Building wheel for klustakwik2 (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/samuel/.virtualenvs/py38/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-0ied5eru/klustakwik2/setup.py'"'"'; __file__='"'"'/tmp/pip-install-0ied5eru/klustakwik2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-c7b5_hxd
cwd: /tmp/pip-install-0ied5eru/klustakwik2/
Complete output (384 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/clustering.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/monitoring.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/data.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/logger.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/input_output.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/mask_starts.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/precomputations.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/linear_algebra.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/default_parameters.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/debugtools.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2
creating build/lib.linux-x86_64-3.8/klustakwik2/numerics
copying klustakwik2/numerics/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics
creating build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/e_step.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/compute_cluster_masks.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/m_step.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/compute_cluster_penalties.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/masks.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
creating build/lib.linux-x86_64-3.8/klustakwik2/numerics/numbalib
copying klustakwik2/numerics/numbalib/m_step.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/numbalib
copying klustakwik2/numerics/numbalib/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/numbalib
creating build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_io.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_compute_cluster_masks.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_partitioning.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_synthetic_data.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_compute_covariance_matrix.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_linear_algebra.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_mask_starts.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
creating build/lib.linux-x86_64-3.8/klustakwik2/scripts
copying klustakwik2/scripts/kk2_legacy.py -> build/lib.linux-x86_64-3.8/klustakwik2/scripts
copying klustakwik2/scripts/tools.py -> build/lib.linux-x86_64-3.8/klustakwik2/scripts
copying klustakwik2/scripts/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2/scripts
running egg_info
writing klustakwik2.egg-info/PKG-INFO
writing dependency_links to klustakwik2.egg-info/dependency_links.txt
writing entry points to klustakwik2.egg-info/entry_points.txt
writing top-level names to klustakwik2.egg-info/top_level.txt
reading manifest file 'klustakwik2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.pyxbld' under directory 'klustakwik2/numerics/cylib'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
writing manifest file 'klustakwik2.egg-info/SOURCES.txt'
copying klustakwik2/numerics/cylib/compute_cluster_masks_cy.c -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/compute_cluster_masks_cy.pyx -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/compute_cluster_penalties_cy.pyx -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/e_step_cy.cpp -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/e_step_cy.pyx -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/m_step_cy.c -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/m_step_cy.pyx -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/masks_cy.cpp -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/masks_cy.pyx -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
running build_ext
building 'klustakwik2.numerics.cylib.compute_cluster_masks_cy' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/klustakwik2
creating build/temp.linux-x86_64-3.8/klustakwik2/numerics
creating build/temp.linux-x86_64-3.8/klustakwik2/numerics/cylib
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include -I/home/samuel/.virtualenvs/py38/include -I/usr/include/python3.8 -c klustakwik2/numerics/cylib/compute_cluster_masks_cy.c -o build/temp.linux-x86_64-3.8/klustakwik2/numerics/cylib/compute_cluster_masks_cy.o
In file included from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from klustakwik2/numerics/cylib/compute_cluster_masks_cy.c:623:
/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/klustakwik2/numerics/cylib/compute_cluster_masks_cy.o -o build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib/compute_cluster_masks_cy.cpython-38-x86_64-linux-gnu.so
building 'klustakwik2.numerics.cylib.compute_cluster_penalties_cy' extension
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include -I/home/samuel/.virtualenvs/py38/include -I/usr/include/python3.8 -c klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c -o build/temp.linux-x86_64-3.8/klustakwik2/numerics/cylib/compute_cluster_penalties_cy.o
In file included from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:265:
/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘PyInit_compute_cluster_penalties_cy’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18762:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18762 | __pyx_type___pyx_array.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18765:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18765 | __pyx_type___pyx_MemviewEnum.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18776:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18776 | __pyx_type___pyx_memoryview.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18785:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18785 | __pyx_type___pyx_memoryviewslice.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionSave’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19186:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19186 | *type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19187:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19187 | *value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19188:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19188 | *tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionReset’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19200:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19200 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19201:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19201 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19202:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19202 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19203:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19203 | tstate->exc_type = type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19204:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19204 | tstate->exc_value = value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19205:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19205 | tstate->exc_traceback = tb;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_GetException’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19248:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19248 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19249:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19249 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19250:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19250 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19251:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19251 | tstate->exc_type = local_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19252:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19252 | tstate->exc_value = local_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19253:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19253 | tstate->exc_traceback = local_tb;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionSwap’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20713:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
