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eggnogdb / eggnog-mapper

Fast genome-wide functional annotation through orthology assignment
http://eggnog-mapper.embl.de
GNU Affero General Public License v3.0
563 stars 105 forks source link

errors while installing the dependencies #526

Open faithoni opened 3 months ago

faithoni commented 3 months ago

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 1

pip 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 <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/jlap/fetch.py", line 259, in download_and_hash
    repodata.write(block)
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/jlap/fetch.py", line 218, in write
    return self.backing.write(b)
           ^^^^^^^^^^^^^^^^^^^^^
OSError: [Errno 122] Disk quota exceeded

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/exception_handler.py", line 18, in __call__
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/cli/main.py", line 84, in main_subshell
    exit_code = do_call(args, parser)
                ^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/cli/conda_argparse.py", line 200, in do_call
    result = getattr(module, func_name)(args, parser)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/notices/core.py", line 132, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/cli/main_install.py", line 152, in execute
    return install(args, parser, "install")
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/cli/install.py", line 377, in install
    unlink_link_transaction = solver.solve_for_transaction(
                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/core/solve.py", line 153, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(
                               ^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/core/solve.py", line 222, in solve_for_diff
    final_precs = self.solve_final_state(
                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda_libmamba_solver/solver.py", line 207, in solve_final_state
    index = IndexHelper(
            ^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda_libmamba_solver/index.py", line 136, in __init__
    self._index = self._load_channels()
                  ^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda_libmamba_solver/index.py", line 332, in _load_channels
    jsons = {url: str(path) for (url, path) in executor.map(self._fetch_channel, urls)}
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 619, in result_iterator
    yield _result_or_cancel(fs.pop())
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 317, in _result_or_cancel
    return fut.result(timeout)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 456, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/home/faith/miniconda3/lib/python3.12/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda_libmamba_solver/index.py", line 254, in _fetch_channel
    json_path, _ = subdir_data.repo_fetch.fetch_latest_path()
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/__init__.py", line 749, in fetch_latest_path
    _, state = self.fetch_latest()
               ^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/__init__.py", line 847, in fetch_latest
    raw_repodata = repo.repodata_parsed(cache.state)  # type: ignore
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/jlap/interface.py", line 87, in repodata_parsed
    repodata_json_or_none = fetch.request_url_jlap_state(
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/jlap/fetch.py", line 309, in request_url_jlap_state
    response = download_and_hash(
               ^^^^^^^^^^^^^^^^^^
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/jlap/fetch.py", line 257, in download_and_hash
    with writer as repodata:
  File "/home/faith/miniconda3/lib/python3.12/site-packages/conda/gateways/repodata/jlap/fetch.py", line 221, in close
    self.backing.close()
OSError: [Errno 122] Disk quota exceeded

$ /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=

 active environment : base
active env location : /home/faith/miniconda3
        shell level : 1
   user config file : /home/faith/.condarc

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

knarrff commented 2 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