After installing in my Jupyter Notebook (as a container of JupyterLab as jovan user without access to root) the libmagic while having cmake 3.26.4 already installed in the conda env. I try to install install libmagic with pip:
pip install python-libmagic
but I keep getting error:
Collecting python-libmagic
Using cached python_libmagic-0.4.0-py3-none-any.whl
Collecting cffi==1.7.0 (from python-libmagic)
Using cached cffi-1.7.0.tar.gz (400 kB)
Preparing metadata (setup.py) ... done
Requirement already satisfied: pycparser in /opt/conda/envs/cho_env/lib/python3.10/site-packages (from cffi==1.7.0->python-libmagic) (2.21)
Building wheels for collected packages: cffi
Building wheel for cffi (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [254 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-310
creating build/lib.linux-x86_64-cpython-310/cffi
copying cffi/ffiplatform.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/cffi_opcode.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/verifier.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/commontypes.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/vengine_gen.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/setuptools_ext.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/vengine_cpy.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/recompiler.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/cparser.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/lock.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/backend_ctypes.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/__init__.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/model.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/api.py -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/_cffi_include.h -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/parse_c_type.h -> build/lib.linux-x86_64-cpython-310/cffi
copying cffi/_embedding.h -> build/lib.linux-x86_64-cpython-310/cffi
running build_ext
building '_cffi_backend' extension
creating build/temp.linux-x86_64-cpython-310
creating build/temp.linux-x86_64-cpython-310/c
gcc -pthread -B /opt/conda/envs/cho_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/envs/cho_env/include -fPIC -O2 -isystem /opt/conda/envs/cho_env/include -fPIC -DUSE__THREAD -I/usr/include/ffi -I/usr/include/libffi -I/opt/conda/envs/cho_env/include/python3.10 -c c/_cffi_backend.c -o build/temp.linux-x86_64-cpython-310/c/_cffi_backend.o
In file included from c/_cffi_backend.c:274:
c/minibuffer.h: In function ‘mb_ass_slice’:
c/minibuffer.h:66:5: warning: ‘PyObject_AsReadBuffer’ is deprecated [-Wdeprecated-declarations]
66 | if (PyObject_AsReadBuffer(other, &buffer, &buffer_len) < 0)
| ^~
In file included from /opt/conda/envs/cho_env/include/python3.10/genobject.h:12,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:110,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/abstract.h:343:17: note: declared here
343 | PyAPI_FUNC(int) PyObject_AsReadBuffer(PyObject *obj,
| ^~~~~~~~~~~~~~~~~~~~~
In file included from c/_cffi_backend.c:277:
c/file_emulator.h: In function ‘PyFile_AsFile’:
c/file_emulator.h:54:14: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
54 | mode = PyText_AsUTF8(ob_mode);
| ^
In file included from c/_cffi_backend.c:281:
c/wchar_helper.h: In function ‘_my_PyUnicode_AsSingleWideChar’:
c/wchar_helper.h:83:5: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
83 | Py_UNICODE *u = PyUnicode_AS_UNICODE(unicode);
| ^~~~~~~~~~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
In file included from c/_cffi_backend.c:281:
c/wchar_helper.h:84:5: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
84 | if (PyUnicode_GET_SIZE(unicode) == 1) {
| ^~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from c/_cffi_backend.c:281:
c/wchar_helper.h:84:5: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
84 | if (PyUnicode_GET_SIZE(unicode) == 1) {
| ^~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
In file included from c/_cffi_backend.c:281:
c/wchar_helper.h:84:5: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
84 | if (PyUnicode_GET_SIZE(unicode) == 1) {
| ^~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from c/_cffi_backend.c:281:
c/wchar_helper.h: In function ‘_my_PyUnicode_SizeAsWideChar’:
c/wchar_helper.h:99:5: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
99 | Py_ssize_t length = PyUnicode_GET_SIZE(unicode);
| ^~~~~~~~~~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from c/_cffi_backend.c:281:
c/wchar_helper.h:99:5: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
99 | Py_ssize_t length = PyUnicode_GET_SIZE(unicode);
| ^~~~~~~~~~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
In file included from c/_cffi_backend.c:281:
c/wchar_helper.h:99:5: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
99 | Py_ssize_t length = PyUnicode_GET_SIZE(unicode);
| ^~~~~~~~~~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from c/_cffi_backend.c:281:
c/wchar_helper.h: In function ‘_my_PyUnicode_AsWideChar’:
c/wchar_helper.h:118:5: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
118 | Py_UNICODE *u = PyUnicode_AS_UNICODE(unicode);
| ^~~~~~~~~~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
c/_cffi_backend.c: In function ‘ctypedescr_dealloc’:
c/_cffi_backend.c:352:23: error: lvalue required as left operand of assignment
352 | Py_REFCNT(ct) = 43;
| ^
c/_cffi_backend.c:355:23: error: lvalue required as left operand of assignment
355 | Py_REFCNT(ct) = 0;
| ^
c/_cffi_backend.c: In function ‘cast_to_integer_or_char’:
c/_cffi_backend.c:3331:26: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
3331 | PyUnicode_GET_SIZE(ob), ct->ct_name);
| ^~~~~~~~~~~~~~~~~~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
c/_cffi_backend.c:3331:26: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