20713 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20714:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
20714 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20715:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
20715 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20716:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
20716 | tstate->exc_type = *type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20717:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
20717 | tstate->exc_value = *value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20718:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
20718 | tstate->exc_traceback = *tb;
| ^~~~~~~~~~~~~
| curexc_traceback
In file included from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:21,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:265:
At top level:
/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
1463 | _import_array(void)
| ^~~~~~~~~~~~~
running bdist_wheel
running build
running build_py
running egg_info
writing klustakwik2.egg-info/PKG-INFO
writing dependency_links to klustakwik2.egg-info/dependency_links.txt
writing entry points to klustakwik2.egg-info/entry_points.txt
writing top-level names to klustakwik2.egg-info/top_level.txt
reading manifest file 'klustakwik2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.pyxbld' under directory 'klustakwik2/numerics/cylib'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
writing manifest file 'klustakwik2.egg-info/SOURCES.txt'
running build_ext
building 'klustakwik2.numerics.cylib.compute_cluster_penalties_cy' extension
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include -I/home/samuel/.virtualenvs/py38/include -I/usr/include/python3.8 -I/home/samuel/.virtualenvs/py38/include -I/usr/include/python3.8 -c klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c -o build/temp.linux-x86_64-3.8/klustakwik2/numerics/cylib/compute_cluster_penalties_cy.o
In file included from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:265:
/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘PyInit_compute_cluster_penalties_cy’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18762:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18762 | __pyx_type___pyx_array.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18765:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18765 | __pyx_type___pyx_MemviewEnum.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18776:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18776 | __pyx_type___pyx_memoryview.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18785:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18785 | __pyx_type___pyx_memoryviewslice.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionSave’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19186:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19186 | *type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19187:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19187 | *value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19188:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19188 | *tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionReset’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19200:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19200 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19201:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19201 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19202:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19202 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19203:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19203 | tstate->exc_type = type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19204:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19204 | tstate->exc_value = value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19205:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19205 | tstate->exc_traceback = tb;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_GetException’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19248:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19248 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19249:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19249 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19250:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19250 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19251:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19251 | tstate->exc_type = local_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19252:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19252 | tstate->exc_value = local_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19253:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19253 | tstate->exc_traceback = local_tb;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionSwap’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20713:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
20713 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20714:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
20714 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20715:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
20715 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20716:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
20716 | tstate->exc_type = *type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20717:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
20717 | tstate->exc_value = *value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20718:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
20718 | tstate->exc_traceback = *tb;
| ^~~~~~~~~~~~~
| curexc_traceback
In file included from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:21,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:265:
At top level:
/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
1463 | _import_array(void)
| ^~~~~~~~~~~~~
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for klustakwik2
Running setup.py clean for klustakwik2
Failed to build klustakwik2
Installing collected packages: klusta, klustakwik2
Running setup.py install for klustakwik2 ... error
ERROR: Command errored out with exit status 1:
command: /home/samuel/.virtualenvs/py38/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-0ied5eru/klustakwik2/setup.py'"'"'; __file__='"'"'/tmp/pip-install-0ied5eru/klustakwik2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-m0hrs9fv/install-record.txt --single-version-externally-managed --compile --install-headers /home/samuel/.virtualenvs/py38/include/site/python3.8/klustakwik2
cwd: /tmp/pip-install-0ied5eru/klustakwik2/
Complete output (384 lines):
