I have been trying to build giotto-ph from source following the developer guidelines at https://giotto-ai.github.io/giotto-ph/build/html/installation.html#developer-installation. My system is MacOS 13.4 with Intel i9 processor, and I am running this in a new Conda environment, I get the following error when I run python -m pip install -e ".[dev]"
. Any clues as to what is going on? Thanks.
Downloading ipykernel-6.25.0-py3-none-any.whl (153 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 153.9/153.9 kB 6.1 MB/s eta 0:00:00
Downloading prometheus_client-0.17.1-py3-none-any.whl (60 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 kB 2.1 MB/s eta 0:00:00
Downloading websocket_client-1.6.1-py3-none-any.whl (56 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.9/56.9 kB 2.0 MB/s eta 0:00:00
Downloading comm-0.1.4-py3-none-any.whl (6.6 kB)
Downloading ipython-8.14.0-py3-none-any.whl (798 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 798.7/798.7 kB 18.9 MB/s eta 0:00:00
Downloading nest_asyncio-1.5.7-py3-none-any.whl (5.3 kB)
Downloading jedi-0.19.0-py2.py3-none-any.whl (1.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 28.0 MB/s eta 0:00:00
Downloading jsonpointer-2.4-py2.py3-none-any.whl (7.8 kB)
Downloading prompt_toolkit-3.0.39-py3-none-any.whl (385 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 385.2/385.2 kB 11.7 MB/s eta 0:00:00
Downloading uri_template-1.3.0-py3-none-any.whl (11 kB)
Building wheels for collected packages: jupyter_contrib_nbextensions, jupyter_contrib_core
Building wheel for jupyter_contrib_nbextensions (setup.py) ... done
Created wheel for jupyter_contrib_nbextensions: filename=jupyter_contrib_nbextensions-0.7.0-py2.py3-none-any.whl size=23428780 sha256=50bf0f06f71a5c34c1c15e9a5205f6c57e1dd78140c49203ef58db2351a18a55
Stored in directory: /Users/longyuxi/Library/Caches/pip/wheels/cd/25/fe/cb6f3e82f5b1921b0157ac9e32adb2e54806ec1befc446be21
Building wheel for jupyter_contrib_core (setup.py) ... done
Created wheel for jupyter_contrib_core: filename=jupyter_contrib_core-0.4.2-py2.py3-none-any.whl size=17482 sha256=854fe4234b006d28702b177286248bdaf08eddbc5e39294171e27f9d2622e522
Stored in directory: /Users/longyuxi/Library/Caches/pip/wheels/37/c3/18/be7a983c1120f15dc0c2d1cb9c33749871a93b034185e00ced
Successfully built jupyter_contrib_nbextensions jupyter_contrib_core
Installing collected packages: webencodings, wcwidth, sortedcontainers, snowballstemmer, py-cpuinfo, pure-eval, ptyprocess, pickleshare, jupyter_highlight_selected_word, json5, ipython_genutils, fastjsonschema, executing, backcall, appnope, websocket-client, webcolors, urllib3, uri-template, traitlets, tornado, tinycss2, threadpoolctl, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, pyzmq, pyyaml, python-json-logger, pygments, pyflakes, pycparser, pycodestyle, psutil, prompt-toolkit, prometheus-client, pluggy, platformdirs, pexpect, parso, pandocfilters, packaging, overrides, numpy, nest-asyncio, mistune, mccabe, markupsafe, lxml, jupyterlab-pygments, jsonpointer, joblib, iniconfig, imagesize, idna, fqdn, docutils, defusedxml, decorator, debugpy, coverage, charset-normalizer, certifi, babel, attrs, async-lru, alabaster, terminado, scipy, rfc3339-validator, requests, referencing, python-dateutil, pytest, matplotlib-inline, jupyter_core, jinja2, jedi, hypothesis, flake8, comm, cffi, bleach, beautifulsoup4, asttokens, anyio, stack-data, sphinx, scikit-learn, pytest-nunit, pytest-cov, pytest-benchmark, jupyter-server-terminals, jupyter-client, jsonschema-specifications, arrow, argon2-cffi-bindings, sphinxcontrib-jquery, sphinx-issues, pytest-azurepipelines, numpydoc, jsonschema, isoduration, ipython, giotto-ph, argon2-cffi, sphinx_rtd_theme, nbformat, ipykernel, nbclient, jupyter-events, nbconvert, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, notebook, jupyter_contrib_core, jupyter_nbextensions_configurator, jupyter_contrib_nbextensions
Running setup.py develop for giotto-ph
error: subprocess-exited-with-error
× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [363 lines of output]
/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/dist.py:745: SetuptoolsDeprecationWarning: Invalid dash-separated options
!!
