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fujiisoup / py3nj

Wigner's 3J, 6J, 9J symbols for python
https://py3nj.readthedocs.io/
Apache License 2.0
18 stars 5 forks source link

Installation error #35

Open Peter010103 opened 9 months ago

Peter010103 commented 9 months ago

Hello,

I am having a bit of trouble trying to install this library.

I am using Python 3.7 on Ubuntu 22. I have previously had success working with py3nj in Ubuntu 20, but I really am not sure what the issue is.

I have installed a fortran compiler and openmp as discussed in other issue posts.

Apologies for the long build log. This is trying pip install py3nj

      The Meson build system
      Version: 1.3.2
      Source dir: /tmp/pip-install-iwhx32mp/py3nj_d541e20a2d7c4a2c8b1a8151d00ad062
      Build dir: /tmp/pip-install-iwhx32mp/py3nj_d541e20a2d7c4a2c8b1a8151d00ad062/.mesonpy-1dhmpk80
      Build type: native build
      Project name: py3nj
      Project version: 0.2.0
      Fortran compiler for the host machine: gfortran (gcc 11.4.0 "GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0")
      Fortran linker for the host machine: gfortran ld.bfd 2.38
      C compiler for the host machine: cc (gcc 11.4.0 "cc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0")
      C linker for the host machine: cc ld.bfd 2.38
      Host machine cpu family: x86_64
      Host machine cpu: x86_64
      Program python found: YES (/usr/bin/python3)
      Run-time dependency OpenMP found: YES 4.5
      Found pkg-config: YES (/usr/bin/pkg-config) 0.29.2
      Run-time dependency python found: YES 3.7
      Build targets in project: 2

      py3nj 0.2.0

        User defined options
          Native files: /tmp/pip-install-iwhx32mp/py3nj_d541e20a2d7c4a2c8b1a8151d00ad062/.mesonpy-1dhmpk80/meson-python-native-file.ini
          buildtype   : release
          b_ndebug    : if-release
          b_vscrt     : md

      Found ninja-1.11.1.git.kitware.jobserver-1 at /tmp/pip-build-env-js67n858/normal/bin/ninja
      + /tmp/pip-build-env-js67n858/normal/bin/ninja
      [1/11] Generating _wignermodule.c with a custom command
      Reading fortran codes...
          Reading file '../fortran/_wigner.pyf' (format:free)
      Post-processing...
          Block: _wigner
                          Block: drc3jj_int
                          Block: drc6j_int
                          Block: drc3jj_vec
                          Block: drc6j_vec
      Post-processing (stage 2)...
      Building modules...
          Building module "_wigner"...
                  Constructing wrapper function "drc3jj_int"...
                    l1min,l1max,thrcof,ier = drc3jj_int(two_l2,two_l3,two_m2,two_m3,ndim)
                  Constructing wrapper function "drc6j_int"...
                    l1min,l1max,sixcof,ier = drc6j_int(two_l2,two_l3,two_l4,two_l5,two_l6,ndim)
                  Constructing wrapper function "drc3jj_vec"...
                    thrcof,ier = drc3jj_vec(two_l2,two_l3,two_m2,two_m3,ndim,[nvec])
                  Constructing wrapper function "drc6j_vec"...
                    sixcof,ier = drc6j_vec(two_l2,two_l3,two_l4,two_l5,two_l6,ndim,[nvec])
          Wrote C/API module "_wigner" to file "./_wignermodule.c"
      [2/11] Compiling C object _wigner.cpython-37m-x86_64-linux-gnu.so.p/6828d8b2494646bca5b8d59c2e3422f9c8f4cbea_site-packages_numpy_f2py_src_fortranobject.c.o
      In file included from /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
                       from /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                       from /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                       from /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/f2py/src/fortranobject.h:13,
                       from /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/f2py/src/fortranobject.c:2:
      /tmp/pip-build-env-js67n858/overlay/lib/python3.7/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 " \
            |  ^~~~~~~
      /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/f2py/src/fortranobject.c: In function ‘fortran_call’:
      /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/f2py/src/fortranobject.c:466:23: warning: cast between incompatible function types from ‘f2py_init_func’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} to ‘PyObject * (*)(PyObject *, PyObject *, PyObject *, void *)’ {aka ‘struct _object * (*)(struct _object *, struct _object *, struct _object *, void *)’} [-Wcast-function-type]
        466 |             return (*((fortranfunc)(fp->defs[i].func)))((PyObject *)fp,arg,kw,NULL);
            |                       ^
      /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/f2py/src/fortranobject.c:468:23: warning: cast between incompatible function types from ‘f2py_init_func’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} to ‘PyObject * (*)(PyObject *, PyObject *, PyObject *, void *)’ {aka ‘struct _object * (*)(struct _object *, struct _object *, struct _object *, void *)’} [-Wcast-function-type]
        468 |             return (*((fortranfunc)(fp->defs[i].func)))((PyObject *)fp,arg,kw,
            |                       ^
      [3/11] Module scanner.
      FAILED: _wigner.cpython-37m-x86_64-linux-gnu.so.p/depscan.dd
      /tmp/pip-build-env-js67n858/overlay/bin/meson --internal depscan _wigner.cpython-37m-x86_64-linux-gnu.so.p/_wigner.cpython-37m-x86_64-linux-gnu.dat _wigner.cpython-37m-x86_64-linux-gnu.so.p/depscan.dd /tmp/pip-install-iwhx32mp/py3nj_d541e20a2d7c4a2c8b1a8151d00ad062/.mesonpy-1dhmpk80/_wigner.cpython-37m-x86_64-linux-gnu.so.p/_wigner.cpython-37m-x86_64-linux-gnu-deps.json
      Traceback (most recent call last):
        File "/tmp/pip-build-env-js67n858/overlay/bin/meson", line 8, in <module>
          sys.exit(main())
        File "/tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/mesonbuild/mesonmain.py", line 294, in main
          return run(sys.argv[1:], launcher)
        File "/tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/mesonbuild/mesonmain.py", line 282, in run
          return run_script_command(args[1], args[2:])
        File "/tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/mesonbuild/mesonmain.py", line 223, in run_script_command
          return module.run(script_args)
        File "/tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/mesonbuild/scripts/depscan.py", line 208, in run
          return scanner.scan()
        File "/tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/mesonbuild/scripts/depscan.py", line 158, in scan
          self.scan_file(s)
        File "/tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/mesonbuild/scripts/depscan.py", line 58, in scan_file
          self.scan_fortran_file(fname)
        File "/tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/mesonbuild/scripts/depscan.py", line 67, in scan_fortran_file
          for line in fpath.read_text(encoding='utf-8', errors='ignore').split('\n'):
        File "/usr/lib/python3.7/pathlib.py", line 1221, in read_text
          with self.open(mode='r', encoding=encoding, errors=errors) as f:
        File "/usr/lib/python3.7/pathlib.py", line 1208, in open
          opener=self._opener)
        File "/usr/lib/python3.7/pathlib.py", line 1063, in _opener
          return self._accessor.open(self, flags, mode)
      FileNotFoundError: [Errno 2] No such file or directory: '_wigner-f2pywrappers.f'
      [4/11] Compiling C object _wigner.cpython-37m-x86_64-linux-gnu.so.p/meson-generated_..__wignermodule.c.o
      In file included from /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
                       from /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                       from /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                       from /tmp/pip-build-env-js67n858/overlay/lib/python3.7/site-packages/numpy/f2py/src/fortranobject.h:13,
                       from _wignermodule.c:16:
      /tmp/pip-build-env-js67n858/overlay/lib/python3.7/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 " \
            |  ^~~~~~~
      _wignermodule.c: In function ‘f2py_rout__wigner_drc3jj_int’:
      _wignermodule.c:217:63: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
        217 | static PyObject *f2py_rout__wigner_drc3jj_int(const PyObject *capi_self,
            |                                               ~~~~~~~~~~~~~~~~^~~~~~~~~
      _wignermodule.c: In function ‘f2py_rout__wigner_drc6j_int’:
      _wignermodule.c:351:62: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
        351 | static PyObject *f2py_rout__wigner_drc6j_int(const PyObject *capi_self,
            |                                              ~~~~~~~~~~~~~~~~^~~~~~~~~
      _wignermodule.c: In function ‘f2py_rout__wigner_drc3jj_vec’:
      _wignermodule.c:491:63: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
        491 | static PyObject *f2py_rout__wigner_drc3jj_vec(const PyObject *capi_self,
            |                                               ~~~~~~~~~~~~~~~~^~~~~~~~~
      _wignermodule.c: In function ‘f2py_rout__wigner_drc6j_vec’:
      _wignermodule.c:689:62: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
        689 | static PyObject *f2py_rout__wigner_drc6j_vec(const PyObject *capi_self,
            |                                              ~~~~~~~~~~~~~~~~^~~~~~~~~
      _wignermodule.c: At top level:
      _wignermodule.c:906:70: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
        906 |   {"drc3jj_int",-1,{{-1}},0,(char *)F_FUNC_US(drc3jj_int,DRC3JJ_INT),(f2py_init_func)f2py_rout__wigner_drc3jj_int,doc_f2py_rout__wigner_drc3jj_int},
            |                                                                      ^
      _wignermodule.c:907:67: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
        907 |   {"drc6j_int",-1,{{-1}},0,(char *)F_FUNC_US(drc6j_int,DRC6J_INT),(f2py_init_func)f2py_rout__wigner_drc6j_int,doc_f2py_rout__wigner_drc6j_int},
            |                                                                   ^
      _wignermodule.c:908:70: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
        908 |   {"drc3jj_vec",-1,{{-1}},0,(char *)F_FUNC_US(drc3jj_vec,DRC3JJ_VEC),(f2py_init_func)f2py_rout__wigner_drc3jj_vec,doc_f2py_rout__wigner_drc3jj_vec},
            |                                                                      ^
      _wignermodule.c:909:67: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
        909 |   {"drc6j_vec",-1,{{-1}},0,(char *)F_FUNC_US(drc6j_vec,DRC6J_VEC),(f2py_init_func)f2py_rout__wigner_drc6j_vec,doc_f2py_rout__wigner_drc6j_vec},
            |                                                                   ^
      _wignermodule.c:917:3: warning: missing initializer for field ‘ml_flags’ of ‘PyMethodDef’ [-Wmissing-field-initializers]
        917 |   {NULL,NULL}
            |   ^
      In file included from /usr/include/python3.7m/Python.h:113,
                       from _wignermodule.c:14:
      /usr/include/python3.7m/methodobject.h:59:17: note: ‘ml_flags’ declared here
         59 |     int         ml_flags;   /* Combination of METH_xxx flags, which mostly
            |                 ^~~~~~~~
      _wignermodule.c:109:12: warning: ‘f2py_size’ defined but not used [-Wunused-function]
        109 | static int f2py_size(PyArrayObject* var, ...)
            |            ^~~~~~~~~
      ninja: build stopped: subcommand failed.
fujiisoup commented 9 months ago

