Open faithoni opened 3 months ago
Stumbling across this as well. The following from https://docs.python.org/3/c-api/structures.html#c.Py_TYPE might be related: "_Changed in version 3.11: PyTYPE() is changed to an inline static function. The parameter type is no longer const PyObject*."
The issue was opened in biopython: https://github.com/biopython/biopython/issues/4643 and closed March 1 2024. This means the fix should be in version 184 of biopython. Thus, one way to fix this might be by upgrading the dependency on biopython to that version. However, this is only necessary for Python 3.11: users of older versions would not see that problem and might not want the upgrade.
As a sidenote: assuming you have all dependencies already installed, this might help as well:
pip install --no-deps eggnog_mapper
Dear authors, I tried to install the dependencies for the tool after cloning the github but I get error messages with all three methods.
python setup.py install
check.warn(importable) Bio/cpairwise2module.c: In function ‘_get_match_score’: Bio/cpairwise2module.c:58:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 58 | if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist))) | ^~ In file included from /home/faith/miniconda3/include/python3.12/Python.h:95, from Bio/cpairwise2module.c:14: /home/faith/miniconda3/include/python3.12/ceval.h:27:43: note: declared here 27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^
~~~~~~~~ Bio/trie.c: In function ‘_with_prefix_helper.constprop’: Bio/trie.c:595:13: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 595 | strncat(current_key, suffix, suffixlen); | ^~~~~~~~~~~ Bio/trie.c:561:21: note: length computed here 561 | suffixlen = strlen(suffix); | ^~~~~~ Bio/triemodule.c: In function ‘PyInit_trie’: Bio/triemodule.c:837:25: error: lvalue required as left operand of assignment 837 | Py_TYPE(&Trie_Type) = &PyType_Type; | ^ error: Setup script exited with error: command '/usr/lib64/ccache/gcc' failed with exit code 1pip install -r requirements.txt
note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for biopython Running setup.py clean for biopython Failed to build biopython ERROR: Could not build wheels for biopython, which is required to install pyproject.toml-based projects
conda install --file requirements.txt
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
$ /home/faith/miniconda3/bin/conda install --file requirements.txt
environment variables: CIO_TEST=
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/faith/miniconda3/bin/conda
CONDA_PREFIX=/home/faith/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/faith/miniconda3/bin/python
CONDA_ROOT=/home/faith/miniconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=
LD_PRELOAD=
MANPATH=/home/faith/.nvm/versions/node/v21.7.3/share/man:/software/lmod/lmod/s
hare/man:
MODULEPATH=/software/skylake/modules/all/Core:/software/modulefiles
PATH=/work/faith/eggnog-mapper:/work/faith/eggnog-
mapper/eggnogmapper/bin:/home/faith/bin:/home/faith/ncbi-blast-
2.14.0+/bin:/home/faith/.nvm/versions/node/v21.7.3/bin:/work/faith/bla
st/ncbi-blast-
2.15.0+/bin:/home/faith/miniconda3/bin:/home/faith/miniconda3/condabin
:/global/local/bin:/global/local/just-dont-bin:/usr/lib64/ccache:/usr/
local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
populated config files : /home/faith/.condarc conda version : 24.5.0 conda-build version : not installed python version : 3.12.2.final.0 solver : libmamba (default) virtual packages : __archspec=1=skylake_avx512 conda=24.5.0=0 glibc=2.34=0 linux=5.14.0=0 unix=0=0 base environment : /home/faith/miniconda3 (writable) conda av data dir : /home/faith/miniconda3/etc/conda conda av metadata url : None channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /home/faith/miniconda3/pkgs /home/faith/.conda/pkgs envs directories : /home/faith/miniconda3/envs /home/faith/.conda/envs platform : linux-64 user-agent : conda/24.5.0 requests/2.32.2 CPython/3.12.2 Linux/5.14.0-284.11.1.el9_2.x86_64 rocky/9.1 glibc/2.34 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8 aau/0.4.4 c/. s/. e/. UID:GID : 66819:2400 netrc file : None offline mode : False
An unexpected error has occurred. Conda has prepared the above report. If you suspect this error is being caused by a malfunctioning plugin, consider using the --no-plugins option to turn off plugins.
Example: conda --no-plugins install
Alternatively, you can set the CONDA_NO_PLUGINS environment variable on the command line to run the command without plugins enabled.
Example: CONDA_NO_PLUGINS=true conda install
If submitted, this report will be used by core maintainers to improve future releases of conda. Would you like conda to send this report to the core maintainers? [y/N]: Timeout reached. No report sent.
please how can i handle this? Thank you