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sidhomj / DeepTCR

Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
https://sidhomj.github.io/DeepTCR/
MIT License
113 stars 40 forks source link

Installation issue (v1.4, v2.0) #87

Open zyzllik opened 1 month ago

zyzllik commented 1 month ago

Hi!

I have some issues during installation of the package. It works for all versions until 1.3., but not for the later ones.

v1.4 cannot be found, which is very weird since pip3 lists 1.4.x versions:

$ pip3 install DeepTCR==1.4
ERROR: Could not find a version that satisfies the requirement DeepTCR==1.4 (from versions: 1.0.0, 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.1.0, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.2.4, 1.2.5, 1.2.6, 1.2.7, 1.2.8, 1.2.9, 1.2.10, 1.2.11, 1.2.12, 1.2.13, 1.2.14, 1.2.15, 1.2.16, 1.2.17, 1.2.18, 1.2.19, 1.2.20, 1.2.21, 1.2.23, 1.2.24, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.3.4, 1.3.5, 1.3.6, 1.3.7, 1.3.8, 1.3.8.1, 1.3.8.2, 1.3.9, 1.3.9.1, 1.3.10, 1.3.11, 1.3.12, 1.3.13, 1.3.14, 1.3.15, 1.3.16, 1.3.17, 1.3.18, 1.3.19, 1.3.20, 1.3.21, 1.3.22, 1.3.23, 1.3.24, 1.3.25, 1.3.26, 1.3.27, 1.3.28, 1.3.29, 1.3.30, 1.3.31, 1.3.32, 1.4.1, 1.4.2, 1.4.2.1, 1.4.3, 1.4.4, 1.4.5, 1.4.6, 1.4.7, 1.4.8, 1.4.9, 1.4.10, 1.4.11, 1.4.12, 1.4.13, 1.4.14, 1.4.15, 1.4.16, 1.4.17, 1.4.18, 1.4.19, 1.4.20, 1.4.21, 1.4.22, 1.4.23, 2.0, 2.0.1, 2.0.2, 2.0.3, 2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.9, 2.0.10, 2.0.11, 2.0.12, 2.1.0, 2.1.1, 2.1.2, 2.1.3, 2.1.4, 2.1.5, 2.1.6, 2.1.7, 2.1.8, 2.1.9, 2.1.10, 2.1.11, 2.1.12, 2.1.13, 2.1.14, 2.1.15, 2.1.16, 2.1.17, 2.1.18, 2.1.19, 2.1.20, 2.1.21, 2.1.22, 2.1.23, 2.1.24, 2.1.25, 2.1.26, 2.1.27)
ERROR: No matching distribution found for DeepTCR==1.4

During installation of v2.0 I get the following error:

$ pip3 install DeepTCR==2.0
Collecting DeepTCR==2.0
  Downloading DeepTCR-2.0.tar.gz (214 kB)
  Preparing metadata (setup.py) ... done
Collecting absl-py==0.11.0 (from DeepTCR==2.0)
  Using cached absl_py-0.11.0-py3-none-any.whl.metadata (2.4 kB)
Collecting astunparse==1.6.3 (from DeepTCR==2.0)
  Using cached astunparse-1.6.3-py2.py3-none-any.whl.metadata (4.4 kB)
Collecting biopython==1.76 (from DeepTCR==2.0)
  Using cached biopython-1.76.tar.gz (16.3 MB)
  Preparing metadata (setup.py) ... done
Collecting cachetools==4.1.1 (from DeepTCR==2.0)
  Using cached cachetools-4.1.1-py3-none-any.whl.metadata (4.4 kB)
Collecting certifi==2020.12.5 (from DeepTCR==2.0)
  Using cached certifi-2020.12.5-py2.py3-none-any.whl.metadata (3.0 kB)
Collecting chardet==3.0.4 (from DeepTCR==2.0)
  Using cached chardet-3.0.4-py2.py3-none-any.whl.metadata (3.2 kB)
Collecting cycler==0.10.0 (from DeepTCR==2.0)
  Using cached cycler-0.10.0-py2.py3-none-any.whl.metadata (722 bytes)
Collecting gast==0.3.3 (from DeepTCR==2.0)
  Using cached gast-0.3.3-py2.py3-none-any.whl.metadata (1.1 kB)
Collecting google-auth==1.23.0 (from DeepTCR==2.0)
  Using cached google_auth-1.23.0-py2.py3-none-any.whl.metadata (3.3 kB)
Collecting google-auth-oauthlib==0.4.2 (from DeepTCR==2.0)
  Using cached google_auth_oauthlib-0.4.2-py2.py3-none-any.whl.metadata (2.4 kB)
Collecting google-pasta==0.2.0 (from DeepTCR==2.0)
  Using cached google_pasta-0.2.0-py3-none-any.whl.metadata (814 bytes)
Collecting grpcio==1.34.0 (from DeepTCR==2.0)
  Using cached grpcio-1.34.0.tar.gz (21.0 MB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [16 lines of output]
      /tmp/pip-install-zej631z9/grpcio_d2a2786d00284430a6efaa264fb9383c/setup.py:31: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
        import pkg_resources
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-zej631z9/grpcio_d2a2786d00284430a6efaa264fb9383c/setup.py", line 229, in <module>
          if check_linker_need_libatomic():
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-install-zej631z9/grpcio_d2a2786d00284430a6efaa264fb9383c/setup.py", line 176, in check_linker_need_libatomic
          cpp_test = subprocess.Popen([cxx, '-x', 'c++', '-std=c++11', '-'],
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/mnt/Data/Liza/deeptcr_env/lib/python3.12/subprocess.py", line 1026, in __init__
          self._execute_child(args, executable, preexec_fn, close_fds,
        File "/mnt/Data/Liza/deeptcr_env/lib/python3.12/subprocess.py", line 1955, in _execute_child
          raise child_exception_type(errno_num, err_msg, err_filename)
      FileNotFoundError: [Errno 2] No such file or directory: 'c++'
      [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.