I looked at your error log, but honestly I have no idea about the error.

Our testing suite runs on Ubuntu 22 as well, so the OS should not be the issue. One thing I can think of is the numpy version. numpy==1.7 seems quite old. Could you try installing py3nj again after updating numpy?

DanielChaseButterfield commented 4 months ago

I had a very similar error, but I was able to resolve it. In order to prepare, I ran the following commands:

pip install meson
pip install ninja
sudo aptitude install gfortran

After doing this, and trying to install this library with the pip install py3nj, I got the following error output. Note I'm on an Ubuntu 22.04.4 LTS system:

Defaulting to user installation because normal site-packages is not writeable
Collecting py3nj
  Using cached py3nj-0.2.1.tar.gz (49 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [142 lines of output]
      + meson setup /tmp/pip-install-akj_6f81/py3nj_efef4f608a8f4c2c8b65551bf5334f4f /tmp/pip-install-akj_6f81/py3nj_efef4f608a8f4c2c8b65551bf5334f4f/.mesonpy-k93r4fq2 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/tmp/pip-install-akj_6f81/py3nj_efef4f608a8f4c2c8b65551bf5334f4f/.mesonpy-k93r4fq2/meson-python-native-file.ini
      The Meson build system
      Version: 1.5.0
      Source dir: /tmp/pip-install-akj_6f81/py3nj_efef4f608a8f4c2c8b65551bf5334f4f
      Build dir: /tmp/pip-install-akj_6f81/py3nj_efef4f608a8f4c2c8b65551bf5334f4f/.mesonpy-k93r4fq2
      Build type: native build
      Project name: py3nj
      Project version: 0.2.1
      Fortran compiler for the host machine: gfortran (gcc 11.4.0 "GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0")
      Fortran linker for the host machine: gfortran ld.bfd 2.38
      C compiler for the host machine: cc (gcc 11.4.0 "cc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0")
      C linker for the host machine: cc ld.bfd 2.38
      Host machine cpu family: x86_64
      Host machine cpu: x86_64
      Program python found: YES (/usr/bin/python3)
      Run-time dependency OpenMP found: YES 4.5
      Found pkg-config: YES (/usr/bin/pkg-config) 0.29.2
      Run-time dependency python found: YES 3.10
      Build targets in project: 2

      py3nj 0.2.1

        User defined options
          Native files: /tmp/pip-install-akj_6f81/py3nj_efef4f608a8f4c2c8b65551bf5334f4f/.mesonpy-k93r4fq2/meson-python-native-file.ini
          buildtype   : release
          b_ndebug    : if-release
          b_vscrt     : md

