3.0           pyhd8ed1ab_0         conda-forge
  virtualenv                     20.29.0         pyhd8ed1ab_0         conda-forge
  wayland                        1.23.1          h3e06ad9_0           conda-forge
  wcwidth                        0.2.13          pyhd8ed1ab_1         conda-forge
  webcolors                      24.11.1         pyhd8ed1ab_0         conda-forge
  webencodings                   0.5.1           pyhd8ed1ab_3         conda-forge
  websocket-client               1.8.0           pyhd8ed1ab_1         conda-forge
  wheel                          0.45.1          pyhd8ed1ab_1         conda-forge
  xcb-util                       0.4.1           hb711507_2           conda-forge
  xcb-util-cursor                0.1.5           hb9d3cd8_0           conda-forge
  xcb-util-image                 0.4.0           hb711507_2           conda-forge
  xcb-util-keysyms               0.4.1           hb711507_0           conda-forge
  xcb-util-renderutil            0.3.10          hb711507_0           conda-forge
  xcb-util-wm                    0.4.2           hb711507_0           conda-forge
  xkeyboard-config               2.43            hb9d3cd8_0           conda-forge
  xorg-libice                    1.1.2           hb9d3cd8_0           conda-forge
  xorg-libsm                     1.2.5           he73a12e_0           conda-forge
  xorg-libx11                    1.8.10          h4f16b4b_1           conda-forge
  xorg-libxau                    1.0.12          hb9d3cd8_0           conda-forge
  xorg-libxcomposite             0.4.6           hb9d3cd8_2           conda-forge
  xorg-libxcursor                1.2.3           hb9d3cd8_0           conda-forge
  xorg-libxdamage                1.1.6           hb9d3cd8_0           conda-forge
  xorg-libxdmcp                  1.1.5           hb9d3cd8_0           conda-forge
  xorg-libxext                   1.3.6           hb9d3cd8_0           conda-forge
  xorg-libxfixes                 6.0.1           hb9d3cd8_0           conda-forge
  xorg-libxi                     1.8.2           hb9d3cd8_0           conda-forge
  xorg-libxrandr                 1.5.4           hb9d3cd8_0           conda-forge
  xorg-libxrender                0.9.12          hb9d3cd8_0           conda-forge
  xorg-libxtst                   1.2.5           hb9d3cd8_3           conda-forge
  xorg-libxxf86vm                1.1.6           hb9d3cd8_0           conda-forge
  yaml                           0.2.5           h7f98852_2           conda-forge
  yaml-cpp                       0.8.0           h59595ed_0           conda-forge
  zeromq                         4.3.5           h3b0a872_7           conda-forge
  zipp                           3.21.0          pyhd8ed1ab_1         conda-forge
  zstandard                      0.23.0          py312hef9b889_1      conda-forge
  zstd                           1.5.6           ha6fb4c9_0           conda-forge

Environment info

libmamba version : 2.0.5
     micromamba version : 2.0.5
           curl version : libcurl/8.11.1 OpenSSL/3.4.0 zlib/1.3.1 zstd/1.5.6 libssh2/1.11.1 nghttp2/1.64.0
     libarchive version : libarchive 3.7.7 zlib/1.3.1 bz2lib/1.0.8 libzstd/1.5.6
       envs directories : .../micromamba/envs
          package cache : .../micromamba/pkgs
                          .../.mamba/pkgs
            environment : scipy-dev (active)
           env location : .../micromamba/envs/scipy-dev
      user config files : .../.mambarc
 populated config files : .../.condarc
       virtual packages : __unix=0=0
                          __linux=5.15.0=0
                          __glibc=2.35=0
                          __archspec=1=x86_64_v3
               channels : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
       base environment : .../micromamba
               platform : linux-64
@Sola85 Sola85 added the bug Something isn't working label Jan 17, 2025
@h-vetinari
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Can you say which commit from scipy you're trying to build? Please try to reproduce with a specific version or commit, without any local changes.

@Sola85 Sola85 mentioned this issue Jan 17, 2025
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@Sola85
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Sola85 commented Jan 17, 2025

I was trying to build the branch in the linked PR (not mine), which builds without errors in CI, so I thought its unlikely to be an issue with the branch. The commit id is scipy/scipy@800c663 and I have no local changes.

@h-vetinari h-vetinari mentioned this issue Jan 19, 2025
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@h-vetinari
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I've opened an issue in scipy to discuss this: scipy/scipy#22362

Any help on reproducing/debugging this would of course be beneficial! :)
(e.g. install these requirements, check out scipy/scipy@800c663, run python dev.py build)

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