mattjones315
commented
3 years ago Hello,
Thank you for posting this issue and I'm sorry that this isn't installing well. I unfortunately have not seen this issue before. Can you please let me know which python version you're using and confirm that Cython is installed with the correct python version?
xliu-uth
Hi Developers,
I failed at install Cassiopeia at "python3 setup.py build". It looks like the arguments for PyCode_New are not in the correct format.
Please see the log below. Do you have any suggestions? Thanks!
running build running build_py running egg_info writing cassiopeia_lineage.egg-info/PKG-INFO writing dependency_links to cassiopeia_lineage.egg-info/dependency_links.txt writing entry points to cassiopeia_lineage.egg-info/entry_points.txt writing requirements to cassiopeia_lineage.egg-info/requires.txt writing top-level names to cassiopeia_lineage.egg-info/top_level.txt reading manifest file 'cassiopeia_lineage.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '' under directory 'cython' writing manifest file 'cassiopeia_lineage.egg-info/SOURCES.txt' running build_ext building 'cassiopeia.TreeSolver.lineage_solver.solver_utils' extension gcc -pthread -B /data/xliu23/binaries/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/data/xliu23/binaries/anaconda3/include/python3.8 -c cassiopeia/TreeSolver/lineage_solver/solver_utils.c -o build/temp.linux-x86_64-3.8/cassiopeia/TreeSolver/lineage_solver/solver_utils.o cassiopeia/TreeSolver/lineage_solver/solver_utils.c: In function ‘Pyx_InitCachedConstants’: cassiopeia/TreeSolver/lineage_solver/solver_utils.c:5934:3: warning: passing argument 6 of ‘PyCode_New’ makes pointer from integer without a cast [enabled by default] pyx_codeobj__11 = (PyObject)Pyx_PyCode_New(2, 0, 6, 0, CO_OPTIMIZED|CO_NEWLOCALS, pyx_empty_bytes, pyx_empty_tuple, pyx_empty_tuple, pyx_tuple10, pyx_empty_tuple, pyx_empty_tuple, pyx_kp_s_cassiopeia_TreeSolver_lineage_so_2, pyx_n_s_node_parent, 6, pyx_empty_bytes); if (unlikely(!pyx_codeobj11)) PYX_ERR(0, 6, pyx_L1_error) ^ In file included from /data/xliu23/binaries/anaconda3/include/python3.8/compile.h:5:0, from /data/xliu23/binaries/anaconda3/include/python3.8/Python.h:138, from cassiopeia/TreeSolver/lineage_solver/solver_utils.c:16: /data/xliu23/binaries/anaconda3/include/python3.8/code.h:122:28: note: expected ‘struct PyObject ’ but argument is of type ‘int’ PyAPI_FUNC(PyCodeObject ) PyCode_New( ^ cassiopeia/TreeSolver/lineage_solver/solver_utils.c:5934:3: warning: passing argument 14 of ‘PyCode_New’ makes integer from pointer without a cast [enabled by default] __pyx_codeobj11 = (PyObject)Pyx_PyCode_New(2, 0, 6, 0, CO_OPTIMIZED|CO_NEWLOCALS, pyx_empty_bytes, pyx_empty_tuple, pyx_empty_tuple, pyx_tuple10, pyx_empty_tuple, pyx_empty_tuple, pyx_kp_s_cassiopeia_TreeSolver_lineage_so_2, pyx_n_s_node_parent, 6, pyx_empty_bytes); if (unlikely(!pyx_codeobj11)) PYX_ERR(0, 6, __pyx_L1_error) ^ In file included from /data/xliu23/binaries/anaconda3/include/python3.8/compile.h:5:0, from /data/xliu23/binaries/anaconda3/include/python3.8/Python.h:138, from cassiopeia/TreeSolver/lineage_solver/solver_utils.c:16: /data/xliu23/binaries/anaconda3/include/python3.8/code.h:122:28: note: expected ‘int’ but argument is of type ‘struct PyObject ’ PyAPI_FUNC(PyCodeObject ) PyCode_New( ^ cassiopeia/TreeSolver/lineage_solver/solver_utils.c:5934:3: warning: passing argument 15 of ‘PyCode_New’ makes pointer from integer without a cast [enabled by default] __pyx_codeobj__11 = (PyObject)Pyx_PyCode_New(2, 0, 6, 0, CO_OPTIMIZED|CO_NEWLOCALS, pyx_empty_bytes, pyx_empty_tuple, pyx_empty_tuple, pyx_tuple10, pyx_empty_tuple, pyx_empty_tuple, pyx_kp_s_cassiopeia_TreeSolver_lineage_so_2, pyx_n_s_node_parent, 6, pyx_empty_bytes); if (unlikely(!pyx_codeobj11)) PYX_ERR(0, 6, pyx_L1_error) ^ In file included from /data/xliu23/binaries/anaconda3/include/python3.8/compile.h:5:0, from /data/xliu23/binaries/anaconda3/include/python3.8/Python.h:138, from cassiopeia/TreeSolver/lineage_solver/solver_utils.c:16: /data/xliu23/binaries/anaconda3/include/python3.8/code.h:122:28: note: expected ‘struct PyObject ’ but argument is of type ‘int’ PyAPI_FUNC(PyCodeObject ) PyCode_New( ^ cassiopeia/TreeSolver/lineage_solver/solver_utils.c:5934:3: error: too many arguments to function ‘PyCode_New’ __pyx_codeobj11 = (PyObject)Pyx_PyCode_New(2, 0, 6, 0, CO_OPTIMIZED|CO_NEWLOCALS, pyx_empty_bytes, pyx_empty_tuple, pyx_empty_tuple, pyx_tuple10, pyx_empty_tuple, pyx_empty_tuple, pyx_kp_s_cassiopeia_TreeSolver_lineage_so_2, pyx_n_s_node_parent, 6, pyx_empty_bytes); if (unlikely(!pyx_codeobj11)) PYX_ERR(0, 6, __pyx_L1_error) ^ In file included from /data/xliu23/binaries/anaconda/include/python3.8/compile.h:5:0, from /data/xliu23/binaries/anaconda3/include/python3.8/Python.h:138, from cassiopeia/TreeSolver/lineage_solver/solver_utils.c:16: /data/xliu23/binaries/anaconda3/include/python3.8/code.h:122:28: note: declared here PyAPI_FUNC(PyCodeObject ) PyCode_New(