      Found ninja-1.11.1.git.kitware.jobserver-1 at /home/dbutterfield3/.local/bin/ninja
      + /home/dbutterfield3/.local/bin/ninja
      [1/11] Generating _wignermodule.c with a custom command
      Reading fortran codes...
          Reading file '../fortran/_wigner.pyf' (format:free)
      Post-processing...
          Block: _wigner
                          Block: drc3jj_int
                          Block: drc6j_int
                          Block: drc3jj_vec
                          Block: drc6j_vec
      Post-processing (stage 2)...
      Building modules...
          Building module "_wigner"...
                  Constructing wrapper function "drc3jj_int"...
                    l1min,l1max,thrcof,ier = drc3jj_int(two_l2,two_l3,two_m2,two_m3,ndim)
                  Constructing wrapper function "drc6j_int"...
                    l1min,l1max,sixcof,ier = drc6j_int(two_l2,two_l3,two_l4,two_l5,two_l6,ndim)
                  Constructing wrapper function "drc3jj_vec"...
                    thrcof,ier = drc3jj_vec(two_l2,two_l3,two_m2,two_m3,ndim,[nvec])
                  Constructing wrapper function "drc6j_vec"...
                    sixcof,ier = drc6j_vec(two_l2,two_l3,two_l4,two_l5,two_l6,ndim,[nvec])
          Wrote C/API module "_wigner" to file "./_wignermodule.c"
      [2/11] Compiling C object _wigner.cpython-310-x86_64-linux-gnu.so.p/_usr_lib_python3_dist-packages_numpy_f2py_src_fortranobject.c.o
      In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
                       from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                       from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                       from /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.h:13,
                       from /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.c:2:
      /usr/lib/python3/dist-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 " \
            |  ^~~~~~~
      /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.c: In function ‘fortran_call’:
      /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.c:466:23: warning: cast between incompatible function types from ‘f2py_init_func’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} to ‘PyObject * (*)(PyObject *, PyObject *, PyObject *, void *)’ {aka ‘struct _object * (*)(struct _object *, struct _object *, struct _object *, void *)’} [-Wcast-function-type]
        466 |             return (*((fortranfunc)(fp->defs[i].func)))((PyObject *)fp,arg,kw,NULL);
            |                       ^
      /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.c:468:23: warning: cast between incompatible function types from ‘f2py_init_func’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} to ‘PyObject * (*)(PyObject *, PyObject *, PyObject *, void *)’ {aka ‘struct _object * (*)(struct _object *, struct _object *, struct _object *, void *)’} [-Wcast-function-type]
        468 |             return (*((fortranfunc)(fp->defs[i].func)))((PyObject *)fp,arg,kw,
            |                       ^
      [3/11] Module scanner.
      FAILED: _wigner.cpython-310-x86_64-linux-gnu.so.p/depscan.dd
      /home/dbutterfield3/.local/bin/meson --internal depscan  _wigner.cpython-310-x86_64-linux-gnu.so.p/depscan.dd _wigner.cpython-310-x86_64-linux-gnu.so.p/_wigner.cpython-310-x86_64-linux-gnu.dat
      Traceback (most recent call last):
        File "/home/dbutterfield3/.local/bin/meson", line 8, in <module>
          sys.exit(main())
        File "/tmp/pip-build-env-wnwlzhkl/overlay/local/lib/python3.10/dist-packages/mesonbuild/mesonmain.py", line 288, in main
          return run(sys.argv[1:], launcher)
        File "/tmp/pip-build-env-wnwlzhkl/overlay/local/lib/python3.10/dist-packages/mesonbuild/mesonmain.py", line 276, in run
          return run_script_command(args[1], args[2:])
        File "/tmp/pip-build-env-wnwlzhkl/overlay/local/lib/python3.10/dist-packages/mesonbuild/mesonmain.py", line 217, in run_script_command
          return module.run(script_args)
        File "/tmp/pip-build-env-wnwlzhkl/overlay/local/lib/python3.10/dist-packages/mesonbuild/scripts/depscan.py", line 173, in run
          return scanner.scan()
        File "/tmp/pip-build-env-wnwlzhkl/overlay/local/lib/python3.10/dist-packages/mesonbuild/scripts/depscan.py", line 125, in scan
          self.scan_file(s, lang)
        File "/tmp/pip-build-env-wnwlzhkl/overlay/local/lib/python3.10/dist-packages/mesonbuild/scripts/depscan.py", line 45, in scan_file
          self.scan_fortran_file(fname)
        File "/tmp/pip-build-env-wnwlzhkl/overlay/local/lib/python3.10/dist-packages/mesonbuild/scripts/depscan.py", line 52, in scan_fortran_file
          for line in fpath.read_text(encoding='utf-8', errors='ignore').split('\n'):
        File "/usr/lib/python3.10/pathlib.py", line 1134, in read_text
          with self.open(mode='r', encoding=encoding, errors=errors) as f:
        File "/usr/lib/python3.10/pathlib.py", line 1119, in open
          return self._accessor.open(self, mode, buffering, encoding, errors,
      FileNotFoundError: [Errno 2] No such file or directory: '_wigner-f2pywrappers.f'
      [4/11] Compiling C object _wigner.cpython-310-x86_64-linux-gnu.so.p/meson-generated_..__wignermodule.c.o
      In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
                       from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                       from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                       from /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.h:13,
                       from _wignermodule.c:16:
      /usr/lib/python3/dist-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 " \
            |  ^~~~~~~
      _wignermodule.c: In function ‘f2py_rout__wigner_drc3jj_int’:
      _wignermodule.c:217:63: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
        217 | static PyObject *f2py_rout__wigner_drc3jj_int(const PyObject *capi_self,
            |                                               ~~~~~~~~~~~~~~~~^~~~~~~~~
      _wignermodule.c: In function ‘f2py_rout__wigner_drc6j_int’:
      _wignermodule.c:351:62: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
        351 | static PyObject *f2py_rout__wigner_drc6j_int(const PyObject *capi_self,
            |                                              ~~~~~~~~~~~~~~~~^~~~~~~~~
      _wignermodule.c: In function ‘f2py_rout__wigner_drc3jj_vec’:
      _wignermodule.c:491:63: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
        491 | static PyObject *f2py_rout__wigner_drc3jj_vec(const PyObject *capi_self,
            |                                               ~~~~~~~~~~~~~~~~^~~~~~~~~
      _wignermodule.c: In function ‘f2py_rout__wigner_drc6j_vec’:
      _wignermodule.c:689:62: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
        689 | static PyObject *f2py_rout__wigner_drc6j_vec(const PyObject *capi_self,
            |                                              ~~~~~~~~~~~~~~~~^~~~~~~~~
      _wignermodule.c: At top level:
      _wignermodule.c:906:70: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
        906 |   {"drc3jj_int",-1,{{-1}},0,(char *)F_FUNC_US(drc3jj_int,DRC3JJ_INT),(f2py_init_func)f2py_rout__wigner_drc3jj_int,doc_f2py_rout__wigner_drc3jj_int},
            |                                                                      ^
      _wignermodule.c:907:67: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
        907 |   {"drc6j_int",-1,{{-1}},0,(char *)F_FUNC_US(drc6j_int,DRC6J_INT),(f2py_init_func)f2py_rout__wigner_drc6j_int,doc_f2py_rout__wigner_drc6j_int},
            |                                                                   ^
      _wignermodule.c:908:70: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
        908 |   {"drc3jj_vec",-1,{{-1}},0,(char *)F_FUNC_US(drc3jj_vec,DRC3JJ_VEC),(f2py_init_func)f2py_rout__wigner_drc3jj_vec,doc_f2py_rout__wigner_drc3jj_vec},
            |                                                                      ^
      _wignermodule.c:909:67: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
        909 |   {"drc6j_vec",-1,{{-1}},0,(char *)F_FUNC_US(drc6j_vec,DRC6J_VEC),(f2py_init_func)f2py_rout__wigner_drc6j_vec,doc_f2py_rout__wigner_drc6j_vec},
            |                                                                   ^
      _wignermodule.c:917:3: warning: missing initializer for field ‘ml_flags’ of ‘PyMethodDef’ [-Wmissing-field-initializers]
        917 |   {NULL,NULL}
            |   ^
      In file included from /usr/include/python3.10/Python.h:97,
                       from _wignermodule.c:14:
      /usr/include/python3.10/methodobject.h:38:17: note: ‘ml_flags’ declared here
         38 |     int         ml_flags;   /* Combination of METH_xxx flags, which mostly
            |                 ^~~~~~~~
      _wignermodule.c:109:12: warning: ‘f2py_size’ defined but not used [-Wunused-function]
        109 | static int f2py_size(PyArrayObject* var, ...)
            |            ^~~~~~~~~
      ninja: build stopped: subcommand failed.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Funnily enough, I also had the error: ```#warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION", but when I checked what version of NumPY I had in my python environment, it stated: 

Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (1.21.5)

This made me think that the issue was due to Meson or Ninja using a different numpy installation. Since I was operating in a conda environment, I decided to try installing numpy directly through python:

conda install numpy

After this, I was able to build the repository:

Collecting py3nj
  Downloading py3nj-0.2.1.tar.gz (49 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 50.0/50.0 kB 2.8 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in /home/dbutterfield3/miniconda3/envs/morph/lib/python3.12/site-packages (from py3nj) (1.26.4)
Building wheels for collected packages: py3nj
  Building wheel for py3nj (pyproject.toml) ... done
  Created wheel for py3nj: filename=py3nj-0.2.1-cp312-cp312-linux_x86_64.whl size=44908 sha256=b90334a5ea4c5dc5facd91177148d07b1f4332252916b3299e30984884ee8d39
  Stored in directory: /home/dbutterfield3/.cache/pip/wheels/8a/fb/37/2d95d35a34d09f4e0758e53138466650cb6643d8383f4bf605
Successfully built py3nj
Installing collected packages: py3nj
Successfully installed py3nj-0.2.1

Not sure how this fixed the issue, but my theory is that installing numpy directly through conda led the build system to use the proper updated version of NumPy, instead of ignoring the pip installation to use some older numpy version installed on the computer. @Peter010103 Does this work for you?

fujiisoup commented 4 months ago

Thank you, @DanielChaseButterfield for your investigation. This should be the answer. ~Yes, we are using conda install numpy in the test suite, which does not show errors in the installation.~ I will try reproducing this symptom.

fujiisoup commented 4 months ago

Yes, we are using conda install numpy in the test suite, which does not show errors in the installation.

I noticed that our current test suite do not use conda, but just running pip install ..

Let me clarify, @DanielChaseButterfield.

Do you have more than one python environment (e.g., one in usr/bin/python3 and ~/Library/Python/3.7/site-packages )? And then while you are installing py3nj into your user python environment, Meson or Ninja picks up the numpy in the other environment?

