lap dependency does not install correctly on Linux

[bootcap]

I am trying to setup Self-Orgaizing-Gaussian, and I got a error when install submodule PLAS. I have googled the error but I got nothing.
Could you help me figure out why?

The error massage goes like this:
...
...
In file included from /home/cap/micromamba/envs/sogs/include/python3.10/Python.h:74,
from lap/_lapjv.cpp:4:
lap/_lapjv.cpp: In function ‘PyObject* __pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr*)’:
lap/_lapjv.cpp:5068:41: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘subarray’
5068 | __Pyx_INCREF(((PyObject*)__pyx_v_d->subarray->shape));
| ^~~~~~~~
/home/cap/micromamba/envs/sogs/include/python3.10/object.h:112:41: note: in definition of macro ‘_PyObject_CAST’
112 | #define _PyObject_CAST(op) ((PyObject*)(op))
| ^~
lap/_lapjv.cpp:1146:27: note: in expansion of macro ‘Py_INCREF’
1146 | #define __Pyx_INCREF(r) Py_INCREF(r)
| ^~~~~~~~~
lap/_lapjv.cpp:5068:5: note: in expansion of macro ‘__Pyx_INCREF’
5068 | __Pyx_INCREF(((PyObject*)__pyx_v_d->subarray->shape));
| ^~~~~~~~~~~~
lap/_lapjv.cpp:5069:38: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘subarray’
5069 | __pyx_r = ((PyObject*)__pyx_v_d->subarray->shape);
| ^~~~~~~~
lap/_lapjv.cpp: In function ‘char* __pyx_f_5numpy__util_dtypestring(PyArray_Descr*, char*, char*, int*)’:
lap/_lapjv.cpp:5164:31: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’
5164 | if (unlikely(__pyx_v_descr->names == Py_None)) {
| ^~~~~
lap/_lapjv.cpp:767:43: note: in definition of macro ‘unlikely’
767 | #define unlikely(x) __builtin_expect(!!(x), 0)
| ^
lap/_lapjv.cpp:5168:30: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’
5168 | __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
| ^~~~~
lap/_lapjv.cpp:5187:33: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’
5187 | if (unlikely(__pyx_v_descr->fields == Py_None)) {
| ^~~~~~
lap/_lapjv.cpp:767:43: note: in definition of macro ‘unlikely’
767 | #define unlikely(x) __builtin_expect(!!(x), 0)
| ^
lap/_lapjv.cpp:5191:53: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’
5191 | __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 806, __pyx_L1_error)
| ^~~~~~
lap/_lapjv.cpp:5392:81: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘elsize’
5392 | (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize);
| ^~~~~~
In file included from /home/cap/micromamba/envs/sogs/include/python3.10/unicodeobject.h:1046,
from /home/cap/micromamba/envs/sogs/include/python3.10/Python.h:83,
from lap/_lapjv.cpp:4:
lap/_lapjv.cpp: In function ‘int __Pyx_ParseOptionalKeywords(PyObject*, PyObject***, PyObject*, PyObject**, Py_ssize_t, const char*)’:
/home/cap/micromamba/envs/sogs/include/python3.10/cpython/unicodeobject.h:451:61: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations]
....
....
error: Command "g++ -pthread -B /home/cap/micromamba/envs/sogs/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/cap/micromamba/envs/sogs/include -fPIC -O2 -isystem /home/cap/micromamba/envs/sogs/include -fPIC -I/home/cap/micromamba/envs/sogs/lib/python3.10/site-packages/numpy/_core/include -Ilap -I/home/cap/micromamba/envs/sogs/lib/python3.10/site-packages/numpy/_core/include -Ibuild/src.linux-x86_64-3.10/numpy/distutils/include -I/home/cap/micromamba/envs/sogs/include/python3.10 -c lap/_lapjv.cpp -o build/temp.linux-x86_64-cpython-310/lap/_lapjv.o -MMD -MF build/temp.linux-x86_64-cpython-310/lap/_lapjv.o.d -msse -msse2 -msse3" failed with exit status 1
INFO:
########### EXT COMPILER OPTIMIZATION ###########
INFO: Platform :
Architecture: x64
Compiler : gcc

  CPU baseline  :
    Requested   : 'min'
    Enabled     : SSE SSE2 SSE3
    Flags       : -msse -msse2 -msse3
    Extra checks: none

  CPU dispatch  :
    Requested   : 'max -xop -fma4'
    Enabled     : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2 AVX512F AVX512CD AVX512_KNL AVX512_KNM AVX512_SKX AVX512_CLX AVX512_CNL AVX512_ICL
    Generated   : none
  INFO: CCompilerOpt.cache_flush[864] : write cache to path -> /tmp/pip-install-fbyoq_ra/lap_3d1ab2a8493e44b5a97065660169e633/build/temp.linux-x86_64-cpython-310/ccompiler_opt_cache_ext.py
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for lap
Running setup.py clean for lap
Successfully built plas
Failed to build lap
ERROR: Could not build wheels for lap, which is required to install pyproject.toml-based projects

[w-m]

I can have a look at the problem next week. As an interim quick fix, do the following:

• check out the code locally
• edit setup.py and remove the line with "lap" (which is only used for FLAS comparison, not for PLAS)
• pip install -e local/dir/to/PLAS

As the error you show is with installing lap, the install should then hopefully go through.

[bootcap]

I can have a look at the problem next week. As an interim quick fix, do the following:

* check out the code locally

* edit setup.py and remove the line with "lap" (which is only used for FLAS comparison, not for PLAS)

* pip install -e local/dir/to/PLAS

As the error you show is with installing lap, the install should then hopefully go through.

Problem solved! Thanks for your help!

[Sevenyt777]

Good evening everyone, I'm new to github and the world of programming, in reality I've been focusing on python programming since December 2023, I would like to know if anyone could help me with a python pip installation error, I'm looking for how to fix it But I can't find it, which is slowing me down in the process of various programs, I hope you can help me!

[w-m]

@Sevenyt777 this is the issue tracker of the PLAS project. It is not the right place to get support for installing a Python environment.

(You are getting a permissions error, as your Python was installed for all users, in the Program Files folder. And you're trying to install pip there, with a Terminal that does not have the right permissions. I suggest you follow a tutorial on how to install Python (+Pip) for the current user only, with the correct permissions.)

[Sevenyt777]

OK!! Got it, thanks for the help, I'll look for a new tutorial