********************************************************************************
Usage of dash-separated 'description-file' will not be supported in future
versions. Please use the underscore name 'description_file' instead.
By 2023-Sep-26, you need to update your project and remove deprecated calls
or your builds will no longer be supported.
See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
********************************************************************************
!!
opt = self.warn_dash_deprecation(opt, section)
running develop
/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/command/develop.py:40: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` and ``easy_install``.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://github.com/pypa/setuptools/issues/917 for details.
********************************************************************************
!!
easy_install.initialize_options(self)
/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
running egg_info
creating giotto_ph.egg-info
writing giotto_ph.egg-info/PKG-INFO
writing dependency_links to giotto_ph.egg-info/dependency_links.txt
writing requirements to giotto_ph.egg-info/requires.txt
writing top-level names to giotto_ph.egg-info/top_level.txt
writing manifest file 'giotto_ph.egg-info/SOURCES.txt'
reading manifest file 'giotto_ph.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'giotto_ph.egg-info/SOURCES.txt'
running build_ext
Submodule 'giotto_ph/ext/junction' (https://github.com/preshing/junction) registered for path 'gph/ext/junction'
Submodule 'src/pybind11' (https://github.com/pybind/pybind11) registered for path 'gph/ext/pybind11'
Submodule 'giotto_ph/ext/turf' (https://github.com/preshing/turf) registered for path 'gph/ext/turf'
Cloning into '/Users/longyuxi/Downloads/giotto-ph/gph/ext/junction'...
Cloning into '/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11'...
Cloning into '/Users/longyuxi/Downloads/giotto-ph/gph/ext/turf'...
Submodule path 'gph/ext/junction': checked out '5ad3be7ce1d3f16b9f7ed6065bbfeacd2d629a08'
Submodule path 'gph/ext/pybind11': checked out '48534089f7f1b0229bc7ae2e4d0f21dc9ad169b5'
Submodule path 'gph/ext/turf': checked out '9ae0d4b984fa95ed5f823274b39c87ee742f6650'
-- The CXX compiler identification is AppleClang 14.0.3.14030022
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at gph/ext/pybind11/CMakeLists.txt:8 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- pybind11 v2.6.2 dev1
CMake Warning (dev) at gph/ext/pybind11/tools/FindPythonLibsNew.cmake:96 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed. Run "cmake --help-policy CMP0148" for policy details. Use
the cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
gph/ext/pybind11/tools/pybind11Tools.cmake:38 (find_package)
gph/ext/pybind11/tools/pybind11Common.cmake:201 (include)
gph/ext/pybind11/CMakeLists.txt:169 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found PythonInterp: /Users/longyuxi/mambaforge/envs/gph-dev/bin/python (found version "3.11.4")
-- Found PythonLibs: /Users/longyuxi/mambaforge/envs/gph-dev/lib/libpython3.11.dylib
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Performing Test HAS_FLTO_THIN
-- Performing Test HAS_FLTO_THIN - Success
CMake Deprecation Warning at gph/ext/junction/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
CMake Deprecation Warning at gph/ext/turf/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
Checking for <stdint.h> -- yes
Checking for noexcept keyword -- no
Checking for constexpr keyword -- no
Checking for override keyword -- yes
Checking for long long -- yes
Checking for static_assert -- no
Checking for std::move -- yes
-- Configuring done (7.6s)
-- Generating done (0.1s)
-- Build files have been written to: /Users/longyuxi/Downloads/giotto-ph/build/temp.macosx-10.9-x86_64-cpython-311
[ 6%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/Core.cpp.o
[ 6%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/ConcurrentMap_Grampa.cpp.o
[ 9%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/Heap.cpp.o
/Users/longyuxi/Downloads/giotto-ph/gph/ext/turf/turf/Heap.cpp:32:6: warning: function previously declared with an explicit exception specification redeclared with an implicit exception specification [-Wimplicit-exception-spec-mismatch]
void operator delete(void* ptr) TURF_NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/new:193:36: note: previous declaration is here
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete(void* __p) _NOEXCEPT;
^
/Users/longyuxi/Downloads/giotto-ph/gph/ext/turf/turf/Heap.cpp:36:6: warning: function previously declared with an explicit exception specification redeclared with an implicit exception specification [-Wimplicit-exception-spec-mismatch]
void operator delete[](void* ptr) TURF_NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/new:201:36: note: previous declaration is here
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete[](void* __p) _NOEXCEPT;
^
2 warnings generated.
