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Error Attempting to Run medaka after pip install #544

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foreignsand opened this issue Dec 4, 2024 · 9 comments
Open

Error Attempting to Run medaka after pip install #544

foreignsand opened this issue Dec 4, 2024 · 9 comments
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@foreignsand
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Describe the bug
A clear and concise description of what the bug is including the command that you have run.

I have successfully installed medaka and all dependencies in a venv using the instructions for installing using pip.

(medaka) (base) lemurbear@MacBook-Pro-10 bin % pip install medaka
Requirement already satisfied: medaka in ./medaka/lib/python3.8/site-packages (1.12.1)

Logging
When I attempt to run medaka, however, I get the following error:

. ./medaka/bin/activate
(medaka) (base) lemurbear@MacBook-Pro-10 bin % medaka
Traceback (most recent call last):
  File "/usr/local/bin/medaka/bin/medaka", line 5, in <module>
    from medaka.medaka import main
  File "/usr/local/bin/medaka/lib/python3.8/site-packages/medaka/medaka.py", line 7, in <module>
    import medaka.common
  File "/usr/local/bin/medaka/lib/python3.8/site-packages/medaka/common.py", line 19, in <module>
    import libmedaka
ImportError: dlopen(/usr/local/bin/medaka/lib/python3.8/site-packages/libmedaka.abi3.so, 0x0002): symbol not found in flat namespace '_libdeflate_alloc_compressor'

Environment (if you do not have a GPU, write No GPU):

  • Installation method: pip install
  • OS: MacOS 15.1
  • medaka version: 1.12.1
  • GPU model: No GPU
  • Nvidia driver version: Unknown
  • CUDA version: Unknown
  • cuDNN version: Unknown

Additional context
libdeflate is installed and I have reinstalled it with pip, but the error message keeps getting thrown.

Any help would be much appreciated!
@foreignsand foreignsand added the bug label Dec 4, 2024
@cjw85
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cjw85 commented Dec 4, 2024

From the fact that you shell prompt contains both (medaka) and (base) I would guess that you have created a python virtual environment inside a base conda environment. I would not recommend doing this, and instead deactivate the conda environment before creating and using a python virtual environment.

@foreignsand
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foreignsand commented Dec 5, 2024 •
edited
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i uninstalled medaka from within the conda base environment, deactivated the base environment, and reinstalled medaka using pip in the virtual environment and i am still getting the same error:

Installing collected packages: medaka
Successfully installed medaka-1.12.1
(medaka) lemurbear@MacBook-Pro-10 bin % medaka
Traceback (most recent call last):
  File "/usr/local/bin/medaka/bin/medaka", line 5, in <module>
    from medaka.medaka import main
  File "/usr/local/bin/medaka/lib/python3.8/site-packages/medaka/medaka.py", line 7, in <module>
    import medaka.common
  File "/usr/local/bin/medaka/lib/python3.8/site-packages/medaka/common.py", line 19, in <module>
    import libmedaka
ImportError: dlopen(/usr/local/bin/medaka/lib/python3.8/site-packages/libmedaka.abi3.so, 0x0002): symbol not found in flat namespace '_libdeflate_alloc_compressor'

i was really hoping reinstalling outside of the conda env would work!

@cjw85
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cjw85 commented Dec 5, 2024

Can you please provide the full output of the pip install command having created a new virtual environment.

@foreignsand
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of course! here it is:

lemurbear@MacBook-Pro-10 bin % . ./medaka/bin/activate
(medaka) lemurbear@MacBook-Pro-10 bin % pip install --upgrade pip
Requirement already satisfied: pip in ./medaka/lib/python3.8/site-packages (24.3.1)
(medaka) lemurbear@MacBook-Pro-10 bin % pip install medaka
Collecting medaka
  Using cached medaka-2.0.1.tar.gz (9.6 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: cffi in ./medaka/lib/python3.8/site-packages (from medaka) (1.15.0)
Requirement already satisfied: edlib in ./medaka/lib/python3.8/site-packages (from medaka) (1.3.9.post1)
Requirement already satisfied: h5py~=3.10.0 in ./medaka/lib/python3.8/site-packages (from medaka) (3.10.0)
Requirement already satisfied: intervaltree in ./medaka/lib/python3.8/site-packages (from medaka) (3.1.0)
Requirement already satisfied: numpy<2.0.0,>=1.21.0 in ./medaka/lib/python3.8/site-packages (from medaka) (1.24.4)
Collecting ont-mappy (from medaka)
  Using cached ont_mappy-2.28.tar.gz (136 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: ont-fast5-api in ./medaka/lib/python3.8/site-packages (from medaka) (4.1.3)
Requirement already satisfied: ont-parasail in ./medaka/lib/python3.8/site-packages (from medaka) (1.3.4)
Requirement already satisfied: pysam>=0.16.0.1 in ./medaka/lib/python3.8/site-packages (from medaka) (0.22.1)
Requirement already satisfied: pyspoa>=0.2.1 in ./medaka/lib/python3.8/site-packages (from medaka) (0.2.1)
Requirement already satisfied: requests in ./medaka/lib/python3.8/site-packages (from medaka) (2.32.3)
INFO: pip is looking at multiple versions of medaka to determine which version is compatible with other requirements. This could take a while.
Collecting medaka
  Using cached medaka-2.0.0.tar.gz (9.6 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
  Using cached medaka-1.12.1-cp38-cp38-macosx_10_9_x86_64.whl
Requirement already satisfied: grpcio in ./medaka/lib/python3.8/site-packages (from medaka) (1.68.1)
Requirement already satisfied: tensorflow~=2.10.0 in ./medaka/lib/python3.8/site-packages (from medaka) (2.10.1)
Requirement already satisfied: mappy in ./medaka/lib/python3.8/site-packages (from medaka) (2.28)
Requirement already satisfied: wurlitzer in ./medaka/lib/python3.8/site-packages (from medaka) (3.1.1)
Requirement already satisfied: pycparser in ./medaka/lib/python3.8/site-packages (from cffi->medaka) (2.22)
Requirement already satisfied: absl-py>=1.0.0 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (2.1.0)
Requirement already satisfied: astunparse>=1.6.0 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (1.6.3)
Requirement already satisfied: flatbuffers>=2.0 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (24.3.25)
Requirement already satisfied: gast<=0.4.0,>=0.2.1 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (0.4.0)
Requirement already satisfied: google-pasta>=0.1.1 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (0.2.0)
Requirement already satisfied: keras-preprocessing>=1.1.1 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (1.1.2)
Requirement already satisfied: libclang>=13.0.0 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (18.1.1)
Requirement already satisfied: opt-einsum>=2.3.2 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (3.4.0)
Requirement already satisfied: packaging in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (24.2)
Requirement already satisfied: protobuf<3.20,>=3.9.2 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (3.19.6)
Requirement already satisfied: setuptools in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (41.2.0)
Requirement already satisfied: six>=1.12.0 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (1.17.0)
Requirement already satisfied: termcolor>=1.1.0 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (2.4.0)
Requirement already satisfied: typing-extensions>=3.6.6 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (4.12.2)
Requirement already satisfied: wrapt>=1.11.0 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (1.17.0)
Requirement already satisfied: tensorflow-io-gcs-filesystem>=0.23.1 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (0.34.0)
Requirement already satisfied: tensorboard<2.11,>=2.10 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (2.10.1)
Requirement already satisfied: tensorflow-estimator<2.11,>=2.10.0 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (2.10.0)