DanielChaseButterfield commented 4 months ago

I do have multiple python environments. I have my /usr environment, and multiple conda environments. This is the python version and numpy version for each:

/usr/bin/python
Python 3.10.12
'1.21.5'
/home/dbutterfield3/miniconda3/envs/morph/bin/python
Python 3.9.19
'1.26.4'
/home/dbutterfield3/miniconda3/envs/gnn/bin/python
Python 3.11.9
'2.0.0'
/home/dbutterfield3/miniconda3/bin/python    (the base conda environment)
Python 3.12.4
ModuleNotFoundError: No module named 'numpy'

Notably, all of my installed NumPy versions are 1.21+, which doesn't seem to make sense due to the 1.7 NumPy deprecated message... But presuming that the build system was unable to see the numpy installation in my morph environment, maybe it fell back to the base conda environment. And since numpy isn't installed there, maybe one of the other packages in the base environment has an internal numpy that it ended up using? All of these are sort of wild theories... I'm not sure what happened exactly.

fujiisoup commented 4 months ago

Thank you, @DanielChaseButterfield

I assumed you have Numpy 1.7 somewhere, but it does not seem so. It is weird.

@kalekundert Do you have any idea for this issue? Meson seems like failing to find an appropriate numpy in the environment.

I believe that according to the official document meson will use the python environment which is used to run Meson,

That argument is optional, if not provided then the returned python installation will be the one used to run Meson.

So it should not matter...

fujiisoup commented 4 months ago

I am trying to reproduce this symptom in our GithubActions https://github.com/fujiisoup/py3nj/actions/workflows/test.yml but no success.

I thought it is caused by the conflict between Anaconda's environment and system environment, so I prepared an Anaconda without numpy installed, and install py3nj to this environment. Unfortunately, I didn't get the error.

kalekundert commented 4 months ago

I'm also not sure what's causing these installations to fail, but I don't think the numpy 1.7 warning is relevant. The pip output is just saying that f2py is using the old numpy API in the C code it's generating, perhaps because it hasn't been updated to generate the new API yet. It's not saying that numpy 1.7 is installed somewhere. Also, the two steps that generate this warning ([2/11] and [4/11]) both ultimately succeed.

It seems like the build fails due to the [3/11] step, which is unable to find _wigner-f2pywrappers.f. Maybe this file wasn't created for some reason, or maybe it was created in the wrong place? I don't really know what this step is supposed to do, and it succeeds on my system with no output. I looked for other errors related to this step, and this is the closest I found, but I couldn't really tell if it's relevant to our problem here.

@DanielChaseButterfield I'm curious what output the following commands produce:

$ which python
$ python --version
$ python -m venv venv
$ . venv/bin/activate
$ which python
$ python --version
$ python -m pip install --no-cache-dir -vvv py3nj

@fujiisoup The best solution to installation problems like this might be to upload binaries to PyPI. Right now PyPI has only a source distribution, so everyone who wants to use py3nj has to compile it themselves. It should be possible to use cibuildwheel to build binaries for all the most common systems on the CI server, where we already have the build working, and then upload the results to PyPI. I've done this for one of my projects, which may be useful as a reference: see here. Note that this config uses a tool called "semantic release" to automatically bump the version number, but in retrospect I'd recommend against doing that.

Just to give some background info, when pip needs to build a package like py3nj, it creates a temporary virtual environment and installs all of the necessary build dependencies there. This completely isolates the build process from any other python packages installed on the system, and makes the build process much more reliable[^1]. So if the build process were being affected by the version of any python package you have installed anywhere, that would be a pretty shocking bug in pip.

Similarly, there's no need to do pip install meson or pip install ninja before pip install py3nj. Meson is a pure python package and will automatically be installed in the build environment. Any version installed outside the build environment will be invisible to the build process anyways. The ninja executable (like the fortran compiler) does need to be installed and on your $PATH, but it doesn't need to be pip-installed.

[^1]: The transition to this process, though, has been pretty traumatic. Packages weren't previously built in isolated environments, and it turns out that a lot of existing packages, including py3nj before #23, fail when built like this. I definitely think this transition will be a good thing in the long run, but right now it's still pretty painful.

DanielChaseButterfield commented 4 months ago

@kalekundert Here is the output of running those commands (except the last one):

dbutterfield@<computer>:~/Research/deep-contact-estimator$ which python
/usr/bin/python
dbutterfield@<computer>:~/Research/deep-contact-estimator$ python --version
Python 3.10.12
butterfield@<computer>:~/Research/deep-contact-estimator$ python -m venv venv2
dbutterfield@<computer>:~/Research/deep-contact-estimator$ . venv2/bin/activate
(venv2) dbutterfield@<computer>:~/Research/deep-contact-estimator$ which python
/home/dbutterfield3/Research/deep-contact-estimator/venv2/bin/python
(venv2) dbutterfield@<computer>:~/Research/deep-contact-estimator$ python --version
Python 3.10.12

And, here is the output of running the last command:

Using pip 22.0.2 from /home/dbutterfield3/Research/deep-contact-estimator/venv2/lib/python3.10/site-packages/pip (python 3.10)
Non-user install because user site-packages disabled
Created temporary directory: /tmp/pip-ephem-wheel-cache-9_b07dyf
Created temporary directory: /tmp/pip-req-tracker-0k5qwjil
Initialized build tracking at /tmp/pip-req-tracker-0k5qwjil
Created build tracker: /tmp/pip-req-tracker-0k5qwjil
Entered build tracker: /tmp/pip-req-tracker-0k5qwjil
Created temporary directory: /tmp/pip-install-bmulf47w
1 location(s) to search for versions of py3nj:
* https://pypi.org/simple/py3nj/
Fetching project page and analyzing links: https://pypi.org/simple/py3nj/
Getting page https://pypi.org/simple/py3nj/
Found index url https://pypi.org/simple
Starting new HTTPS connection (1): pypi.org:443
https://pypi.org:443 "GET /simple/py3nj/ HTTP/1.1" 200 812
  Found link https://files.pythonhosted.org/packages/25/0b/b23aaa457c1cc2357f6bb8f12947c5cbf51f98e9b60dfc555287a6f38039/py3nj-0.0.1.tar.gz#sha256=e2288c78b99505a447a7c9180cefd52cf1eed7a8c078f1b2a978f76725a628ba (from https://pypi.org/simple/py3nj/), version: 0.0.1
  Found link https://files.pythonhosted.org/packages/78/d7/e058ffad8b72225edea5a17401b6a72b9a66d2e65561b3713c2f193a5afd/py3nj-0.1.0.tar.gz#sha256=cec3d825bd5d8bd2bc25916f700b65755bd971a4f96d745759764a5faa0fdf2d (from https://pypi.org/simple/py3nj/), version: 0.1.0
  Found link https://files.pythonhosted.org/packages/f4/10/edd6cc68949c914a9c08e1947e302a9d8569ea0e9f348dd28b0fcaca1303/py3nj-0.1.1.tar.gz#sha256=e192ced2a0b5c1350ba9c55ecd1eb1dcf9c5988dbb5aaad0bf8ea2c05dcefff9 (from https://pypi.org/simple/py3nj/), version: 0.1.1
  Found link https://files.pythonhosted.org/packages/f4/6f/5aa1bea141da27f65f8d9e138669cf75f3de916c705ca15f82ada8fae074/py3nj-0.1.2.tar.gz#sha256=d1c68634381c82d2a5642e8dc9fc109faaf89e7c9fc5844f287713634fbc2cd7 (from https://pypi.org/simple/py3nj/), version: 0.1.2
  Found link https://files.pythonhosted.org/packages/21/f9/799cfe5dcc73e0fcd15ccb7776272f13071bc339d3e33c4e39f87f4648b0/py3nj-0.2.0.tar.gz#sha256=8a25820d5375ea677344d9752b190115bf0b46129979279e8d82e744d870a374 (from https://pypi.org/simple/py3nj/), version: 0.2.0
  Found link https://files.pythonhosted.org/packages/79/39/608a0b4fa24bd07e42acfbe914eff4f32382e3861d81853d81f2c6d9fa7b/py3nj-0.2.1.tar.gz#sha256=3f9a79b3b18a51570c835c174a941f3cd3b552d1d3414debebeb70ce759512fe (from https://pypi.org/simple/py3nj/) (requires-python:~=3.8), version: 0.2.1
Skipping link: not a file: https://pypi.org/simple/py3nj/
Given no hashes to check 6 links for project 'py3nj': discarding no candidates
Collecting py3nj
  Created temporary directory: /tmp/pip-unpack-6u4plwqm
  Starting new HTTPS connection (1): files.pythonhosted.org:443
  https://files.pythonhosted.org:443 "GET /packages/79/39/608a0b4fa24bd07e42acfbe914eff4f32382e3861d81853d81f2c6d9fa7b/py3nj-0.2.1.tar.gz HTTP/1.1" 200 49969
  Downloading py3nj-0.2.1.tar.gz (49 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 50.0/50.0 KB 2.8 MB/s eta 0:00:00
  Added py3nj from https://files.pythonhosted.org/packages/79/39/608a0b4fa24bd07e42acfbe914eff4f32382e3861d81853d81f2c6d9fa7b/py3nj-0.2.1.tar.gz#sha256=3f9a79b3b18a51570c835c174a941f3cd3b552d1d3414debebeb70ce759512fe to build tracker '/tmp/pip-req-tracker-0k5qwjil'
  Created temporary directory: /tmp/pip-build-env-9f_ms7wm
  Created temporary directory: /tmp/pip-standalone-pip-upiuz2j7
  Installing build dependencies: started
  Running command pip subprocess to install build dependencies
  Using pip 22.0.2 from /tmp/pip-standalone-pip-upiuz2j7/__env_pip__.zip/pip (python 3.10)
  Collecting meson-python
    Using cached meson_python-0.16.0-py3-none-any.whl (26 kB)
  Collecting numpy
    Using cached numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.3 MB)
  Collecting packaging>=19.0
    Using cached packaging-24.1-py3-none-any.whl (53 kB)
  Collecting meson>=0.63.3
    Using cached meson-1.5.0-py3-none-any.whl
  Collecting pyproject-metadata>=0.7.1
    Using cached pyproject_metadata-0.8.0-py3-none-any.whl (7.5 kB)
  Collecting tomli>=1.0.0
    Using cached tomli-2.0.1-py3-none-any.whl (12 kB)
  Installing collected packages: tomli, packaging, numpy, meson, pyproject-metadata, meson-python
    Creating /tmp/pip-build-env-9f_ms7wm/overlay/bin
    changing mode of /tmp/pip-build-env-9f_ms7wm/overlay/bin/f2py to 755
    changing mode of /tmp/pip-build-env-9f_ms7wm/overlay/bin/numpy-config to 755
    changing mode of /tmp/pip-build-env-9f_ms7wm/overlay/bin/meson to 755
  Successfully installed meson-1.5.0 meson-python-0.16.0 numpy-2.0.0 packaging-24.1 pyproject-metadata-0.8.0 tomli-2.0.1
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Running command Getting requirements to build wheel
  Getting requirements to build wheel: finished with status 'done'
  Created temporary directory: /tmp/pip-standalone-pip-pa6fo73o
  Installing backend dependencies: started
  Running command pip subprocess to install backend dependencies
  Using pip 22.0.2 from /tmp/pip-standalone-pip-pa6fo73o/__env_pip__.zip/pip (python 3.10)
  Collecting ninja>=1.8.2
    Using cached ninja-1.11.1.1-py2.py3-none-manylinux1_x86_64.manylinux_2_5_x86_64.whl (307 kB)
  Collecting patchelf>=0.11.0
    Using cached patchelf-0.17.2.1-py2.py3-none-manylinux_2_5_x86_64.manylinux1_x86_64.musllinux_1_1_x86_64.whl (425 kB)
  Installing collected packages: patchelf, ninja
    changing mode of /tmp/pip-build-env-9f_ms7wm/normal/bin/ninja to 755
  Successfully installed ninja-1.11.1.1 patchelf-0.17.2.1
  Installing backend dependencies: finished with status 'done'
  Created temporary directory: /tmp/pip-modern-metadata-1kayw8k1
  Preparing metadata (pyproject.toml): started
  Running command Preparing metadata (pyproject.toml)
  + meson setup /tmp/pip-install-bmulf47w/py3nj_9e080df0e8ed4f279ad54e252a61bd2e /tmp/pip-install-bmulf47w/py3nj_9e080df0e8ed4f279ad54e252a61bd2e/.mesonpy-int4jxik -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/tmp/pip-install-bmulf47w/py3nj_9e080df0e8ed4f279ad54e252a61bd2e/.mesonpy-int4jxik/meson-python-native-file.ini
  The Meson build system
  Version: 1.5.0
  Source dir: /tmp/pip-install-bmulf47w/py3nj_9e080df0e8ed4f279ad54e252a61bd2e
  Build dir: /tmp/pip-install-bmulf47w/py3nj_9e080df0e8ed4f279ad54e252a61bd2e/.mesonpy-int4jxik
  Build type: native build
  Project name: py3nj
  Project version: 0.2.1
  Fortran compiler for the host machine: gfortran (gcc 11.4.0 "GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0")
  Fortran linker for the host machine: gfortran ld.bfd 2.38
  C compiler for the host machine: cc (gcc 11.4.0 "cc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0")
  C linker for the host machine: cc ld.bfd 2.38
  Host machine cpu family: x86_64
  Host machine cpu: x86_64
  Program python found: YES (/home/dbutterfield3/Research/deep-contact-estimator/venv2/bin/python)
  Run-time dependency OpenMP found: YES 4.5
  Found pkg-config: YES (/usr/bin/pkg-config) 0.29.2
  Run-time dependency python found: YES 3.10
  Build targets in project: 2

  py3nj 0.2.1

    User defined options
      Native files: /tmp/pip-install-bmulf47w/py3nj_9e080df0e8ed4f279ad54e252a61bd2e/.mesonpy-int4jxik/meson-python-native-file.ini
      buildtype   : release
      b_ndebug    : if-release
      b_vscrt     : md