[ 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/turf/CMakeFiles/turf.dir/turf/extra/Random.cpp.o
[ 25%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/ConcurrentMap_Linear.cpp.o
[ 29%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/extra/TimeWaster.cpp.o
[ 32%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Affinity_FreeBSD.cpp.o
[ 35%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/QSBR.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/turf/CMakeFiles/turf.dir/turf/impl/Affinity_Win32.cpp.o
[ 45%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Heap_DL.cpp.o
[ 48%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Trace_Counters.cpp.o
[ 51%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/details/Grampa.cpp.o
[ 54%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Trace_MemLog.cpp.o
[ 58%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/details/Leapfrog.cpp.o
[ 61%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Trace_Null.cpp.o
[ 64%] Linking CXX static library libturf.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Core.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_FreeBSD.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_Linux.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_Win32.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Heap_DL.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Core.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_FreeBSD.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_Linux.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_Win32.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Heap_DL.cpp.o) has no symbols
[ 67%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/details/Linear.cpp.o
[ 67%] Built target turf
[ 70%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/extra/MemHook_NBDS.cpp.o
[ 74%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/extra/MemHook_TBB.cpp.o
[ 77%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/striped/ConditionBank.cpp.o
[ 80%] Building CXX object CMakeFiles/gph_collapser.dir/gph/bindings/collapser_bindings.cpp.o
clang: warning: argument unused during compilation: '-shared' [-Wunused-command-line-argument]
[ 83%] Linking CXX static library libjunction.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Grampa.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Leapfrog.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Linear.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Grampa.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Leapfrog.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Linear.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(MemHook_NBDS.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(MemHook_TBB.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Grampa.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Leapfrog.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Linear.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Grampa.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Leapfrog.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Linear.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(MemHook_NBDS.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(MemHook_TBB.cpp.o) has no symbols
[ 83%] Built target junction
[ 87%] Building CXX object CMakeFiles/gph_ripser.dir/gph/bindings/ripser_bindings.cpp.o
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:446:36: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
" " + handle(frame->f_code->co_filename).cast<std::string>() +
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:448:29: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
handle(frame->f_code->co_name).cast<std::string>() + "\n";
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:449:26: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame = frame->f_back;
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2291:49: error: no member named 'frame' in '_ts'
PyFrameObject *frame = PyThreadState_Get()->frame;
~~~~~~~~~~~~~~~~~~~ ^
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2292:41: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
if (frame && (std::string) str(frame->f_code->co_name) == name &&
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2293:14: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_code->co_argcount > 0) {
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:18: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:52: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:446:36: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
" " + handle(frame->f_code->co_filename).cast<std::string>() +
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:448:29: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
handle(frame->f_code->co_name).cast<std::string>() + "\n";
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:449:26: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame = frame->f_back;
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2291:49: error: no member named 'frame' in '_ts'
PyFrameObject *frame = PyThreadState_Get()->frame;
~~~~~~~~~~~~~~~~~~~ ^
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2292:41: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
if (frame && (std::string) str(frame->f_code->co_name) == name &&
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2293:14: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_code->co_argcount > 0) {
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:18: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:52: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
8 errors generated.
make[2]: *** [CMakeFiles/gph_collapser.dir/gph/bindings/collapser_bindings.cpp.o] Error 1
make[1]: *** [CMakeFiles/gph_collapser.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
8 errors generated.
make[2]: *** [CMakeFiles/gph_ripser.dir/gph/bindings/ripser_bindings.cpp.o] Error 1
make[1]: *** [CMakeFiles/gph_ripser.dir/all] Error 2
make: *** [all] Error 2
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/Users/longyuxi/Downloads/giotto-ph/setup.py", line 147, in <module>
setup(name=DISTNAME,
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/__init__.py", line 107, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/command/develop.py", line 34, in run
self.install_for_development()
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/command/develop.py", line 111, in install_for_development
self.run_command('build_ext')
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/Users/longyuxi/Downloads/giotto-ph/setup.py", line 104, in run
self.build_extension(ext)
File "/Users/longyuxi/Downloads/giotto-ph/setup.py", line 143, in build_extension
subprocess.check_call(["cmake", "--build", "."] + build_args,
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [363 lines of output]
/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/dist.py:745: SetuptoolsDeprecationWarning: Invalid dash-separated options
!!
********************************************************************************
Usage of dash-separated 'description-file' will not be supported in future
versions. Please use the underscore name 'description_file' instead.
By 2023-Sep-26, you need to update your project and remove deprecated calls
or your builds will no longer be supported.
See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
********************************************************************************
!!
opt = self.warn_dash_deprecation(opt, section)
running develop
/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/command/develop.py:40: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` and ``easy_install``.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://github.com/pypa/setuptools/issues/917 for details.