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/clustering.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/monitoring.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/data.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/logger.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/input_output.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/mask_starts.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/precomputations.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/linear_algebra.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/default_parameters.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/debugtools.py -> build/lib.linux-x86_64-3.8/klustakwik2
copying klustakwik2/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2
creating build/lib.linux-x86_64-3.8/klustakwik2/numerics
copying klustakwik2/numerics/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics
creating build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/e_step.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/compute_cluster_masks.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/m_step.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/compute_cluster_penalties.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/masks.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
creating build/lib.linux-x86_64-3.8/klustakwik2/numerics/numbalib
copying klustakwik2/numerics/numbalib/m_step.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/numbalib
copying klustakwik2/numerics/numbalib/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/numbalib
creating build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_io.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_compute_cluster_masks.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_partitioning.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_synthetic_data.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_compute_covariance_matrix.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_linear_algebra.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/test_mask_starts.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
copying klustakwik2/tests/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2/tests
creating build/lib.linux-x86_64-3.8/klustakwik2/scripts
copying klustakwik2/scripts/kk2_legacy.py -> build/lib.linux-x86_64-3.8/klustakwik2/scripts
copying klustakwik2/scripts/tools.py -> build/lib.linux-x86_64-3.8/klustakwik2/scripts
copying klustakwik2/scripts/__init__.py -> build/lib.linux-x86_64-3.8/klustakwik2/scripts
running egg_info
writing klustakwik2.egg-info/PKG-INFO
writing dependency_links to klustakwik2.egg-info/dependency_links.txt
writing entry points to klustakwik2.egg-info/entry_points.txt
writing top-level names to klustakwik2.egg-info/top_level.txt
reading manifest file 'klustakwik2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.pyxbld' under directory 'klustakwik2/numerics/cylib'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
writing manifest file 'klustakwik2.egg-info/SOURCES.txt'
copying klustakwik2/numerics/cylib/compute_cluster_masks_cy.c -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/compute_cluster_masks_cy.pyx -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/compute_cluster_penalties_cy.pyx -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/e_step_cy.cpp -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/e_step_cy.pyx -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/m_step_cy.c -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/m_step_cy.pyx -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/masks_cy.cpp -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
copying klustakwik2/numerics/cylib/masks_cy.pyx -> build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib
running build_ext
building 'klustakwik2.numerics.cylib.compute_cluster_masks_cy' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/klustakwik2
creating build/temp.linux-x86_64-3.8/klustakwik2/numerics
creating build/temp.linux-x86_64-3.8/klustakwik2/numerics/cylib
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include -I/home/samuel/.virtualenvs/py38/include -I/usr/include/python3.8 -c klustakwik2/numerics/cylib/compute_cluster_masks_cy.c -o build/temp.linux-x86_64-3.8/klustakwik2/numerics/cylib/compute_cluster_masks_cy.o
In file included from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from klustakwik2/numerics/cylib/compute_cluster_masks_cy.c:623:
/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/klustakwik2/numerics/cylib/compute_cluster_masks_cy.o -o build/lib.linux-x86_64-3.8/klustakwik2/numerics/cylib/compute_cluster_masks_cy.cpython-38-x86_64-linux-gnu.so
building 'klustakwik2.numerics.cylib.compute_cluster_penalties_cy' extension
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include -I/home/samuel/.virtualenvs/py38/include -I/usr/include/python3.8 -c klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c -o build/temp.linux-x86_64-3.8/klustakwik2/numerics/cylib/compute_cluster_penalties_cy.o
In file included from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:265:
/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘PyInit_compute_cluster_penalties_cy’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18762:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18762 | __pyx_type___pyx_array.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18765:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18765 | __pyx_type___pyx_MemviewEnum.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18776:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18776 | __pyx_type___pyx_memoryview.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18785:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18785 | __pyx_type___pyx_memoryviewslice.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionSave’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19186:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19186 | *type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19187:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19187 | *value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19188:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19188 | *tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionReset’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19200:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19200 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19201:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19201 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19202:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19202 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19203:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19203 | tstate->exc_type = type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19204:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19204 | tstate->exc_value = value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19205:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19205 | tstate->exc_traceback = tb;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_GetException’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19248:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19248 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19249:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19249 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19250:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19250 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19251:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19251 | tstate->exc_type = local_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19252:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19252 | tstate->exc_value = local_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19253:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19253 | tstate->exc_traceback = local_tb;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionSwap’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20713:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