Requirement already satisfied: keras<2.11,>=2.10.0 in ./medaka/lib/python3.8/site-packages (from tensorflow~=2.10.0->medaka) (2.10.0)
Requirement already satisfied: sortedcontainers<3.0,>=2.0 in ./medaka/lib/python3.8/site-packages (from intervaltree->medaka) (2.4.0)
Requirement already satisfied: progressbar33>=2.3.1 in ./medaka/lib/python3.8/site-packages (from ont-fast5-api->medaka) (2.4)
Requirement already satisfied: charset-normalizer<4,>=2 in ./medaka/lib/python3.8/site-packages (from requests->medaka) (3.4.0)
Requirement already satisfied: idna<4,>=2.5 in ./medaka/lib/python3.8/site-packages (from requests->medaka) (3.10)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./medaka/lib/python3.8/site-packages (from requests->medaka) (2.2.3)
Requirement already satisfied: certifi>=2017.4.17 in ./medaka/lib/python3.8/site-packages (from requests->medaka) (2024.8.30)
Requirement already satisfied: wheel<1.0,>=0.23.0 in ./medaka/lib/python3.8/site-packages (from astunparse>=1.6.0->tensorflow~=2.10.0->medaka) (0.45.1)
Requirement already satisfied: google-auth<3,>=1.6.3 in ./medaka/lib/python3.8/site-packages (from tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (2.36.0)
Requirement already satisfied: google-auth-oauthlib<0.5,>=0.4.1 in ./medaka/lib/python3.8/site-packages (from tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (0.4.6)
Requirement already satisfied: markdown>=2.6.8 in ./medaka/lib/python3.8/site-packages (from tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (3.7)
Requirement already satisfied: tensorboard-data-server<0.7.0,>=0.6.0 in ./medaka/lib/python3.8/site-packages (from tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (0.6.1)
Requirement already satisfied: tensorboard-plugin-wit>=1.6.0 in ./medaka/lib/python3.8/site-packages (from tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (1.8.1)
Requirement already satisfied: werkzeug>=1.0.1 in ./medaka/lib/python3.8/site-packages (from tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (3.0.6)
Requirement already satisfied: cachetools<6.0,>=2.0.0 in ./medaka/lib/python3.8/site-packages (from google-auth<3,>=1.6.3->tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (5.5.0)
Requirement already satisfied: pyasn1-modules>=0.2.1 in ./medaka/lib/python3.8/site-packages (from google-auth<3,>=1.6.3->tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (0.4.1)
Requirement already satisfied: rsa<5,>=3.1.4 in ./medaka/lib/python3.8/site-packages (from google-auth<3,>=1.6.3->tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (4.9)
Requirement already satisfied: requests-oauthlib>=0.7.0 in ./medaka/lib/python3.8/site-packages (from google-auth-oauthlib<0.5,>=0.4.1->tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (2.0.0)
Requirement already satisfied: importlib-metadata>=4.4 in ./medaka/lib/python3.8/site-packages (from markdown>=2.6.8->tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (8.5.0)
Requirement already satisfied: MarkupSafe>=2.1.1 in ./medaka/lib/python3.8/site-packages (from werkzeug>=1.0.1->tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (2.1.5)
Requirement already satisfied: zipp>=3.20 in ./medaka/lib/python3.8/site-packages (from importlib-metadata>=4.4->markdown>=2.6.8->tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (3.20.2)
Requirement already satisfied: pyasn1<0.7.0,>=0.4.6 in ./medaka/lib/python3.8/site-packages (from pyasn1-modules>=0.2.1->google-auth<3,>=1.6.3->tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (0.6.1)
Requirement already satisfied: oauthlib>=3.0.0 in ./medaka/lib/python3.8/site-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard<2.11,>=2.10->tensorflow~=2.10.0->medaka) (3.2.2)
Installing collected packages: medaka
Successfully installed medaka-1.12.1
(medaka) lemurbear@MacBook-Pro-10 bin % medaka
Traceback (most recent call last):
  File "/usr/local/bin/medaka/bin/medaka", line 5, in <module>
    from medaka.medaka import main
  File "/usr/local/bin/medaka/lib/python3.8/site-packages/medaka/medaka.py", line 7, in <module>
    import medaka.common
  File "/usr/local/bin/medaka/lib/python3.8/site-packages/medaka/common.py", line 19, in <module>
    import libmedaka
ImportError: dlopen(/usr/local/bin/medaka/lib/python3.8/site-packages/libmedaka.abi3.so, 0x0002): symbol not found in flat namespace '_libdeflate_alloc_compressor'

