Closed immunoliver closed 1 year ago
I'm having this same issue - any chance you ended up resolving it?
The same question
same error, could this please resolved?
The team was disbanded last year, so there's not gonna be any fixes, unless there's community efforts.
Hello,
I'm trying to install ESMfold locally and am struggling. When I paste the following code into the terminal, I get an error message.
pip install "fair-esm[esmfold]" pip install 'dllogger @ git+https://github.com/NVIDIA/dllogger.git' pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307'
It seems that pip install "fair-esm[esmfold]" works, as does pip install 'dllogger @ git+https://github.com/NVIDIA/dllogger.git', but when I try to install openfold I get the error below:
rekgowr@CS00056653:/mnt/c/Users/rekgowr/Documents/Lab/Structural_Biology$ pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307' Defaulting to user installation because normal site-packages is not writeable Collecting openfold@ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307 Cloning https://github.com/aqlaboratory/openfold.git (to revision 4b41059694619831a7db195b7e0988fc4ff3a307) to /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695 Running command git clone --filter=blob:none --quiet https://github.com/aqlaboratory/openfold.git /tmp/pip-install-pxkdmj8r/openfold_3b67dd159eb04815b2101d5537d3d695 Running command git rev-parse -q --verify 'sha^4b41059694619831a7db195b7e0988fc4ff3a307' Running command git fetch -q https://github.com/aqlaboratory/openfold.git 4b41059694619831a7db195b7e0988fc4ff3a307 Running command git checkout -q 4b41059694619831a7db195b7e0988fc4ff3a307 Resolved https://github.com/aqlaboratory/openfold.git to commit 4b41059694619831a7db195b7e0988fc4ff3a307 Preparing metadata (setup.py) ... done Building wheels for collected packages: openfold Building wheel for openfold (setup.py) ... error error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [289 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/openfold copying openfold/config.py -> build/lib.linux-x86_64-cpython-310/openfold copying openfold/init.py -> build/lib.linux-x86_64-cpython-310/openfold creating build/lib.linux-x86_64-cpython-310/openfold/data copying openfold/data/templates.py -> build/lib.linux-x86_64-cpython-310/openfold/data copying openfold/data/feature_pipeline.py -> build/lib.linux-x86_64-cpython-310/openfold/data copying openfold/data/data_modules.py -> build/lib.linux-x86_64-cpython-310/openfold/data copying openfold/data/errors.py -> build/lib.linux-x86_64-cpython-310/openfold/data copying openfold/data/input_pipeline.py -> build/lib.linux-x86_64-cpython-310/openfold/data copying openfold/data/parsers.py -> build/lib.linux-x86_64-cpython-310/openfold/data copying openfold/data/data_pipeline.py -> build/lib.linux-x86_64-cpython-310/openfold/data copying openfold/data/mmcif_parsing.py -> build/lib.linux-x86_64-cpython-310/openfold/data copying openfold/data/data_transforms.py -> build/lib.linux-x86_64-cpython-310/openfold/data copying openfold/data/init.py -> build/lib.linux-x86_64-cpython-310/openfold/data creating build/lib.linux-x86_64-cpython-310/openfold/np copying openfold/np/residue_constants.py -> build/lib.linux-x86_64-cpython-310/openfold/np copying openfold/np/init.py -> build/lib.linux-x86_64-cpython-310/openfold/np copying openfold/np/protein.py -> build/lib.linux-x86_64-cpython-310/openfold/np creating build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/template.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/primitives.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/triangular_multiplicative_update.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/embedders.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/evoformer.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/outer_product_mean.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/structure_module.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/msa.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/model.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/triangular_attention.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/heads.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/torchscript.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/dropout.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/pair_transition.py -> build/lib.linux-x86_64-cpython-310/openfold/model copying openfold/model/init.py -> build/lib.linux-x86_64-cpython-310/openfold/model creating build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/superimposition.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/seed.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/tensor_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/lr_schedulers.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/argparse.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/rigid_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/loss.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/logger.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/trace_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/feats.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/callbacks.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/chunk_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/validation_metrics.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/init.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/checkpointing.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/suppress_output.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/import_weights.py -> build/lib.linux-x86_64-cpython-310/openfold/utils copying openfold/utils/exponential_moving_average.py -> build/lib.linux-x86_64-cpython-310/openfold/utils creating build/lib.linux-x86_64-cpython-310/openfold/resources copying openfold/resources/init.py -> build/lib.linux-x86_64-cpython-310/openfold/resources creating build/lib.linux-x86_64-cpython-310/openfold/data/tools copying openfold/data/tools/utils.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools copying openfold/data/tools/kalign.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools copying openfold/data/tools/hhblits.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools copying openfold/data/tools/hhsearch.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools copying openfold/data/tools/init.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools copying openfold/data/tools/jackhmmer.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools creating build/lib.linux-x86_64-cpython-310/openfold/np/relax copying openfold/np/relax/utils.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax copying openfold/np/relax/relax.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax copying openfold/np/relax/cleanup.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax copying openfold/np/relax/amber_minimize.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax copying openfold/np/relax/init.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax creating build/lib.linux-x86_64-cpython-310/openfold/utils/kernel copying openfold/utils/kernel/attention_core.py -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel copying openfold/utils/kernel/init.py -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel running egg_info creating openfold.egg-info writing openfold.egg-info/PKG-INFO writing dependency_links to openfold.egg-info/dependency_links.txt writing top-level names to openfold.egg-info/top_level.txt writing manifest file 'openfold.egg-info/SOURCES.txt' reading manifest file 'openfold.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'openfold.egg-info/SOURCES.txt' /home/rekgowr/.local/lib/python3.10/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'openfold.utils.kernel.csrc' is absent from the
packages
configuration. !!note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for openfold Running setup.py clean for openfold Failed to build openfold ERROR: Could not build wheels for openfold, which is required to install pyproject.toml-based projects
I'm very new to this and have less than a month's experience using the terminal - I appreciate that this is likely a simple problem. I have been able to troubleshoot everything else I've done so far using ChatGPT and Github, but this seems like there's something going on within the code I'm importing from you guys and I can't tell what's not compatible at my end unfortunately.
Please advise?
Thanks!