3331 | PyUnicode_GET_SIZE(ob), ct->ct_name);
| ^~~~~~~~~~~~~~~~~~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
c/_cffi_backend.c:3331:26: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
3331 | PyUnicode_GET_SIZE(ob), ct->ct_name);
| ^~~~~~~~~~~~~~~~~~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
c/_cffi_backend.c: In function ‘b_complete_struct_or_union’:
c/_cffi_backend.c:4251:17: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations]
4251 | do_align = PyText_GetSize(fname) > 0;
| ^~~~~~~~
In file included from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:177:43: note: declared here
177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize(
| ^~~~~~~~~~~~~~~~~
c/_cffi_backend.c:4283:13: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations]
4283 | if (PyText_GetSize(fname) == 0 &&
| ^~
In file included from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:177:43: note: declared here
177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize(
| ^~~~~~~~~~~~~~~~~
c/_cffi_backend.c:4353:17: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations]
4353 | if (PyText_GetSize(fname) > 0) {
| ^~
In file included from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:177:43: note: declared here
177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize(
| ^~~~~~~~~~~~~~~~~
c/_cffi_backend.c: In function ‘prepare_callback_info_tuple’:
c/_cffi_backend.c:5214:5: warning: ‘PyEval_InitThreads’ is deprecated [-Wdeprecated-declarations]
5214 | PyEval_InitThreads();
| ^~~~~~~~~~~~~~~~~~
In file included from /opt/conda/envs/cho_env/include/python3.10/Python.h:130,
from c/_cffi_backend.c:2:
/opt/conda/envs/cho_env/include/python3.10/ceval.h:122:37: note: declared here
122 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void);
| ^~~~~~~~~~~~~~~~~~
c/_cffi_backend.c: In function ‘b_callback’:
c/_cffi_backend.c:5255:5: warning: ‘ffi_prep_closure’ is deprecated: use ffi_prep_closure_loc instead [-Wdeprecated-declarations]
5255 | if (ffi_prep_closure(closure, &cif_descr->cif,
| ^~
In file included from c/_cffi_backend.c:15:
/opt/conda/envs/cho_env/include/ffi.h:347:1: note: declared here
347 | ffi_prep_closure (ffi_closure*,
| ^~~~~~~~~~~~~~~~
In file included from /opt/conda/envs/cho_env/include/python3.10/unicodeobject.h:1046,
from /opt/conda/envs/cho_env/include/python3.10/Python.h:83,
from c/_cffi_backend.c:2:
c/ffi_obj.c: In function ‘_ffi_type’:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:744:29: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
744 | #define _PyUnicode_AsString PyUnicode_AsUTF8
| ^~~~~~~~~~~~~~~~
c/_cffi_backend.c:72:25: note: in expansion of macro ‘_PyUnicode_AsString’
72 | # define PyText_AS_UTF8 _PyUnicode_AsString
| ^~~~~~~~~~~~~~~~~~~
c/ffi_obj.c:191:32: note: in expansion of macro ‘PyText_AS_UTF8’
191 | char *input_text = PyText_AS_UTF8(arg);
| ^~~~~~~~~~~~~~
c/lib_obj.c: In function ‘lib_build_cpython_func’:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:744:29: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
744 | #define _PyUnicode_AsString PyUnicode_AsUTF8
| ^~~~~~~~~~~~~~~~
c/_cffi_backend.c:72:25: note: in expansion of macro ‘_PyUnicode_AsString’
72 | # define PyText_AS_UTF8 _PyUnicode_AsString
| ^~~~~~~~~~~~~~~~~~~
c/lib_obj.c:129:21: note: in expansion of macro ‘PyText_AS_UTF8’
129 | char *libname = PyText_AS_UTF8(lib->l_libname);
| ^~~~~~~~~~~~~~
c/lib_obj.c: In function ‘lib_build_and_cache_attr’:
/opt/conda/envs/cho_env/include/python3.10/cpython/unicodeobject.h:744:29: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
744 | #define _PyUnicode_AsString PyUnicode_AsUTF8
| ^~~~~~~~~~~~~~~~
c/_cffi_backend.c:71:24: note: in expansion of macro ‘_PyUnicode_AsString’
71 | # define PyText_AsUTF8 _PyUnicode_AsString /* PyUnicode_AsUTF8 in Py3.3 */
| ^~~~~~~~~~~~~~~~~~~
c/lib_obj.c:208:15: note: in expansion of macro ‘PyText_AsUTF8’
208 | char *s = PyText_AsUTF8(name);
| ^~~~~~~~~~~~~
In file included from c/cffi1_module.c:16,
from c/_cffi_backend.c:6636:
c/lib_obj.c: In function ‘lib_getattr’:
c/lib_obj.c:506:7: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
506 | p = PyText_AsUTF8(name);
| ^
In file included from c/cffi1_module.c:19,
from c/_cffi_backend.c:6636:
c/call_python.c: In function ‘_get_interpstate_dict’:
c/call_python.c:20:30: error: dereferencing pointer to incomplete type ‘PyInterpreterState’ {aka ‘struct _is’}
20 | builtins = tstate->interp->builtins;
| ^~
c/call_python.c: In function ‘_ffi_def_extern_decorator’:
c/call_python.c:73:11: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
73 | s = PyText_AsUTF8(name);
| ^
error: command '/usr/bin/gcc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for cffi
Running setup.py clean for cffi
Failed to build cffi
ERROR: Could not build wheels for cffi, which is required to install pyproject.toml-based projects```
how can I fix this?
Correct me, if I'm wrong, but I guess you want to install the python bindings for libmagic.
Find them here: https://pypi.org/project/python-magic/ and here https://github.com/ahupp/python-magic
pip install python-magic
There was an issue request 6 years ago by its maintainer to the person sitting on the abandoned "python-libmagic" name to change it, to no avail.
The pip package "libmagic" from here https://pypi.org/project/libmagic/ is an even older bindings (basically a python interface to the library) and not the same as the library either. This package looks abandoned as well.
And this abandoned pip package seems to interfere with the conda package that you need to install, so:
pip uninstall libmagic
And with conda install the actual library like you did:
conda install -c conda-forge libmagic
Just for reference in other cases, one can install system packages for libmagic, for instance:
apt install libmagic1 libmagic-dev