Comments (4)
gmacon
commented on May 21, 2024
This looks like an incompatibility with Python 3.11. #71 says that it fixes the issue.
from giotto-ph.
poke1024
commented on May 21, 2024
I'm still seeing this issue today with Python 3.11, building from head of git. Looks like giotto-ph/gph/ext/pybind11 is still old.
-- Build files have been written to: /home/liebl/prj/giotto/giotto-ph/build/temp.linux-x86_64-cpython-311
[ 3%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/ConcurrentMap_Grampa.cpp.o
[ 6%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/Core.cpp.o
[ 9%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/Heap.cpp.o
[ 12%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/UTCTime.cpp.o
[ 16%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/extra/Options.cpp.o
[ 19%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/ConcurrentMap_Leapfrog.cpp.o
[ 22%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/ConcurrentMap_Linear.cpp.o
[ 25%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/extra/Random.cpp.o
[ 29%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/QSBR.cpp.o
[ 32%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/extra/TimeWaster.cpp.o
[ 35%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Affinity_FreeBSD.cpp.o
[ 38%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Affinity_Linux.cpp.o
[ 41%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/details/Grampa.cpp.o
[ 45%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Affinity_Win32.cpp.o
[ 48%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Heap_DL.cpp.o
[ 51%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/details/Leapfrog.cpp.o
[ 54%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Trace_Counters.cpp.o
[ 58%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Trace_MemLog.cpp.o
[ 61%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/details/Linear.cpp.o
[ 64%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Trace_Null.cpp.o
[ 67%] Linking CXX static library libturf.a
[ 67%] Built target turf
[ 70%] Building CXX object CMakeFiles/gph_collapser.dir/gph/bindings/collapser_bindings.cpp.o
[ 74%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/extra/MemHook_NBDS.cpp.o
[ 77%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/extra/MemHook_TBB.cpp.o
[ 80%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/striped/ConditionBank.cpp.o
[ 83%] Linking CXX static library libjunction.a
[ 83%] Built target junction
[ 87%] Building CXX object CMakeFiles/gph_ripser.dir/gph/bindings/ripser_bindings.cpp.o
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h: In function ‘std::string pybind11::detail::error_string()’:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:446:36: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
446 | " " + handle(frame->f_code->co_filename).cast<std::string>() +
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:446:75: error: expected primary-expression before ‘>’ token
446 | " " + handle(frame->f_code->co_filename).cast<std::string>() +
| ^
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:446:77: error: expected primary-expression before ‘)’ token
446 | " " + handle(frame->f_code->co_filename).cast<std::string>() +
| ^
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:448:29: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
448 | handle(frame->f_code->co_name).cast<std::string>() + "\n";
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:448:64: error: expected primary-expression before ‘>’ token
448 | handle(frame->f_code->co_name).cast<std::string>() + "\n";
| ^
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:448:66: error: expected primary-expression before ‘)’ token
448 | handle(frame->f_code->co_name).cast<std::string>() + "\n";
| ^
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:449:26: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
449 | frame = frame->f_back;
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h: In function ‘pybind11::function pybind11::detail::get_type_override(const void*, const pybind11::detail::type_info*, const char*)’:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2291:49: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’; did you mean ‘cframe’?
2291 | PyFrameObject *frame = PyThreadState_Get()->frame;
| ^~~~~
| cframe
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2292:41: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
2292 | if (frame && (std::string) str(frame->f_code->co_name) == name &&
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2293:14: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
2293 | frame->f_code->co_argcount > 0) {
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:18: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
2296 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:38,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:30: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
2296 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
| ^~~~~~~~~~~~~~~~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
/home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp: In lambda function:
/home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:74:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
74 | for (size_t k = 0; k < size; ++k)
| ~~^~~~~~
/home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp: In lambda function:
/home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:96:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘pybind11::ssize_t’ {aka ‘long int’} [-Wsign-compare]
96 | for (size_t i = 0; i < dm.shape(0); i++)
| ~~^~~~~~~~~~~~~
/home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:97:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘pybind11::ssize_t’ {aka ‘long int’} [-Wsign-compare]
97 | for (size_t j = 0; j < dm.shape(1); j++)
| ~~^~~~~~~~~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:6:
/home/liebl/prj/giotto/giotto-ph/gph/src/Flag_complex_edge_collapser.h: In instantiation of ‘Gudhi::collapse::Flag_complex_edge_collapser<int, float>::edge_is_dominated(int, int, Gudhi::collapse::Flag_complex_edge_collapser<int, float>::edge_idx_t)::<lambda(auto:8&)> [with auto:8 = const int]’:
/home/liebl/prj/giotto/giotto-ph/gph/src/Flag_complex_edge_collapser.h:220:25: required from ‘void Gudhi::collapse::Flag_complex_edge_collapser<vertex_t, filt_t>::custom_intersection(vertex_t, vertex_t, Gudhi::collapse::Flag_complex_edge_collapser<vertex_t, filt_t>::edge_idx_t, const Func&) [with Func = Gudhi::collapse::Flag_complex_edge_collapser<int, float>::edge_is_dominated(int, int, Gudhi::collapse::Flag_complex_edge_collapser<int, float>::edge_idx_t)::<lambda(auto:8&)>; vertex_t = int; filt_t = float; Gudhi::collapse::Flag_complex_edge_collapser<vertex_t, filt_t>::edge_idx_t = int]’
