=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Building for py314-scikit-learn-1.8.0 * Building wheel... + meson setup /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/.mesonpy-toar5kga -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/.mesonpy-toar5kga/meson-python-native-file.ini The Meson build system Version: 1.10.1 Source dir: /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0 Build dir: /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/.mesonpy-toar5kga Build type: native build Project name: scikit-learn Project version: 1.8.0 C compiler for the host machine: gcc (gcc 12.5.0 "gcc (nb1 20250721) 12.5.0") C linker for the host machine: gcc ld.bfd 2.42 C++ compiler for the host machine: c++ (gcc 12.5.0 "g++ (nb1 20250721) 12.5.0") C++ linker for the host machine: c++ ld.bfd 2.42 Cython compiler for the host machine: cython-3.14 (cython 3.2.4) Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C supports arguments -Wno-unused-but-set-variable: YES Compiler for C supports arguments -Wno-unused-function: YES Compiler for C supports arguments -Wno-conversion: YES Compiler for C supports arguments -Wno-misleading-indentation: YES Library m found: YES Program sklearn/_build_utils/tempita.py found: YES (/usr/pkg/bin/python3.13 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py) Program python found: YES (/usr/pkg/bin/python3.14) Run-time dependency OpenMP for c found: YES 4.5 Program cython-3.14 found: YES (/usr/pkg/bin/cython-3.14) Found pkg-config: YES (/pbulk/work/math/py-scikit-learn/work/.tools/bin/pkg-config) 2.5.1 Run-time dependency python found: YES 3.14 Build targets in project: 112 scikit-learn 1.8.0 User defined options Native files: /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/.mesonpy-toar5kga/meson-python-native-file.ini b_ndebug : if-release b_vscrt : md buildtype : release Found ninja-1.13.2 at /usr/pkg/bin/ninja + /usr/pkg/bin/ninja [1/253] Copying file sklearn/__init__.py [2/253] Copying file sklearn/_loss/_loss.pxd [3/253] Copying file sklearn/utils/__init__.py [4/253] Copying file sklearn/utils/_cython_blas.pxd [5/253] Copying file sklearn/utils/_heap.pxd [6/253] Copying file sklearn/utils/_openmp_helpers.pxd [7/253] Copying file sklearn/utils/_random.pxd [8/253] Copying file sklearn/utils/_sorting.pxd [9/253] Copying file sklearn/utils/_typedefs.pxd [10/253] Copying file sklearn/utils/_vector_sentinel.pxd [11/253] Copying file sklearn/metrics/__init__.py [12/253] Copying file sklearn/metrics/_pairwise_distances_reduction/__init__.py [13/253] Copying file sklearn/metrics/_pairwise_distances_reduction/_classmode.pxd [14/253] Copying file sklearn/linear_model/__init__.py [15/253] Copying file sklearn/neighbors/__init__.py [16/253] Copying file sklearn/neighbors/_partition_nodes.pxd [17/253] Generating sklearn/utils/_seq_dataset_pxd with a custom command FAILED: [code=1] sklearn/utils/_seq_dataset.pxd /usr/pkg/bin/python3.13 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py ../sklearn/utils/_seq_dataset.pxd.tp -o sklearn/utils Traceback (most recent call last): File "/pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py", line 9, in from Cython import Tempita as tempita ModuleNotFoundError: No module named 'Cython' [18/253] Generating sklearn/utils/_weight_vector_pxd with a custom command FAILED: [code=1] sklearn/utils/_weight_vector.pxd /usr/pkg/bin/python3.13 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py ../sklearn/utils/_weight_vector.pxd.tp -o sklearn/utils Traceback (most recent call last): File "/pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py", line 9, in from Cython import Tempita as tempita ModuleNotFoundError: No module named 'Cython' [19/253] Generating sklearn/metrics/_dist_metrics_pxd with a custom command FAILED: [code=1] sklearn/metrics/_dist_metrics.pxd /usr/pkg/bin/python3.13 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py ../sklearn/metrics/_dist_metrics.pxd.tp -o sklearn/metrics Traceback (most recent call last): File "/pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py", line 9, in from Cython import Tempita as