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Rostlab / SeqVec

Modelling the Language of Life - Deep Learning Protein Sequences
http://embed.protein.properties
MIT License
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ERROR: Could not build wheels for bio-embeddings-bepler which use PEP 517 and cannot be installed directly #22

Closed a14578 closed 3 years ago

a14578 commented 3 years ago

Hi,

I'm trying to install SeqVec on a mac (Mojave v10.14.6) but I seem to be running into some problems. Do you know how I could fix this? Is there an issue with GCC?

pip3 install bio-embeddings[all] Collecting bio-embeddings[all] Using cached bio_embeddings-0.2.0-py3-none-any.whl (88 kB) Collecting ruamel.yaml<0.17.0,>=0.16.10 Using cached ruamel.yaml-0.16.13-py2.py3-none-any.whl (111 kB) Requirement already satisfied: scipy<2.0.0,>=1.4.1 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings[all]) (1.6.1) Requirement already satisfied: appdirs<2.0.0,>=1.4.4 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings[all]) (1.4.4) Requirement already satisfied: scikit-learn<0.25.0,>=0.24.0 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings[all]) (0.24.1) Collecting importlib_metadata<2.0.0,>=1.7.0 Using cached importlib_metadata-1.7.0-py2.py3-none-any.whl (31 kB) Requirement already satisfied: gensim<4.0.0,>=3.8.2 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings[all]) (3.8.3) Collecting umap-learn<0.6.0,>=0.5.1 Using cached umap_learn-0.5.1-py3-none-any.whl Collecting torch<1.9.0,>=1.7.0 Using cached torch-1.8.1-cp38-none-macosx_10_9_x86_64.whl (119.6 MB) Requirement already satisfied: pandas<2.0.0,>=1.2.0 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings[all]) (1.2.3) Collecting plotly<5.0.0,>=4.6.0 Using cached plotly-4.14.3-py2.py3-none-any.whl (13.2 MB) Requirement already satisfied: tqdm<5.0.0,>=4.45.0 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings[all]) (4.56.0) Collecting h5py<4.0.0,>=3.2.1 Using cached h5py-3.2.1-cp38-cp38-macosx_10_9_x86_64.whl (2.9 MB) Requirement already satisfied: numpy<2.0.0,>=1.18.3 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings[all]) (1.19.2) Collecting humanize<4.0.0,>=3.2.0 Using cached humanize-3.6.0-py3-none-any.whl (80 kB) Collecting biopython<2.0,>=1.76 Using cached biopython-1.78-cp38-cp38-macosx_10_9_x86_64.whl (2.2 MB) Collecting lock<2019.0.0,>=2018.3.25 Using cached lock-2018.3.25.2110-py3-none-any.whl Requirement already satisfied: matplotlib<4.0.0,>=3.2.1 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings[all]) (3.3.4) Collecting python-slugify<5.0.0,>=4.0.1 Using cached python_slugify-4.0.1-py2.py3-none-any.whl Collecting bio-embeddings-deepblast==0.1.0 Using cached bio_embeddings_deepblast-0.1.0-py3-none-any.whl (47.3 MB) Collecting fair-esm==0.3.1 Using cached fair_esm-0.3.1-py3-none-any.whl (35 kB) Collecting bio-embeddings-allennlp==0.9.2 Using cached bio_embeddings_allennlp-0.9.2-py3-none-any.whl (7.6 MB) Collecting bio-embeddings-plus==0.1.1 Using cached bio_embeddings_PLUS-0.1.1-py3-none-any.whl (43 kB) Collecting bio-embeddings-cpcprot==0.0.1 Using cached bio_embeddings_CPCProt-0.0.1-py3-none-any.whl (29 kB) Collecting jax-unirep<2.0.0,>=1.0.0 Using cached jax_unirep-1.0.3-py3-none-any.whl (67.7 MB) Collecting transformers<5.0.0,>=4.5.0 Using cached transformers-4.6.1-py3-none-any.whl (2.2 MB) Collecting bio-embeddings-tape-proteins==0.4 Using cached bio_embeddings_tape_proteins-0.4-py3-none-any.whl (69 kB) Collecting bio-embeddings-bepler==0.0.1 Using cached bio_embeddings_bepler-0.0.1.tar.gz (140 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing wheel metadata ... done Collecting jsonpickle Using cached jsonpickle-2.0.0-py2.py3-none-any.whl (37 kB) Requirement already satisfied: nltk in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (3.5) Collecting conllu==4.4 Using cached conllu-4.4-py2.py3-none-any.whl (15 kB) Requirement already satisfied: gevent>=1.3.6 