New install issue on Candide
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python -m pip install . returns:
[ 98%] Linking CXX executable dl_dl2d
[ 98%] Built target dl_denoise_image
[ 98%] Linking CXX executable dl_estimate_redshift
libdiclearn.a(C_DL1D.cc.o): In function void arma::syrk<false, false, false>::apply_blas_type<double, arma::Mat<double> >(arma::Mat<double>&, arma::Mat<double> const&, double, double) [clone .isra.0]': C_DL1D.cc:(.text+0x8f3): undefined reference to wrapper2_dsyrk_'
C_DL1D.cc:(.text+0xcdc): undefined reference to wrapper2_ddot_' libdiclearn.a(C_DL1D.cc.o): In function void arma::glue_times_redirect2_helper::apply<arma::Mat, arma::Op<arma::Mat, arma::op_htrans> >(arma::Mat<arma::Mat::elem_type>&, arma::Glue<arma::Mat, arma::Op<arma::Mat, arma::op_htrans>, arma::glue_times> const&) [clone .isra.0]':
C_DL1D.cc:(.text.hot+0xf24): undefined reference to wrapper2_dgemm_' C_DL1D.cc:(.text.hot+0x11e1): undefined reference to wrapper2_dgemm_'
C_DL1D.cc:(.text.hot+0x1662): undefined reference to wrapper2_dgemv_' C_DL1D.cc:(.text.hot+0x172c): undefined reference to wrapper2_dgemv_'
C_DL1D.cc:(.text.hot+0x17e5): undefined reference to wrapper2_dgemv_' C_DL1D.cc:(.text.hot+0x18c6): undefined reference to wrapper2_dgemv_'
libdiclearn.a(C_DL1D.cc.o): In function bool arma::auxlib::eig_sym_dc<double>(arma::Col<double>&, arma::Mat<double>&, arma::Mat<double> const&)': C_DL1D.cc:(.text._ZN4arma6auxlib10eig_sym_dcIdEEbRNS_3ColIT_EERNS_3MatIS3_EERKS7_[_ZN4arma6auxlib10eig_sym_dcIdEEbRNS_3ColIT_EERNS_3MatIS3_EERKS7_]+0x438): undefined reference to wrapper2_dsyevd_'
C_DL1D.cc:(.text.ZN4arma6auxlib10eig_sym_dcIdEEbRNS_3ColIT_EERNS_3MatIS3_EERKS7[ZN4arma6auxlib10eig_sym_dcIdEEbRNS_3ColIT_EERNS_3MatIS3_EERKS7]+0x51b): undefined reference to wrapper2_dsyevd_' libdiclearn.a(C_DL1D.cc.o): In function bool arma::auxlib::svd_dc_econ(arma::Mat&, arma::Col&, arma::Mat&, arma::Mat&)':
C_DL1D.cc:(.text.ZN4arma6auxlib11svd_dc_econIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5[ZN4arma6auxlib11svd_dc_econIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5]+0x490): undefined reference to wrapper2_dgesdd_' C_DL1D.cc:(.text._ZN4arma6auxlib11svd_dc_econIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_[_ZN4arma6auxlib11svd_dc_econIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_]+0x95b): undefined reference to wrapper2_dgesdd_'
libdiclearn.a(C_DL1D.cc.o): In function bool arma::auxlib::svd_econ<double>(arma::Mat<double>&, arma::Col<double>&, arma::Mat<double>&, arma::Mat<double>&, char)': C_DL1D.cc:(.text._ZN4arma6auxlib8svd_econIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_c[_ZN4arma6auxlib8svd_econIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_c]+0x30b): undefined reference to wrapper2_dgesvd_'
C_DL1D.cc:(.text._ZN4arma6auxlib8svd_econIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_c[_ZN4arma6auxlib8svd_econIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_c]+0x74d): undefined reference to wrapper2_dgesvd_' libdiclearn.a(C_DL1D.cc.o): In function bool arma::op_pinv::apply_sym(arma::Mat&, arma::Mat const&, arma::get_pod_type::result, unsigned long long)':
C_DL1D.cc:(.text._ZN4arma7op_pinv9apply_symIdEEbRNS_3MatIT_EERKS4_NS_12get_pod_typeIS3_E6resultEy[ZN4arma7op_pinv9apply_symIdEEbRNS_3MatIT_EERKS4_NS_12get_pod_typeIS3_E6resultEy]+0x751): undefined reference to `wrapper2_dsyev'
collect2: error: ld returned 1 exit status
[ 98%] Built target dl_dl2d
make[5]: *** [src/dl_dl1d] Error 1
make[4]: *** [src/CMakeFiles/dl_dl1d.dir/all] Error 2
make[4]: *** Waiting for unfinished jobs....
[ 99%] Linking CXX executable delta_chi2
[ 99%] Linking CXX executable dl_extract_patches
[ 99%] Linking CXX executable mr3d_genus
[ 99%] Built target dl_estimate_redshift
[ 99%] Built target delta_chi2
[ 99%] Built target dl_extract_patches
[ 99%] Linking CXX executable simgauss
[ 99%] Built target mr3d_genus
[ 99%] Linking CXX executable simu_lognormal
[ 99%] Built target simgauss
[ 99%] Built target simu_lognormal
[ 99%] Linking CXX executable lratio
[ 99%] Built target lratio
make[3]: *** [all] Error 2
gmake[2]: *** [sparse2d/src/sparse2d-stamp/sparse2d-build] Error 2
gmake[1]: *** [CMakeFiles/sparse2d.dir/all] Error 2
gmake: *** [all] Error 2
Traceback (most recent call last):
File "/home/tersenov/.conda/envs/pysap/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in
main()
File "/home/tersenov/.conda/envs/pysap/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tersenov/.conda/envs/pysap/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel
whl_basename = backend.build_wheel(metadata_directory, config_settings)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-ojbpv0oc/overlay/lib/python3.11/site-packages/py_build_cmake/build.py", line 67, in build_wheel
whl_name = self.build_wheel_in_dir(wheel_directory, tmp_build_dir,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-ojbpv0oc/overlay/lib/python3.11/site-packages/py_build_cmake/build.py", line 248, in build_wheel_in_dir
self.do_native_cross_cmake_build(paths, cfg, pkg_info)
File "/tmp/pip-build-env-ojbpv0oc/overlay/lib/python3.11/site-packages/py_build_cmake/build.py", line 333, in do_native_cross_cmake_build
self.run_cmake(paths.source_dir, paths.staging_dir, cmake_cfg,
File "/tmp/pip-build-env-ojbpv0oc/overlay/lib/python3.11/site-packages/py_build_cmake/build.py", line 511, in run_cmake
cmaker.build()
File "/tmp/pip-build-env-ojbpv0oc/overlay/lib/python3.11/site-packages/py_build_cmake/cmake.py", line 190, in build
self.run(cmd, cwd=cwd, check=True, env=env)
File "/tmp/pip-build-env-ojbpv0oc/overlay/lib/python3.11/site-packages/py_build_cmake/cmake.py", line 68, in run
return self.runner.run(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-ojbpv0oc/overlay/lib/python3.11/site-packages/py_build_cmake/cmd_runner.py", line 25, in run
return sp_run(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tersenov/.conda/envs/pysap/lib/python3.11/subprocess.py", line 571, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['cmake', '--build', '/home/tersenov/software/cosmostat/.py-build-cmake_cache/cp311-cp311-linux_x86_64', '-j 8']' returned non-zero exit status 2.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.