20713 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20714:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
20714 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20715:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
20715 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20716:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
20716 | tstate->exc_type = *type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20717:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
20717 | tstate->exc_value = *value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20718:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
20718 | tstate->exc_traceback = *tb;
| ^~~~~~~~~~~~~
| curexc_traceback
In file included from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:21,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:265:
At top level:
/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
1463 | _import_array(void)
| ^~~~~~~~~~~~~
running install
running build
running build_py
running egg_info
writing klustakwik2.egg-info/PKG-INFO
writing dependency_links to klustakwik2.egg-info/dependency_links.txt
writing entry points to klustakwik2.egg-info/entry_points.txt
writing top-level names to klustakwik2.egg-info/top_level.txt
reading manifest file 'klustakwik2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.pyxbld' under directory 'klustakwik2/numerics/cylib'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
writing manifest file 'klustakwik2.egg-info/SOURCES.txt'
running build_ext
building 'klustakwik2.numerics.cylib.compute_cluster_penalties_cy' extension
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include -I/home/samuel/.virtualenvs/py38/include -I/usr/include/python3.8 -I/home/samuel/.virtualenvs/py38/include -I/usr/include/python3.8 -c klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c -o build/temp.linux-x86_64-3.8/klustakwik2/numerics/cylib/compute_cluster_penalties_cy.o
In file included from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:265:
/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘PyInit_compute_cluster_penalties_cy’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18762:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18762 | __pyx_type___pyx_array.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18765:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18765 | __pyx_type___pyx_MemviewEnum.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18776:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18776 | __pyx_type___pyx_memoryview.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:18785:3: warning: ‘tp_print’ is deprecated [-Wdeprecated-declarations]
18785 | __pyx_type___pyx_memoryviewslice.tp_print = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/python3.8/object.h:746,
from /usr/include/python3.8/pytime.h:6,
from /usr/include/python3.8/Python.h:85,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:24:
/usr/include/python3.8/cpython/object.h:260:30: note: declared here
260 | Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
| ^~~~~~~~
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionSave’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19186:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19186 | *type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19187:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19187 | *value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19188:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19188 | *tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionReset’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19200:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19200 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19201:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19201 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19202:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19202 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19203:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19203 | tstate->exc_type = type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19204:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19204 | tstate->exc_value = value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19205:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19205 | tstate->exc_traceback = tb;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_GetException’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19248:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19248 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19249:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19249 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19250:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19250 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19251:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
19251 | tstate->exc_type = local_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19252:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
19252 | tstate->exc_value = local_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:19253:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
19253 | tstate->exc_traceback = local_tb;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c: In function ‘__Pyx_ExceptionSwap’:
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20713:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
20713 | tmp_type = tstate->exc_type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20714:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
20714 | tmp_value = tstate->exc_value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20715:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
20715 | tmp_tb = tstate->exc_traceback;
| ^~~~~~~~~~~~~
| curexc_traceback
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20716:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
20716 | tstate->exc_type = *type;
| ^~~~~~~~
| curexc_type
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20717:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
20717 | tstate->exc_value = *value;
| ^~~~~~~~~
| curexc_value
klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:20718:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
20718 | tstate->exc_traceback = *tb;
| ^~~~~~~~~~~~~
| curexc_traceback
In file included from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:21,
from /home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from klustakwik2/numerics/cylib/compute_cluster_penalties_cy.c:265:
At top level:
/home/samuel/.virtualenvs/py38/lib/python3.8/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
1463 | _import_array(void)
| ^~~~~~~~~~~~~
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/samuel/.virtualenvs/py38/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-0ied5eru/klustakwik2/setup.py'"'"'; __file__='"'"'/tmp/pip-install-0ied5eru/klustakwik2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-m0hrs9fv/install-record.txt --single-version-externally-managed --compile --install-headers /home/samuel/.virtualenvs/py38/include/site/python3.8/klustakwik2 Check the logs for full command output.
samuelgarcia
commented
3 years ago