  Found ninja-1.11.1.git.kitware.jobserver-1 at /tmp/pip-build-env-9f_ms7wm/normal/bin/ninja
  + /tmp/pip-build-env-9f_ms7wm/normal/bin/ninja
  [1/11] Generating _wignermodule.c with a custom command
  Reading fortran codes...
        Reading file '../fortran/_wigner.pyf' (format:free)
  Post-processing...
        Block: _wigner
                        Block: drc3jj_int
                        Block: drc6j_int
                        Block: drc3jj_vec
                        Block: drc6j_vec
  Applying post-processing hooks...
    character_backward_compatibility_hook
  Post-processing (stage 2)...
  Building modules...
      Building module "_wigner"...
      Generating possibly empty wrappers"
      Maybe empty "_wigner-f2pywrappers.f"
          Constructing wrapper function "drc3jj_int"...
            l1min,l1max,thrcof,ier = drc3jj_int(two_l2,two_l3,two_m2,two_m3,ndim)
      Generating possibly empty wrappers"
      Maybe empty "_wigner-f2pywrappers.f"
          Constructing wrapper function "drc6j_int"...
            l1min,l1max,sixcof,ier = drc6j_int(two_l2,two_l3,two_l4,two_l5,two_l6,ndim)
      Generating possibly empty wrappers"
      Maybe empty "_wigner-f2pywrappers.f"
          Constructing wrapper function "drc3jj_vec"...
            thrcof,ier = drc3jj_vec(two_l2,two_l3,two_m2,two_m3,ndim,[nvec])
      Generating possibly empty wrappers"
      Maybe empty "_wigner-f2pywrappers.f"
          Constructing wrapper function "drc6j_vec"...
            sixcof,ier = drc6j_vec(two_l2,two_l3,two_l4,two_l5,two_l6,ndim,[nvec])
      Wrote C/API module "_wigner" to file "./_wignermodule.c"
  [2/11] Module scanner.
  [3/11] Compiling Fortran object _wigner.cpython-310-x86_64-linux-gnu.so.p/meson-generated_..__wigner-f2pywrappers.f.o
  [4/11] Compiling Fortran object _wigner.cpython-310-x86_64-linux-gnu.so.p/fortran_d1mach.f.o
  [5/11] Compiling C object _wigner.cpython-310-x86_64-linux-gnu.so.p/b03bbfd662e7e604a51183609e43f00038e11a2e_site-packages_numpy_f2py_src_fortranobject.c.o
  /tmp/pip-build-env-9f_ms7wm/overlay/lib/python3.10/site-packages/numpy/f2py/src/fortranobject.c: In function ‘fortran_call’:
  /tmp/pip-build-env-9f_ms7wm/overlay/lib/python3.10/site-packages/numpy/f2py/src/fortranobject.c:529:23: warning: cast between incompatible function types from ‘f2py_init_func’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} to ‘PyObject * (*)(PyObject *, PyObject *, PyObject *, void *)’ {aka ‘struct _object * (*)(struct _object *, struct _object *, struct _object *, void *)’} [-Wcast-function-type]
    529 |             return (*((fortranfunc)(fp->defs[i].func)))((PyObject *)fp, arg,
        |                       ^
  /tmp/pip-build-env-9f_ms7wm/overlay/lib/python3.10/site-packages/numpy/f2py/src/fortranobject.c:532:23: warning: cast between incompatible function types from ‘f2py_init_func’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} to ‘PyObject * (*)(PyObject *, PyObject *, PyObject *, void *)’ {aka ‘struct _object * (*)(struct _object *, struct _object *, struct _object *, void *)’} [-Wcast-function-type]
    532 |             return (*((fortranfunc)(fp->defs[i].func)))(
        |                       ^
  [6/11] Compiling C object _wigner.cpython-310-x86_64-linux-gnu.so.p/meson-generated_..__wignermodule.c.o
  _wignermodule.c: In function ‘f2py_rout__wigner_drc3jj_int’:
  _wignermodule.c:202:63: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
    202 | static PyObject *f2py_rout__wigner_drc3jj_int(const PyObject *capi_self,
        |                                               ~~~~~~~~~~~~~~~~^~~~~~~~~
  _wignermodule.c: In function ‘f2py_rout__wigner_drc6j_int’:
  _wignermodule.c:338:62: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
    338 | static PyObject *f2py_rout__wigner_drc6j_int(const PyObject *capi_self,
        |                                              ~~~~~~~~~~~~~~~~^~~~~~~~~
  _wignermodule.c: In function ‘f2py_rout__wigner_drc3jj_vec’:
  _wignermodule.c:480:63: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
    480 | static PyObject *f2py_rout__wigner_drc3jj_vec(const PyObject *capi_self,
        |                                               ~~~~~~~~~~~~~~~~^~~~~~~~~
  _wignermodule.c: In function ‘f2py_rout__wigner_drc6j_vec’:
  _wignermodule.c:688:62: warning: unused parameter ‘capi_self’ [-Wunused-parameter]
    688 | static PyObject *f2py_rout__wigner_drc6j_vec(const PyObject *capi_self,
        |                                              ~~~~~~~~~~~~~~~~^~~~~~~~~
  _wignermodule.c: At top level:
  _wignermodule.c:917:78: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
    917 |     {"drc3jj_int",-1,{{-1}},0,0,(char *)  F_FUNC_US(drc3jj_int,DRC3JJ_INT),  (f2py_init_func)f2py_rout__wigner_drc3jj_int,doc_f2py_rout__wigner_drc3jj_int},
        |                                                                              ^
  _wignermodule.c:918:75: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
    918 |     {"drc6j_int",-1,{{-1}},0,0,(char *)  F_FUNC_US(drc6j_int,DRC6J_INT),  (f2py_init_func)f2py_rout__wigner_drc6j_int,doc_f2py_rout__wigner_drc6j_int},
        |                                                                           ^
  _wignermodule.c:919:78: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
    919 |     {"drc3jj_vec",-1,{{-1}},0,0,(char *)  F_FUNC_US(drc3jj_vec,DRC3JJ_VEC),  (f2py_init_func)f2py_rout__wigner_drc3jj_vec,doc_f2py_rout__wigner_drc3jj_vec},
        |                                                                              ^
  _wignermodule.c:920:75: warning: cast between incompatible function types from ‘PyObject * (*)(const PyObject *, PyObject *, PyObject *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’ {aka ‘struct _object * (*)(const struct _object *, struct _object *, struct _object *, void (*)(int *, int *, int *, int *, int *, int *, double *, int *, int *))’} to ‘void (*)(int *, npy_intp *, void (*)(char *, npy_intp *), int *)’ {aka ‘void (*)(int *, long int *, void (*)(char *, long int *), int *)’} [-Wcast-function-type]
    920 |     {"drc6j_vec",-1,{{-1}},0,0,(char *)  F_FUNC_US(drc6j_vec,DRC6J_VEC),  (f2py_init_func)f2py_rout__wigner_drc6j_vec,doc_f2py_rout__wigner_drc6j_vec},
        |                                                                           ^
  _wignermodule.c:928:5: warning: missing initializer for field ‘ml_flags’ of ‘PyMethodDef’ [-Wmissing-field-initializers]
    928 |     {NULL,NULL}
        |     ^
  In file included from /usr/include/python3.10/Python.h:97,
                   from _wignermodule.c:18:
  /usr/include/python3.10/methodobject.h:38:17: note: ‘ml_flags’ declared here
     38 |     int         ml_flags;   /* Combination of METH_xxx flags, which mostly
        |                 ^~~~~~~~
  [7/11] Compiling Fortran object _wigner.cpython-310-x86_64-linux-gnu.so.p/fortran_drc3jj.f.o
  ../fortran/drc3jj.f:204:72:

    204 |       IF(NDIM-NFIN)  21, 23, 23
        |                                                                        1
  Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
  ../fortran/drc3jj.f:237:72:

    237 |       IF(LSTEP-2)  32, 32, 31
        |                                                                        1
  Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
  ../fortran/drc3jj.f:280:72:

    280 |    70 THRCOF(I) = THRCOF(I) / SRHUGE
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 70 at (1)
  ../fortran/drc3jj.f:290:72:

    290 |    80 IF(C1OLD-ABS(C1))   100, 100, 30
        |                                                                        1
  Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
  ../fortran/drc3jj.f:367:72:

    367 |   130 THRCOF(INDEX) = THRCOF(INDEX) / SRHUGE
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 130 at (1)
  ../fortran/drc3jj.f:392:72:

    392 |   210 THRCOF(N) = RATIO * THRCOF(N)
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 210 at (1)
  ../fortran/drc3jj.f:399:72:

    399 |   212 THRCOF(N) = RATIO * THRCOF(N)
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 212 at (1)
  ../fortran/drc3jj.f:414:72:

    414 |       IF(SIGN1*SIGN2) 235,235,236
        |                                                                        1
  Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
  ../fortran/drc3jj.f:420:72:

    420 |   240 THRCOF(N) = CNORM * THRCOF(N)
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 240 at (1)
  ../fortran/drc3jj.f:426:72:

    426 |   251 THRCOF(N) = CNORM * THRCOF(N)
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 251 at (1)
  ../fortran/drc3jj.f:132:69:

    132 |       DOUBLE PRECISION A1, A1S, A2, A2S, C1, C1OLD, C2, CNORM, D1MACH,
        |                                                                     1
  Warning: Unused variable ‘d1mach’ declared at (1) [-Wunused-variable]
  ../fortran/drc3jj.f:400:72:

    400 |       SUMUNI = SUMFOR + RATIO*RATIO*SUMBAC
        |                                                                        ^
  Warning: ‘sumbac’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  ../fortran/drc3jj.f:259:72:

    259 |    60 C2 = - L1 * OLDFAC / DENOM
        |                                                                        ^
  Warning: ‘denom’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  ../fortran/drc3jj.f:290:72:

    290 |    80 IF(C1OLD-ABS(C1))   100, 100, 30
        |                                                                        ^
  Warning: ‘c1old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  [8/11] Compiling Fortran object _wigner.cpython-310-x86_64-linux-gnu.so.p/fortran_drc6j.f.o
  ../fortran/drc6j.f:208:72:

    208 |       IF(NDIM-NFIN)   21, 23, 23
        |                                                                        1
  Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
  ../fortran/drc6j.f:243:72:

    243 |       IF(LSTEP-2)  32, 32, 31
        |                                                                        1
  Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
  ../fortran/drc6j.f:288:72:

    288 |    70 SIXCOF(I) = SIXCOF(I) / SRHUGE
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 70 at (1)
  ../fortran/drc6j.f:299:72:

    299 |    80 IF(C1OLD-ABS(C1))   100, 100, 30
        |                                                                        1
  Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
  ../fortran/drc6j.f:378:72:

    378 |   130 SIXCOF(INDEX) = SIXCOF(INDEX) / SRHUGE
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 130 at (1)
  ../fortran/drc6j.f:402:72:

    402 |   210 SIXCOF(N) = RATIO * SIXCOF(N)
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 210 at (1)
  ../fortran/drc6j.f:409:72:

    409 |   212 SIXCOF(N) = RATIO * SIXCOF(N)
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 212 at (1)
  ../fortran/drc6j.f:424:72:

    424 |       IF(SIGN1*SIGN2) 235,235,236
        |                                                                        1
  Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
  ../fortran/drc6j.f:430:72:

    430 |   240 SIXCOF(N) = CNORM * SIXCOF(N)
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 240 at (1)
  ../fortran/drc6j.f:436:72:

    436 |   251 SIXCOF(N) = CNORM * SIXCOF(N)
        |                                                                        1
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 251 at (1)
  ../fortran/drc6j.f:410:72:

    410 |       SUMUNI = SUMFOR + RATIO*RATIO*SUMBAC
        |                                                                        ^
  Warning: ‘sumbac’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  ../fortran/drc6j.f:266:72:

    266 |    60 C2 = - L1 * OLDFAC / DENOM
        |                                                                        ^
  Warning: ‘denom’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  ../fortran/drc6j.f:299:72:

    299 |    80 IF(C1OLD-ABS(C1))   100, 100, 30
        |                                                                        ^
  Warning: ‘c1old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  [9/11] Compiling Fortran object _wigner.cpython-310-x86_64-linux-gnu.so.p/fortran_xermsg.f.o
  ../fortran/xermsg.f:1414:30:

   1414 |       SUBROUTINE XERHLT (MESSG)
        |                              1
  Warning: Unused dummy argument ‘messg’ at (1) [-Wunused-dummy-argument]
  ../fortran/xermsg.f:1354:67:

   1354 |       SUBROUTINE XERCNT (LIBRAR, SUBROU, MESSG, NERR, LEVEL, KONTRL)
        |                                                                   1
  Warning: Unused dummy argument ‘kontrl’ at (1) [-Wunused-dummy-argument]
  ../fortran/xermsg.f:1354:59:

   1354 |       SUBROUTINE XERCNT (LIBRAR, SUBROU, MESSG, NERR, LEVEL, KONTRL)
        |                                                           1
  Warning: Unused dummy argument ‘level’ at (1) [-Wunused-dummy-argument]
  ../fortran/xermsg.f:1354:31:

   1354 |       SUBROUTINE XERCNT (LIBRAR, SUBROU, MESSG, NERR, LEVEL, KONTRL)
        |                               1
  Warning: Unused dummy argument ‘librar’ at (1) [-Wunused-dummy-argument]
  ../fortran/xermsg.f:1354:46:

   1354 |       SUBROUTINE XERCNT (LIBRAR, SUBROU, MESSG, NERR, LEVEL, KONTRL)
        |                                              1
  Warning: Unused dummy argument ‘messg’ at (1) [-Wunused-dummy-argument]
  ../fortran/xermsg.f:1354:52:

   1354 |       SUBROUTINE XERCNT (LIBRAR, SUBROU, MESSG, NERR, LEVEL, KONTRL)
        |                                                    1
  Warning: Unused dummy argument ‘nerr’ at (1) [-Wunused-dummy-argument]
  ../fortran/xermsg.f:1354:39:

   1354 |       SUBROUTINE XERCNT (LIBRAR, SUBROU, MESSG, NERR, LEVEL, KONTRL)
        |                                       1
  Warning: Unused dummy argument ‘subrou’ at (1) [-Wunused-dummy-argument]
  [10/11] Compiling Fortran object _wigner.cpython-310-x86_64-linux-gnu.so.p/fortran_drc.f90.o
  [11/11] Linking target _wigner.cpython-310-x86_64-linux-gnu.so
  [1/4] /tmp/pip-install-bmulf47w/py3nj_9e080df0e8ed4f279ad54e252a61bd2e/.mesonpy-int4jxik/_wigner.cpython-310-x86_64-linux-gnu.so
  [2/4] /tmp/pip-install-bmulf47w/py3nj_9e080df0e8ed4f279ad54e252a61bd2e/src/__init__.py
  [3/4] /tmp/pip-install-bmulf47w/py3nj_9e080df0e8ed4f279ad54e252a61bd2e/src/_version.py
  [4/4] /tmp/pip-install-bmulf47w/py3nj_9e080df0e8ed4f279ad54e252a61bd2e/src/wigner.py
  Preparing metadata (pyproject.toml): finished with status 'done'
  Source in /tmp/pip-install-bmulf47w/py3nj_9e080df0e8ed4f279ad54e252a61bd2e has version 0.2.1, which satisfies requirement py3nj from https://files.pythonhosted.org/packages/79/39/608a0b4fa24bd07e42acfbe914eff4f32382e3861d81853d81f2c6d9fa7b/py3nj-0.2.1.tar.gz#sha256=3f9a79b3b18a51570c835c174a941f3cd3b552d1d3414debebeb70ce759512fe
  Removed py3nj from https://files.pythonhosted.org/packages/79/39/608a0b4fa24bd07e42acfbe914eff4f32382e3861d81853d81f2c6d9fa7b/py3nj-0.2.1.tar.gz#sha256=3f9a79b3b18a51570c835c174a941f3cd3b552d1d3414debebeb70ce759512fe from build tracker '/tmp/pip-req-tracker-0k5qwjil'
1 location(s) to search for versions of numpy:
* https://pypi.org/simple/numpy/
Fetching project page and analyzing links: https://pypi.org/simple/numpy/
Getting page https://pypi.org/simple/numpy/
Found index url https://pypi.org/simple
https://pypi.org:443 "GET /simple/numpy/ HTTP/1.1" 200 252754
  Skipping link: unsupported archive format: .exe: https://files.pythonhosted.org/packages/b7/53/342ee8490dce7939ed31073a1e1d80f114a56bd7b63ebd8d80df79aba5e0/numpy-1.0.1.dev3460.win32-py2.4.exe#sha256=7a1daab190e8584eadc5461d3518cbe0302f6e38143b451f7138c392a4bfc0d8 (from https://pypi.org/simple/numpy/)
  Found link https://files.pythonhosted.org/packages/ab/67/19e93e3f8c3e077dcf6fc54e84e1cff609c4a7e0a3ce14f70794dde60063/numpy-1.3.0.tar.gz#sha256=7524687cce85aa78103046db5e617c626b0ef871a203a049159f88f35647c90d (from https://pypi.org/simple/numpy/), version: 1.3.0
  Skipping link: unsupported archive format: .exe: https://files.pythonhosted.org/packages/98/b6/d5022159ff85cfb20a063996fe0b5a48199d856a752df20af675001a3fdf/numpy-1.3.0.win32-py2.5.exe#sha256=dadea0e51054a1cce976e143b98de765068e6541f9cd6cdb1819e39c924a5eed (from https://pypi.org/simple/numpy/)
  Found link https://files.pythonhosted.org/packages/6f/16/84dcacfbabd93ac12c378b823330d8665bdcf8ccea89da17d992afcbcb3a/numpy-1.4.1.tar.gz#sha256=e630d1d7960dd65ca9ed7bcd29c604bb22ef2b28ed6f33574e655a65da1146a6 (from https://pypi.org/simple/numpy/), version: 1.4.1
  Found link https://files.pythonhosted.org/packages/f4/7e/ee0605be5f922a85f798bf8ff1849d4d043b08229b026e55527110384c6d/numpy-1.5.0.tar.gz#sha256=06d2181c884c5937c7c475103dd55de4fe4842a9d91bab1ed0965dd973a4661a (from https://pypi.org/simple/numpy/), version: 1.5.0
  Skipping link: unsupported archive format: .exe: https://files.pythonhosted.org/packages/bd/bd/20b14b780f26876796fa7d33ac4e7d59adcd462c8c08006f5aeb11e67a10/numpy-1.5.0.win32-py2.6.exe#sha256=ba4d6b5d59e0646b6b82098db087ee2f9aedeca968354492f125ebb62f091f69 (from https://pypi.org/simple/numpy/)
  Skipping link: none of the wheel's tags (cp27-none-macosx_10_6_intel, cp27-none-macosx_10_9_intel, cp27-none-macosx_10_9_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/ad/d6/0cee332656a0633ff062c13408734dc3c617d5d45d174c491033063668eb/numpy-1.5.1-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.whl#sha256=2d19469a94eadd002b1596cb0ec22e4f27f4f96dd6c83391220d0e187041bd36 (from https://pypi.org/simple/numpy/)
  Found link https://files.pythonhosted.org/packages/73/e1/88932bb0420a0fbe1547ee96d4e7332de5c1ed5a846a6c96ea422c6bf753/numpy-1.5.1.tar.gz#sha256=c36789ec381fec09f519249744ea36a77e5534b69446a59ee73b06cac29542eb (from https://pypi.org/simple/numpy/), version: 1.5.1
  Skipping link: unsupported archive format: .exe: https://files.pythonhosted.org/packages/8b/8e/e20ca84e30db2d93d85370ba23efbe54037bb45348dd6496185e7bbb15fa/numpy-1.5.1.win32-py2.5-nosse.exe#sha256=e45623a65625a22e8c59d5feacc02bdc360eed4ab9f01f3dc619dc58c56336ad (from https://pypi.org/simple/numpy/)
  Skipping link: unsupported archive format: .exe: https://files.pythonhosted.org/packages/d2/fe/2d765a8f923db9a2254f398af2cafdd777b39611e90ac28d5fc3b8fd9cfa/numpy-1.5.1.win32-py2.6-nosse.exe#sha256=bea35acebd89855529f52e418f2b5d5976b50982651a7e1b97d4d6b68ba83130 (from https://pypi.org/simple/numpy/)
  Skipping link: unsupported archive format: .exe: https://files.pythonhosted.org/packages/eb/a9/af5807aeefbc05d574e103212cfc71423ac255ad326de651ed01ddf7f995/numpy-1.5.1.win32-py2.7-nosse.exe#sha256=37d8363be1e76b855ef27eb140caccd00e250244a6a3536dce9cd06a1e56ddbb (from https://pypi.org/simple/numpy/)
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  Found link https://files.pythonhosted.org/packages/58/98/80b1c502a149e4e6de900c0cd16e5a71c47313b12365aacbbd7e2eb206c2/numpy-1.8.1.tar.gz#sha256=3d722fc3ac922a34c50183683e828052cd9bb7e9134a95098441297d7ea1c7a9 (from https://pypi.org/simple/numpy/), version: 1.8.1
  Found link https://files.pythonhosted.org/packages/3e/0c/d8b5d5095988024ef68959bdec151e108138208214dbfe1e2658b1bc50ed/numpy-1.8.1.zip#sha256=80316c1743f10f2fb7d42c8dd70efda2ad9e104d532c1f18f1b665e86f694fa0 (from https://pypi.org/simple/numpy/), version: 1.8.1
  Skipping link: none of the wheel's tags (cp26-cp26m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/87/c1/69515470a99455dcab7b060bd8697bf913d6266ab89b764772eaeff35743/numpy-1.8.2-cp26-cp26m-manylinux1_x86_64.whl#sha256=f9ab980aa9d3d90f1d072fc8c53a6df2e5b2eedabb38fad42d844152940d0fdc (from https://pypi.org/simple/numpy/)
  Skipping link: none of the wheel's tags (cp26-cp26mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d8/2b/f47ceb5e782d4e8e30f11cbc354261fa06d335cf318e1a7494929a0539cb/numpy-1.8.2-cp26-cp26mu-manylinux1_x86_64.whl#sha256=3fd6e20ea9550ceb2e9ebecba35517e855ea7b4f08441f51b2731d4a26663f0a (from https://pypi.org/simple/numpy/)
  Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/1e/1f/42ec033fe7522ea5e16352b5491cca5d08bd05fd1d19b5be9dd9d2a3a15d/numpy-1.8.2-cp27-cp27m-manylinux1_x86_64.whl#sha256=99699e3e7df919fc6bbdfbdbc2ccef86a955c6d782f1b284e656ae735317c1b1 (from https://pypi.org/simple/numpy/)
  Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/17/f3/404bc85be67150663024d2bb5af654c7d16cf678077690dda27b91be14eb/numpy-1.8.2-cp27-cp27mu-manylinux1_x86_64.whl#sha256=ee209ac66442eb5b63bb180a281678ef8204e0b0bb45b83269e13b5158759eca (from https://pypi.org/simple/numpy/)
  Skipping link: none of the wheel's tags (cp27-none-macosx_10_6_intel, cp27-none-macosx_10_9_intel, cp27-none-macosx_10_9_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/6e/00/667a21ff386d4cc6a77bf16d51623dbc9315a50204f6ed01458b10d1fd34/numpy-1.8.2-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.whl#sha256=860afb63f154777e69908b9daef7d10929f8257526aee9553f6548ed962cd5e7 (from https://pypi.org/simple/numpy/)
  Skipping link: none of the wheel's tags (cp33-cp33m-macosx_10_6_intel, cp33-cp33m-macosx_10_9_intel, cp33-cp33m-macosx_10_9_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/c3/29/3aeb193406d7e52cda5b1fafa5b6624ab99bb480c2ce65484b602f4d0cb1/numpy-1.8.2-cp33-cp33m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.whl#sha256=664800623cc68176ea02e23302536e2e75a0f5d3b70e22dc7ca61d67d2b4b630 (from https://pypi.org/simple/numpy/)

I haven't posted the full output, as there are thousands of lines of "Skipping link", but here is the end:

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  Skipping link: none of the wheel's tags (pp39-pypy39_pp73-manylinux2014_x86_64, pp39-pypy39_pp73-manylinux_2_17_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/80/1a/354ad1a6627dbac1d4167591db51ce59ed972064bfb9979f9a37a7782900/numpy-2.0.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=38ecb5b0582cd125f67a629072fed6f83562d9dd04d7e03256c9829bdec027ad (from https://pypi.org/simple/numpy/) (requires-python:>=3.9)
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Skipping link: not a file: https://pypi.org/simple/numpy/
Given no hashes to check 153 links for project 'numpy': discarding no candidates
Collecting numpy
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  Downloading numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.3/19.3 MB 46.8 MB/s eta 0:00:00
  Added numpy from https://files.pythonhosted.org/packages/d6/a8/6a2419c40c7b6f7cb4ef52c532c88e55490c4fa92885964757d507adddce/numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=6d7696c615765091cc5093f76fd1fa069870304beaccfd58b5dcc69e55ef49c1 (from py3nj) to build tracker '/tmp/pip-req-tracker-0k5qwjil'
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Created temporary directory: /tmp/pip-unpack-f26533xh
Building wheels for collected packages: py3nj
  Created temporary directory: /tmp/pip-wheel-vkm6cax0
  Destination directory: /tmp/pip-wheel-vkm6cax0
  Building wheel for py3nj (pyproject.toml): started
  Running command Building wheel for py3nj (pyproject.toml)
  Building wheel for py3nj (pyproject.toml): finished with status 'done'
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Successfully built py3nj
Installing collected packages: numpy, py3nj

  changing mode of /home/dbutterfield3/Research/deep-contact-estimator/venv2/bin/f2py to 755
  changing mode of /home/dbutterfield3/Research/deep-contact-estimator/venv2/bin/numpy-config to 755

Successfully installed numpy-2.0.0 py3nj-0.2.1
Removed build tracker: '/tmp/pip-req-tracker-0k5qwjil'
DanielChaseButterfield commented 4 months ago

I changed the venv environment because I had to create a second one, after the first command's output got erased in the terminal (because it was too long). I also piped the streams to a file using python -m pip install --no-cache-dir -vvv py3nj > log2.txt 2>&1

kalekundert commented 4 months ago

Thanks for running those commands (and carefully reporting the actual commands you ran!). Unfortunately, it seemed to install successfully. I was hoping that it would fail, so I could compare to an unsuccessful log. As it is, that's pretty much the same log as I get when I install py3nj myself.

Do you think you could reproduce the initial failure, but using the extra verbose pip command I gave? If you can, let me know the exact commands used, and the paths to any pythons involved. Right now, it seems to me like maybe the failure only happens if you try to install py3nj with the system python; not with a conda environment or a virtual environment? If that's the case, then (i) maybe the issue is ultimately some sort of permission error and (ii) I feel obliged to say that installing packages into the system python is a bad idea; you can break your OS doing that. But maybe I'm totally off-base.