tempita ModuleNotFoundError: No module named 'Cython' [20/253] Generating sklearn/metrics/_pairwise_distances_reduction/_datasets_pair_pxd with a custom command FAILED: [code=1] sklearn/metrics/_pairwise_distances_reduction/_datasets_pair.pxd /usr/pkg/bin/python3.13 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py ../sklearn/metrics/_pairwise_distances_reduction/_datasets_pair.pxd.tp -o sklearn/metrics/_pairwise_distances_reduction Traceback (most recent call last): File "/pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py", line 9, in from Cython import Tempita as tempita ModuleNotFoundError: No module named 'Cython' [21/253] Generating sklearn/metrics/_pairwise_distances_reduction/_base_pxd with a custom command FAILED: [code=1] sklearn/metrics/_pairwise_distances_reduction/_base.pxd /usr/pkg/bin/python3.13 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py ../sklearn/metrics/_pairwise_distances_reduction/_base.pxd.tp -o sklearn/metrics/_pairwise_distances_reduction Traceback (most recent call last): File "/pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py", line 9, in from Cython import Tempita as tempita ModuleNotFoundError: No module named 'Cython' [22/253] Generating sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer_pxd with a custom command FAILED: [code=1] sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.pxd /usr/pkg/bin/python3.13 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py ../sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.pxd.tp -o sklearn/metrics/_pairwise_distances_reduction Traceback (most recent call last): File "/pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py", line 9, in from Cython import Tempita as tempita ModuleNotFoundError: No module named 'Cython' [23/253] Generating sklearn/metrics/_pairwise_distances_reduction/_argkmin_pxd with a custom command FAILED: [code=1] sklearn/metrics/_pairwise_distances_reduction/_argkmin.pxd /usr/pkg/bin/python3.13 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py ../sklearn/metrics/_pairwise_distances_reduction/_argkmin.pxd.tp -o sklearn/metrics/_pairwise_distances_reduction Traceback (most recent call last): File "/pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py", line 9, in from Cython import Tempita as tempita ModuleNotFoundError: No module named 'Cython' [24/253] Generating sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors_pxd with a custom command FAILED: [code=1] sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.pxd /usr/pkg/bin/python3.13 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py ../sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.pxd.tp -o sklearn/metrics/_pairwise_distances_reduction Traceback (most recent call last): File "/pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py", line 9, in from Cython import Tempita as tempita ModuleNotFoundError: No module named 'Cython' [25/253] Generating sklearn/neighbors/_binary_tree_pxi with a custom command FAILED: [code=1] sklearn/neighbors/_binary_tree.pxi /usr/pkg/bin/python3.13 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py ../sklearn/neighbors/_binary_tree.pxi.tp -o sklearn/neighbors Traceback (most recent call last): File "/pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py", line 9, in from Cython import Tempita as tempita ModuleNotFoundError: No module named 'Cython' [26/253] Generating sklearn/_loss/_loss_pyx with a custom command FAILED: [code=1] sklearn/_loss/_loss.pyx /usr/pkg/bin/python3.13 /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py ../sklearn/_loss/_loss.pyx.tp -o sklearn/_loss Traceback (most recent call last): File "/pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/_build_utils/tempita.py", line 9, in from Cython import Tempita as tempita ModuleNotFoundError: No module named 'Cython' [27/253] Generating 'sklearn/__check_build/_check_build.so.p/_check_build.c' [28/253] Generating 'sklearn/utils/arrayfuncs.so.p/arrayfuncs.c' [29/253] Generating 'sklearn/_isotonic.so.p/_isotonic.c' [30/253] Generating 'sklearn/utils/_typedefs.so.p/_typedefs.c' [31/253] Generating 