/home/liebl/prj/giotto/giotto-ph/gph/src/Flag_complex_edge_collapser.h:278:28: required from ‘const bool Gudhi::collapse::Flag_complex_edge_collapser<vertex_t, filt_t>::edge_is_dominated(vertex_t, vertex_t, Gudhi::collapse::Flag_complex_edge_collapser<vertex_t, filt_t>::edge_idx_t) [with vertex_t = int; filt_t = float; Gudhi::collapse::Flag_complex_edge_collapser<vertex_t, filt_t>::edge_idx_t = int]’
/home/liebl/prj/giotto/giotto-ph/gph/src/Flag_complex_edge_collapser.h:489:18: required from ‘void Gudhi::collapse::Flag_complex_edge_collapser<vertex_t, filt_t>::process_edges(FilteredEdgeOutput) [with FilteredEdgeOutput = Gudhi::collapse::flag_complex_collapse_edges<std::vector<std::tuple<int, int, float> > >(const std::vector<std::tuple<int, int, float> >&)::<lambda(vertex_t, vertex_t, filt_t)>; vertex_t = int; filt_t = float]’
/home/liebl/prj/giotto/giotto-ph/gph/src/Flag_complex_edge_collapser.h:534:37: required from ‘auto Gudhi::collapse::flag_complex_collapse_edges(const FilteredEdgeRange&) [with FilteredEdgeRange = std::vector<std::tuple<int, int, float> >]’
/home/liebl/prj/giotto/giotto-ph/gph/bindings/collapser_bindings.cpp:81:72: required from here
/home/liebl/prj/giotto/giotto-ph/gph/src/Flag_complex_edge_collapser.h:288:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
288 | idx_ongoing < intersection_vec.size()) {
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h: In function ‘std::string pybind11::detail::error_string()’:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:446:36: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
446 | " " + handle(frame->f_code->co_filename).cast<std::string>() +
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:446:75: error: expected primary-expression before ‘>’ token
446 | " " + handle(frame->f_code->co_filename).cast<std::string>() +
| ^
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:446:77: error: expected primary-expression before ‘)’ token
446 | " " + handle(frame->f_code->co_filename).cast<std::string>() +
| ^
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:448:29: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
448 | handle(frame->f_code->co_name).cast<std::string>() + "\n";
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:448:64: error: expected primary-expression before ‘>’ token
448 | handle(frame->f_code->co_name).cast<std::string>() + "\n";
| ^
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:448:66: error: expected primary-expression before ‘)’ token
448 | handle(frame->f_code->co_name).cast<std::string>() + "\n";
| ^
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:449:26: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
449 | frame = frame->f_back;
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h: In function ‘pybind11::function pybind11::detail::get_type_override(const void*, const pybind11::detail::type_info*, const char*)’:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2291:49: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’; did you mean ‘cframe’?
2291 | PyFrameObject *frame = PyThreadState_Get()->frame;
| ^~~~~
| cframe
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2292:41: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
2292 | if (frame && (std::string) str(frame->f_code->co_name) == name &&
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2293:14: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
2293 | frame->f_code->co_argcount > 0) {
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:18: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
2296 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
| ^~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:38,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:30: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’}
2296 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
| ^~~~~~~~~~~~~~~~
In file included from /home/liebl/anaconda3/envs/jupyterlab/include/python3.11/Python.h:42,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/detail/common.h:124,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pytypes.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45,
from /home/liebl/prj/giotto/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12,
from /home/liebl/prj/giotto/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
/home/liebl/anaconda3/envs/jupyterlab/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
gmake[2]: *** [CMakeFiles/gph_collapser.dir/build.make:76: CMakeFiles/gph_collapser.dir/gph/bindings/collapser_bindings.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:193: CMakeFiles/gph_collapser.dir/all] Error 2
gmake[1]: *** Waiting for unfinished jobs....
gmake[2]: *** [CMakeFiles/gph_ripser.dir/build.make:76: CMakeFiles/gph_ripser.dir/gph/bindings/ripser_bindings.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:140: CMakeFiles/gph_ripser.dir/all] Error 2
gmake: *** [Makefile:91: all] Error 2
from giotto-ph.
ulupo
commented on May 21, 2024
Hi! Perhaps this is related to giotto-ai/giotto-tda#689? Maybe a similar fix can be made here? @rballeba what do you think?
from giotto-ph.
rballeba
commented on May 21, 2024
Yes! I updated the giotto-tda version for this reason. I have also created a pull request for giotto-ph. I'm going to tag you there.
from giotto-ph.
Related Issues (20)
- Garbage collection step in python interface is too runtime-costly
- Computation of enclosing radius is too slow
- proof of correctness of your check for the busy loop HOT 5
- Consistency in index dtypes HOT 1
- [BUG] Dead comment in compute_dim_0_pairs/incorrect removal of edges with zero filtration value HOT 4
- Allow computation of barcodes for graphs (no 2-simplices)
- Improve docstrings
- Always treat bars with infinite death as essential bars HOT 4
- maxdim=0 HOT 2
- [CI] Produce wheels for Python 3.10 and Apple Silicon HOT 2
- [CPP] Variable names in binomial_coeff_table
- Incorrect handling of zeros for dense input when a threshold is passed HOT 1
- Extend dense backend to cover case of non-zero diagonal weights HOT 1
- [DOC] Dimension 0 is computed sequentially
- Investigate flaky multithreading tests HOT 2
- Unify LONG_DESCRIPTION in setup.py and use delvewheel to repair Windows wheels
- Generators of persistence diagrams do not correspond to longest edge in hole
- OverflowError
- "undefined symbol __atomic_compare_exchange" when compiled with clang. requires to be linked against "atomic"
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from giotto-ph.