********************************************************************************
!!
easy_install.initialize_options(self)
/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
running egg_info
creating giotto_ph.egg-info
writing giotto_ph.egg-info/PKG-INFO
writing dependency_links to giotto_ph.egg-info/dependency_links.txt
writing requirements to giotto_ph.egg-info/requires.txt
writing top-level names to giotto_ph.egg-info/top_level.txt
writing manifest file 'giotto_ph.egg-info/SOURCES.txt'
reading manifest file 'giotto_ph.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'giotto_ph.egg-info/SOURCES.txt'
running build_ext
Submodule 'giotto_ph/ext/junction' (https://github.com/preshing/junction) registered for path 'gph/ext/junction'
Submodule 'src/pybind11' (https://github.com/pybind/pybind11) registered for path 'gph/ext/pybind11'
Submodule 'giotto_ph/ext/turf' (https://github.com/preshing/turf) registered for path 'gph/ext/turf'
Cloning into '/Users/longyuxi/Downloads/giotto-ph/gph/ext/junction'...
Cloning into '/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11'...
Cloning into '/Users/longyuxi/Downloads/giotto-ph/gph/ext/turf'...
Submodule path 'gph/ext/junction': checked out '5ad3be7ce1d3f16b9f7ed6065bbfeacd2d629a08'
Submodule path 'gph/ext/pybind11': checked out '48534089f7f1b0229bc7ae2e4d0f21dc9ad169b5'
Submodule path 'gph/ext/turf': checked out '9ae0d4b984fa95ed5f823274b39c87ee742f6650'
-- The CXX compiler identification is AppleClang 14.0.3.14030022
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at gph/ext/pybind11/CMakeLists.txt:8 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- pybind11 v2.6.2 dev1
CMake Warning (dev) at gph/ext/pybind11/tools/FindPythonLibsNew.cmake:96 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed. Run "cmake --help-policy CMP0148" for policy details. Use
the cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
gph/ext/pybind11/tools/pybind11Tools.cmake:38 (find_package)
gph/ext/pybind11/tools/pybind11Common.cmake:201 (include)
gph/ext/pybind11/CMakeLists.txt:169 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found PythonInterp: /Users/longyuxi/mambaforge/envs/gph-dev/bin/python (found version "3.11.4")
-- Found PythonLibs: /Users/longyuxi/mambaforge/envs/gph-dev/lib/libpython3.11.dylib
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Performing Test HAS_FLTO_THIN
-- Performing Test HAS_FLTO_THIN - Success
CMake Deprecation Warning at gph/ext/junction/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
CMake Deprecation Warning at gph/ext/turf/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
Checking for <stdint.h> -- yes
Checking for noexcept keyword -- no
Checking for constexpr keyword -- no
Checking for override keyword -- yes
Checking for long long -- yes
Checking for static_assert -- no
Checking for std::move -- yes
-- Configuring done (7.6s)
-- Generating done (0.1s)
-- Build files have been written to: /Users/longyuxi/Downloads/giotto-ph/build/temp.macosx-10.9-x86_64-cpython-311
[ 6%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/Core.cpp.o
[ 6%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/ConcurrentMap_Grampa.cpp.o
[ 9%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/Heap.cpp.o
/Users/longyuxi/Downloads/giotto-ph/gph/ext/turf/turf/Heap.cpp:32:6: warning: function previously declared with an explicit exception specification redeclared with an implicit exception specification [-Wimplicit-exception-spec-mismatch]
void operator delete(void* ptr) TURF_NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/new:193:36: note: previous declaration is here
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete(void* __p) _NOEXCEPT;
^
/Users/longyuxi/Downloads/giotto-ph/gph/ext/turf/turf/Heap.cpp:36:6: warning: function previously declared with an explicit exception specification redeclared with an implicit exception specification [-Wimplicit-exception-spec-mismatch]
void operator delete[](void* ptr) TURF_NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/new:201:36: note: previous declaration is here
_LIBCPP_OVERRIDABLE_FUNC_VIS void operator delete[](void* __p) _NOEXCEPT;
^
2 warnings generated.