'sklearn/utils/_openmp_helpers.so.p/_openmp_helpers.c' [32/253] Generating sklearn/_cyutility.c with a custom command [33/253] Generating 'sklearn/cluster/_hdbscan/_linkage.so.p/_linkage.c' FAILED: [code=1] sklearn/cluster/_hdbscan/_linkage.so.p/_linkage.c /usr/pkg/bin/cython-3.14 --depfile '-X language_level=3' '-X boundscheck=False' '-X wraparound=False' '-X initializedcheck=False' '-X nonecheck=False' '-X cdivision=True' '-X profile=False' --include-dir /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/.mesonpy-toar5kga -Xfreethreading_compatible=True --shared=sklearn._cyutility ../sklearn/cluster/_hdbscan/_linkage.pyx --output-file sklearn/cluster/_hdbscan/_linkage.so.p/_linkage.c Error compiling Cython file: ------------------------------------------------------------ ... cimport numpy as cnp from libc.float cimport DBL_MAX import numpy as np from sklearn.metrics._dist_metrics cimport DistanceMetric64 ^ ------------------------------------------------------------ /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/cluster/_hdbscan/_linkage.pyx:36:0: 'sklearn/metrics/_dist_metrics.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... cimport numpy as cnp from libc.float cimport DBL_MAX import numpy as np from sklearn.metrics._dist_metrics cimport DistanceMetric64 ^ ------------------------------------------------------------ /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/cluster/_hdbscan/_linkage.pyx:36:0: 'sklearn/metrics/_dist_metrics/DistanceMetric64.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... cpdef cnp.ndarray[MST_edge_t, ndim=1, mode='c'] mst_from_data_matrix( const float64_t[:, ::1] raw_data, const float64_t[::1] core_distances, DistanceMetric64 dist_metric, ^ ------------------------------------------------------------ /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/cluster/_hdbscan/_linkage.pyx:114:4: 'DistanceMetric64' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... next_node_min_reach = min_reachability[j] next_node_source = current_sources[j] pair_distance = dist_metric.dist( &raw_data[current_node, 0], ^ ------------------------------------------------------------ /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/cluster/_hdbscan/_linkage.pyx:184:16: Cannot convert 'const float64_t *' to Python object Error compiling Cython file: ------------------------------------------------------------ ... next_node_min_reach = min_reachability[j] next_node_source = current_sources[j] pair_distance = dist_metric.dist( &raw_data[current_node, 0], &raw_data[j, 0], ^ ------------------------------------------------------------ /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/cluster/_hdbscan/_linkage.pyx:185:16: Cannot convert 'const float64_t *' to Python object [34/253] Generating 'sklearn/utils/_sorting.so.p/_sorting.c' [35/253] Generating 'sklearn/ensemble/_hist_gradient_boosting/_gradient_boosting.so.p/_gradient_boosting.c' [36/253] Generating 'sklearn/cluster/_dbscan_inner.so.p/_dbscan_inner.cpp' [37/253] Generating 'sklearn/decomposition/_online_lda_fast.so.p/_online_lda_fast.c' [38/253] Generating 'sklearn/ensemble/_hist_gradient_boosting/_predictor.so.p/_predictor.c' [39/253] Generating 'sklearn/cluster/_k_means_minibatch.so.p/_k_means_minibatch.c' [40/253] Generating 'sklearn/manifold/_utils.so.p/_utils.c' [41/253] Generating 'sklearn/ensemble/_hist_gradient_boosting/common.so.p/common.c' [42/253] Generating 'sklearn/ensemble/_hist_gradient_boosting/_bitset.so.p/_bitset.c' [43/253] Generating 'sklearn/utils/_heap.so.p/_heap.c' [44/253] Generating 'sklearn/utils/_random.so.p/_random.c' [45/253] Generating 'sklearn/utils/murmurhash.so.p/murmurhash.c' [46/253] Generating 'sklearn/utils/_fast_dict.so.p/_fast_dict.cpp' [47/253] Generating 'sklearn/ensemble/_hist_gradient_boosting/histogram.so.p/histogram.c' [48/253] Generating 'sklearn/ensemble/_hist_gradient_boosting/_binning.so.p/_binning.c' [49/253] Generating 'sklearn/feature_extraction/_hashing_fast.so.p/_hashing_fast.cpp' [50/253] Generating 'sklearn/cluster/_k_means_elkan.so.p/_k_means_elkan.c' [51/253] Generating 