@cjw85
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cjw85 commented Dec 5, 2024

I'm not entirely sure what is happening here. Pip is seemingly referencing three different versions of medaka in that logging before finally settling on a rather old version.

It references also x86, is you MacBook an Intel based Mac?

@foreignsand
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it is an intel-based mac

@foreignsand
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now i've deleted the original medaka virtual environment and recreated it and am getting a completely different error when trying to reinstall medaka:

(medaka) lemurbear@MacBook-Pro-10 bin % pip install medaka
Collecting medaka
  Using cached medaka-1.6.1.tar.gz (34.0 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [23 lines of output]
      Cannot import parasail, some features may not be available.
      Cannot import spoa, some features may not be available.
      Bundling models: ['r103_fast_g507', 'r103_fast_snp_g507', 'r103_fast_variant_g507', 'r103_hac_g507', 'r103_hac_snp_g507', 'r103_hac_variant_g507', 'r103_min_high_g345', 'r103_min_high_g360', 'r103_prom_high_g360', 'r103_prom_snp_g3210', 'r103_prom_variant_g3210', 'r103_sup_g507', 'r103_sup_snp_g507', 'r103_sup_variant_g507', 'r1041_e82_400bps_fast_g615', 'r1041_e82_400bps_fast_variant_g615', 'r1041_e82_400bps_hac_g615', 'r1041_e82_400bps_hac_variant_g615', 'r1041_e82_400bps_sup_g615', 'r1041_e82_400bps_sup_variant_g615', 'r104_e81_fast_g5015', 'r104_e81_fast_variant_g5015', 'r104_e81_hac_g5015', 'r104_e81_hac_variant_g5015', 'r104_e81_sup_g5015', 'r104_e81_sup_g610', 'r104_e81_sup_variant_g610', 'r10_min_high_g303', 'r10_min_high_g340', 'r941_e81_fast_g514', 'r941_e81_fast_variant_g514', 'r941_e81_hac_g514', 'r941_e81_hac_variant_g514', 'r941_e81_sup_g514', 'r941_e81_sup_variant_g514', 'r941_min_fast_g303', 'r941_min_fast_g507', 'r941_min_fast_snp_g507', 'r941_min_fast_variant_g507', 'r941_min_hac_g507', 'r941_min_hac_snp_g507', 'r941_min_hac_variant_g507', 'r941_min_high_g303', 'r941_min_high_g330', 'r941_min_high_g340_rle', 'r941_min_high_g344', 'r941_min_high_g351', 'r941_min_high_g360', 'r941_min_sup_g507', 'r941_min_sup_snp_g507', 'r941_min_sup_variant_g507', 'r941_prom_fast_g303', 'r941_prom_fast_g507', 'r941_prom_fast_snp_g507', 'r941_prom_fast_variant_g507', 'r941_prom_hac_g507', 'r941_prom_hac_snp_g507', 'r941_prom_hac_variant_g507', 'r941_prom_high_g303', 'r941_prom_high_g330', 'r941_prom_high_g344', 'r941_prom_high_g360', 'r941_prom_high_g4011', 'r941_prom_snp_g303', 'r941_prom_snp_g322', 'r941_prom_snp_g360', 'r941_prom_sup_g507', 'r941_prom_sup_snp_g507', 'r941_prom_sup_variant_g507', 'r941_prom_variant_g303', 'r941_prom_variant_g322', 'r941_prom_variant_g360', 'r941_sup_plant_g610', 'r941_sup_plant_variant_g610']
      Traceback (most recent call last):
        File "/usr/local/bin/medaka/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/usr/local/bin/medaka/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/usr/local/bin/medaka/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/4n/0ghjrzsd4g393zjlgxy9ympc0000gn/T/pip-build-env-izk_tneb/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 334, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/4n/0ghjrzsd4g393zjlgxy9ympc0000gn/T/pip-build-env-izk_tneb/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires
          self.run_setup()
        File "/private/var/folders/4n/0ghjrzsd4g393zjlgxy9ympc0000gn/T/pip-build-env-izk_tneb/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 522, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/private/var/folders/4n/0ghjrzsd4g393zjlgxy9ympc0000gn/T/pip-build-env-izk_tneb/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 320, in run_setup
          exec(code, locals())
        File "<string>", line 112, in <module>
      RuntimeError: `medaka` is unsupported on your version of python, please use python 3.6-3.9 (inclusive)
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

@foreignsand
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update: the above error resulted from python3 automatically creating a virtual environment with python 3.12, so i created a virtual environment using the following command:

python3.9 -m venv medaka

And then attempted to install medaka again, which seemed to have installed successfully:

python3.9 -m venv medaka 
lemurbear@MacBook-Pro-10 bin % . ./medaka/bin/activate    
(medaka) lemurbear@MacBook-Pro-10 bin % python -V
Python 3.9.18
(medaka) lemurbear@MacBook-Pro-10 bin % pip install --upgrade pip
Requirement already satisfied: pip in ./medaka/lib/python3.9/site-packages (23.3.1)
Collecting pip
  Using cached pip-24.3.1-py3-none-any.whl.metadata (3.7 kB)
Using cached pip-24.3.1-py3-none-any.whl (1.8 MB)
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 23.3.1
    Uninstalling pip-23.3.1:
      Successfully uninstalled pip-23.3.1
Successfully installed pip-24.3.1
(medaka) lemurbear@MacBook-Pro-10 bin % pip install medaka
Collecting medaka
  Using cached medaka-2.0.1.tar.gz (9.6 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting cffi (from medaka)
  Using cached cffi-1.17.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (1.5 kB)
Collecting edlib (from medaka)
  Downloading edlib-1.3.9.post1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (9.1 kB)
Collecting h5py~=3.10.0 (from medaka)
  Downloading h5py-3.10.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.5 kB)
Collecting intervaltree (from medaka)
  Using cached intervaltree-3.1.0.tar.gz (32 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting numpy<2.0.0,>=1.21.0 (from medaka)
  Downloading numpy-1.26.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (61 kB)
Collecting ont-mappy (from medaka)
  Using cached ont_mappy-2.28.tar.gz (136 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting ont_fast5_api (from medaka)
  Using cached ont_fast5_api-4.1.3-py3-none-any.whl.metadata (13 kB)
Collecting ont-parasail (from medaka)
  Using cached ont_parasail-1.3.4-py2.py3-none-macosx_10_9_x86_64.whl.metadata (21 kB)
Collecting pysam>=0.16.0.1 (from medaka)
  Downloading pysam-0.22.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (1.5 kB)
Collecting pyspoa>=0.2.1 (from medaka)
  Downloading pyspoa-0.2.1-cp39-cp39-macosx_10_9_universal2.whl.metadata (1.9 kB)
Collecting requests (from medaka)
  Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
INFO: pip is looking at multiple versions of medaka to determine which version is compatible with other requirements. This could take a while.
Collecting medaka
  Using cached medaka-2.0.0.tar.gz (9.6 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
  Using cached medaka-1.12.1.tar.gz (15.6 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting cffi==1.15.0 (from medaka)
  Using cached cffi-1.15.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (1.2 kB)
Collecting grpcio (from medaka)
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Building wheels for collected packages: medaka, intervaltree, mappy, progressbar33
  Building wheel for medaka (pyproject.toml) ... done
  Created wheel for medaka: filename=medaka-1.12.1-cp39-cp39-macosx_12_0_x86_64.whl size=12556155 sha256=109dad2f3e395d86e049b2c79be3de469de3cb660ce4a7ca96d44a5eea3280e2
  Stored in directory: /Users/lemurbear/Library/Caches/pip/wheels/35/14/d2/63c72ee43d691e8de6bd034b9ab5dbcea861c6a4cd83f9b664
  Building wheel for intervaltree (pyproject.toml) ... done
  Created wheel for intervaltree: filename=intervaltree-3.1.0-py2.py3-none-any.whl size=26097 sha256=cbd51b0a0255470def1fc396ff69c21d1b209bd15af028122b0980943f4533fb
  Stored in directory: /Users/lemurbear/Library/Caches/pip/wheels/ab/fa/1b/75d9a713279796785711bd0bad8334aaace560c0bd28830c8c
  Building wheel for mappy (pyproject.toml) ... done
  Created wheel for mappy: filename=mappy-2.28-cp39-cp39-macosx_12_0_x86_64.whl size=162833 sha256=6228a20129483ee43278ff618896137eab89d929f8ebb06decf30a329c10727b
  Stored in directory: /Users/lemurbear/Library/Caches/pip/wheels/c8/d9/31/e7ee43dbc311a131fcd2c7406bb00667fa5add6c2d9fb02ff4
  Building wheel for progressbar33 (pyproject.toml) ... done
  Created wheel for progressbar33: filename=progressbar33-2.4-py3-none-any.whl size=12143 sha256=26bbfece5d040bd0cc0db66086a0d90d67269265509c5223f988889275124b75
  Stored in directory: /Users/lemurbear/Library/Caches/pip/wheels/b1/84/d4/f9af63e5362a7a4d5b9aada124c81642569fbd53c6e5220a3d
Successfully built medaka intervaltree mappy progressbar33
Installing collected packages: tensorboard-plugin-wit, sortedcontainers, pyspoa, progressbar33, mappy, libclang, keras, flatbuffers, edlib, zipp, wurlitzer, wrapt, wheel, urllib3, typing-extensions, termcolor, tensorflow-io-gcs-filesystem, tensorflow-estimator, tensorboard-data-server, six, pysam, pycparser, pyasn1, protobuf, packaging, opt-einsum, oauthlib, numpy, MarkupSafe, intervaltree, idna, grpcio, gast, charset-normalizer, certifi, cachetools, absl-py, werkzeug, rsa, requests, pyasn1-modules, ont-parasail, keras-preprocessing, importlib-metadata, h5py, google-pasta, cffi, astunparse, requests-oauthlib, ont_fast5_api, markdown, google-auth, google-auth-oauthlib, tensorboard, tensorflow, medaka
Successfully installed MarkupSafe-3.0.2 absl-py-2.1.0 astunparse-1.6.3 cachetools-5.5.0 certifi-2024.8.30 cffi-1.15.0 charset-normalizer-3.4.0 edlib-1.3.9.post1 flatbuffers-24.3.25 gast-0.4.0 google-auth-2.36.0 google-auth-oauthlib-0.4.6 google-pasta-0.2.0 grpcio-1.68.1 h5py-3.10.0 idna-3.10 importlib-metadata-8.5.0 intervaltree-3.1.0 keras-2.10.0 keras-preprocessing-1.1.2 libclang-18.1.1 mappy-2.28 markdown-3.7 medaka-1.12.1 numpy-1.26.4 oauthlib-3.2.2 ont-parasail-1.3.4 ont_fast5_api-4.1.3 opt-einsum-3.4.0 packaging-24.2 progressbar33-2.4 protobuf-3.19.6 pyasn1-0.6.1 pyasn1-modules-0.4.1 pycparser-2.22 pysam-0.22.1 pyspoa-0.2.1 requests-2.32.3 requests-oauthlib-2.0.0 rsa-4.9 six-1.17.0 sortedcontainers-2.4.0 tensorboard-2.10.1 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.1 tensorflow-2.10.1 tensorflow-estimator-2.10.0 tensorflow-io-gcs-filesystem-0.37.1 termcolor-2.5.0 typing-extensions-4.12.2 urllib3-2.2.3 werkzeug-3.1.3 wheel-0.45.1 wrapt-1.17.0 wurlitzer-3.1.1 zipp-3.21.0