[ 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/turf/CMakeFiles/turf.dir/turf/extra/Random.cpp.o
[ 25%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/ConcurrentMap_Linear.cpp.o
[ 29%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/extra/TimeWaster.cpp.o
[ 32%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Affinity_FreeBSD.cpp.o
[ 35%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/QSBR.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/turf/CMakeFiles/turf.dir/turf/impl/Affinity_Win32.cpp.o
[ 45%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Heap_DL.cpp.o
[ 48%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Trace_Counters.cpp.o
[ 51%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/details/Grampa.cpp.o
[ 54%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Trace_MemLog.cpp.o
[ 58%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/details/Leapfrog.cpp.o
[ 61%] Building CXX object gph/ext/junction/turf/CMakeFiles/turf.dir/turf/impl/Trace_Null.cpp.o
[ 64%] Linking CXX static library libturf.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Core.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_FreeBSD.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_Linux.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_Win32.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Heap_DL.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Core.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_FreeBSD.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_Linux.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Affinity_Win32.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libturf.a(Heap_DL.cpp.o) has no symbols
[ 67%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/details/Linear.cpp.o
[ 67%] Built target turf
[ 70%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/extra/MemHook_NBDS.cpp.o
[ 74%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/extra/MemHook_TBB.cpp.o
[ 77%] Building CXX object gph/ext/junction/CMakeFiles/junction.dir/junction/striped/ConditionBank.cpp.o
[ 80%] Building CXX object CMakeFiles/gph_collapser.dir/gph/bindings/collapser_bindings.cpp.o
clang: warning: argument unused during compilation: '-shared' [-Wunused-command-line-argument]
[ 83%] Linking CXX static library libjunction.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Grampa.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Leapfrog.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Linear.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Grampa.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Leapfrog.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Linear.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(MemHook_NBDS.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(MemHook_TBB.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Grampa.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Leapfrog.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(ConcurrentMap_Linear.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Grampa.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Leapfrog.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(Linear.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(MemHook_NBDS.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libjunction.a(MemHook_TBB.cpp.o) has no symbols
[ 83%] Built target junction
[ 87%] Building CXX object CMakeFiles/gph_ripser.dir/gph/bindings/ripser_bindings.cpp.o
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:446:36: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
" " + handle(frame->f_code->co_filename).cast<std::string>() +
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:448:29: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
handle(frame->f_code->co_name).cast<std::string>() + "\n";
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:449:26: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame = frame->f_back;
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2291:49: error: no member named 'frame' in '_ts'
PyFrameObject *frame = PyThreadState_Get()->frame;
~~~~~~~~~~~~~~~~~~~ ^
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2292:41: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
if (frame && (std::string) str(frame->f_code->co_name) == name &&
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2293:14: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_code->co_argcount > 0) {
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:18: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/collapser_bindings.cpp:8:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:52: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:446:36: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
" " + handle(frame->f_code->co_filename).cast<std::string>() +
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:448:29: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
handle(frame->f_code->co_name).cast<std::string>() + "\n";
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:45:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/attr.h:13:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/cast.h:449:26: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame = frame->f_back;
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2291:49: error: no member named 'frame' in '_ts'
PyFrameObject *frame = PyThreadState_Get()->frame;
~~~~~~~~~~~~~~~~~~~ ^
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2292:41: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
if (frame && (std::string) str(frame->f_code->co_name) == name &&
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2293:14: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_code->co_argcount > 0) {
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:18: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/bindings/ripser_bindings.cpp:10:
In file included from /Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/numpy.h:12:
/Users/longyuxi/Downloads/giotto-ph/gph/ext/pybind11/include/pybind11/pybind11.h:2296:52: error: member access into incomplete type 'PyFrameObject' (aka '_frame')
frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
^
/Users/longyuxi/mambaforge/envs/gph-dev/include/python3.11/pytypedefs.h:22:16: note: forward declaration of '_frame'
typedef struct _frame PyFrameObject;
^
8 errors generated.
make[2]: *** [CMakeFiles/gph_collapser.dir/gph/bindings/collapser_bindings.cpp.o] Error 1
make[1]: *** [CMakeFiles/gph_collapser.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
8 errors generated.
make[2]: *** [CMakeFiles/gph_ripser.dir/gph/bindings/ripser_bindings.cpp.o] Error 1
make[1]: *** [CMakeFiles/gph_ripser.dir/all] Error 2
make: *** [all] Error 2
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/Users/longyuxi/Downloads/giotto-ph/setup.py", line 147, in <module>
setup(name=DISTNAME,
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/__init__.py", line 107, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/command/develop.py", line 34, in run
self.install_for_development()
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/command/develop.py", line 111, in install_for_development
self.run_command('build_ext')
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/Users/longyuxi/Downloads/giotto-ph/setup.py", line 104, in run
self.build_extension(ext)
File "/Users/longyuxi/Downloads/giotto-ph/setup.py", line 143, in build_extension
subprocess.check_call(["cmake", "--build", "."] + build_args,
File "/Users/longyuxi/mambaforge/envs/gph-dev/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.