'sklearn/cluster/_k_means_lloyd.so.p/_k_means_lloyd.c' [52/253] Generating 'sklearn/cluster/_hierarchical_fast.so.p/_hierarchical_fast.cpp' FAILED: [code=1] sklearn/cluster/_hierarchical_fast.so.p/_hierarchical_fast.cpp /usr/pkg/bin/cython-3.14 --depfile '-X language_level=3' '-X boundscheck=False' '-X wraparound=False' '-X initializedcheck=False' '-X nonecheck=False' '-X cdivision=True' '-X profile=False' --include-dir /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/.mesonpy-toar5kga -Xfreethreading_compatible=True --shared=sklearn._cyutility --cplus ../sklearn/cluster/_hierarchical_fast.pyx --output-file sklearn/cluster/_hierarchical_fast.so.p/_hierarchical_fast.cpp Error compiling Cython file: ------------------------------------------------------------ ... # SPDX-License-Identifier: BSD-3-Clause import numpy as np cimport cython from sklearn.metrics._dist_metrics cimport DistanceMetric64 ^ ------------------------------------------------------------ /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/cluster/_hierarchical_fast.pyx:7:0: 'sklearn/metrics/_dist_metrics.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... # SPDX-License-Identifier: BSD-3-Clause import numpy as np cimport cython from sklearn.metrics._dist_metrics cimport DistanceMetric64 ^ ------------------------------------------------------------ /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/cluster/_hierarchical_fast.pyx:7:0: 'sklearn/metrics/_dist_metrics/DistanceMetric64.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... # Implements MST-LINKAGE-CORE from https://arxiv.org/abs/1109.2378 def mst_linkage_core( const float64_t [:, ::1] raw_data, DistanceMetric64 dist_metric): ^ ------------------------------------------------------------ /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/cluster/_hierarchical_fast.pyx:431:8: 'DistanceMetric64' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... for j in range(n_samples): if in_tree[j]: continue right_value = current_distances[j] left_value = dist_metric.dist(&raw_data[current_node, 0], ^ ------------------------------------------------------------ /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/cluster/_hierarchical_fast.pyx:491:42: Cannot convert 'const float64_t *' to Python object Error compiling Cython file: ------------------------------------------------------------ ... if in_tree[j]: continue right_value = current_distances[j] left_value = dist_metric.dist(&raw_data[current_node, 0], &raw_data[j, 0], ^ ------------------------------------------------------------ /pbulk/work/math/py-scikit-learn/work/scikit_learn-1.8.0/sklearn/cluster/_hierarchical_fast.pyx:492:42: Cannot convert 'const float64_t *' to Python object [53/253] Generating 'sklearn/ensemble/_gradient_boosting.so.p/_gradient_boosting.c' [54/253] Generating 'sklearn/ensemble/_hist_gradient_boosting/splitting.so.p/splitting.c' [55/253] Generating 'sklearn/utils/_vector_sentinel.so.p/_vector_sentinel.cpp' [56/253] Generating 'sklearn/datasets/_svmlight_format_fast.so.p/_svmlight_format_fast.c' [57/253] Generating 'sklearn/decomposition/_cdnmf_fast.so.p/_cdnmf_fast.c' [58/253] Generating 'sklearn/metrics/_pairwise_fast.so.p/_pairwise_fast.c' [59/253] Generating 'sklearn/cluster/_hdbscan/_reachability.so.p/_reachability.c' [60/253] Generating 'sklearn/metrics/cluster/_expected_mutual_info_fast.so.p/_expected_mutual_info_fast.c' [61/253] Generating 'sklearn/cluster/_hdbscan/_tree.so.p/_tree.c' [62/253] Generating 'sklearn/cluster/_k_means_common.so.p/_k_means_common.c' [63/253] Generating 'sklearn/utils/_isfinite.so.p/_isfinite.c' [64/253] Generating 'sklearn/linear_model/_cd_fast.so.p/_cd_fast.c' [65/253] Generating 'sklearn/utils/_cython_blas.so.p/_cython_blas.c' [66/253] Generating 'sklearn/utils/sparsefuncs_fast.so.p/sparsefuncs_fast.c' ninja: build stopped: subcommand failed. ERROR Backend subprocess exited when trying to invoke build_wheel *** Error code 1 Stop. make[1]: stopped making "all" in /usr/pkgsrc/math/py-scikit-learn *** Error code 1 Stop. make: stopped making "all" in /usr/pkgsrc/math/py-scikit-learn