But then i continue to get the same error:

(medaka) lemurbear@MacBook-Pro-10 bin % medaka                
Traceback (most recent call last):
  File "/usr/local/bin/medaka/bin/medaka", line 5, in <module>
    from medaka.medaka import main
  File "/usr/local/bin/medaka/lib/python3.9/site-packages/medaka/medaka.py", line 7, in <module>
    import medaka.common
  File "/usr/local/bin/medaka/lib/python3.9/site-packages/medaka/common.py", line 19, in <module>
    import libmedaka
ImportError: dlopen(/usr/local/bin/medaka/lib/python3.9/site-packages/libmedaka.abi3.so, 0x0002): symbol not found in flat namespace '_libdeflate_alloc_compressor'

I'm honestly so confused about what's happening. I attempt to reinstall libdeflate using brew:

(medaka) lemurbear@MacBook-Pro-10 bin % brew reinstall libdeflate
==> Downloading https://ghcr.io/v2/homebrew/core/libdeflate/manifests/1.22
Already downloaded: /Users/lemurbear/Library/Caches/Homebrew/downloads/573d8b020d8ee66acf44995bcc1439b1a73534ae78d0f741e3692653b5738d3b--libdeflate-1.22.bottle_manifest.json
==> Fetching libdeflate
==> Downloading https://ghcr.io/v2/homebrew/core/libdeflate/blobs/sha256:34c07181913c15251daa7dcf9801d29f1bb7abfb6719ea6c98054e48e25dc
Already downloaded: /Users/lemurbear/Library/Caches/Homebrew/downloads/3425e217491ac57974897a195d2dccb6004ef39c6cafc77340b788bf436d5bee--libdeflate--1.22.sonoma.bottle.tar.gz
==> Reinstalling libdeflate 
==> Pouring libdeflate--1.22.sonoma.bottle.tar.gz
🍺  /usr/local/Cellar/libdeflate/1.22: 17 files, 277.2KB
==> Running `brew cleanup libdeflate`...
Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP.
Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`).

But this doesn't fix the issue. So confusing!!

@cjw85
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cjw85 commented Dec 6, 2024

You should not need to install libdeflate through brew in order for medaka to work --- its is intended to be included within the medaka code. I will try to reproduce this issue as soon as I've dug out an old Intel macbook from my cupboard.

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