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (21.1.1) Collecting responses>=0.7 Using cached responses-0.13.3-py2.py3-none-any.whl (25 kB) Collecting parsimonious>=0.8.0 Using cached parsimonious-0.8.1-py3-none-any.whl Collecting spacy<3.0,>=2.1.0 Using cached spacy-2.3.5-cp38-cp38-macosx_10_9_x86_64.whl (10.2 MB) Requirement already satisfied: pytz>=2017.3 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (2021.1) Collecting boto3 Using cached boto3-1.17.84-py2.py3-none-any.whl (131 kB) Collecting jsonnet>=0.10.0 Using cached jsonnet-0.17.0.tar.gz (259 kB) Requirement already satisfied: pytest in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (6.2.2) Collecting pytorch-transformers==1.1.0 Using cached pytorch_transformers-1.1.0-py3-none-any.whl (158 kB) Collecting sqlparse>=0.2.4 Using cached sqlparse-0.4.1-py3-none-any.whl (42 kB) Collecting unidecode Using cached Unidecode-1.2.0-py2.py3-none-any.whl (241 kB) Collecting flask-cors>=3.0.7 Using cached Flask_Cors-3.0.10-py2.py3-none-any.whl (14 kB) Collecting pytorch-pretrained-bert>=0.6.0 Using cached pytorch_pretrained_bert-0.6.2-py3-none-any.whl (123 kB) Collecting tensorboardX>=1.2 Using cached tensorboardX-2.2-py2.py3-none-any.whl (120 kB) Collecting flaky Using cached flaky-3.7.0-py2.py3-none-any.whl (22 kB) Collecting ftfy Using cached ftfy-6.0.3-py3-none-any.whl Requirement already satisfied: numpydoc>=0.8.0 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (1.1.0) Requirement already satisfied: flask>=1.0.2 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (1.1.2) Collecting word2number>=1.1 Using cached word2number-1.1-py3-none-any.whl Requirement already satisfied: requests>=2.18 in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (2.25.1) Collecting overrides<5,>=4 Using cached overrides-4.1.2-py3-none-any.whl (11 kB) Collecting editdistance Using cached editdistance-0.5.3.tar.gz (27 kB) Collecting lmdb<2.0,>=1.0 Using cached lmdb-1.2.1-cp38-cp38-macosx_10_14_x86_64.whl (102 kB) Requirement already satisfied: numba in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings-deepblast==0.1.0->bio-embeddings[all]) (0.52.0) Requirement already satisfied: pillow in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings-deepblast==0.1.0->bio-embeddings[all]) (8.1.1) Collecting pytorch-lightning>=0.8.1 Using cached pytorch_lightning-1.3.3-py3-none-any.whl (806 kB) Collecting torch<1.9.0,>=1.7.0 Using cached torch-1.7.1-cp38-none-macosx_10_9_x86_64.whl (108.9 MB) Requirement already satisfied: filelock in /opt/anaconda3/lib/python3.8/site-packages (from bio-embeddings-tape-proteins==0.4->bio-embeddings[all]) (3.0.12) Collecting sentencepiece Using cached sentencepiece-0.1.95-cp38-cp38-macosx_10_6_x86_64.whl (1.1 MB) Requirement already satisfied: regex in /opt/anaconda3/lib/python3.8/site-packages (from pytorch-transformers==1.1.0->bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (2020.11.13) Requirement already satisfied: Jinja2>=2.10.1 in /opt/anaconda3/lib/python3.8/site-packages (from 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jaxlib-0.1.67-cp38-none-macosx_10_9_x86_64.whl (43.5 MB) Collecting optuna Using cached optuna-2.7.0-py3-none-any.whl (293 kB) Collecting jax<0.2.0 Using cached jax-0.1.77-py3-none-any.whl Requirement already satisfied: opt-einsum in /opt/anaconda3/lib/python3.8/site-packages (from jax<0.2.0->jax-unirep<2.0.0,>=1.0.0->bio-embeddings[all]) (3.3.0) Requirement already satisfied: absl-py in /opt/anaconda3/lib/python3.8/site-packages (from jax<0.2.0->jax-unirep<2.0.0,>=1.0.0->bio-embeddings[all]) (0.11.0) Requirement already satisfied: MarkupSafe>=0.23 in /opt/anaconda3/lib/python3.8/site-packages (from Jinja2>=2.10.1->flask>=1.0.2->bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (1.1.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /opt/anaconda3/lib/python3.8/site-packages (from matplotlib<4.0.0,>=3.2.1->bio-embeddings[all]) (2.4.7) Requirement already satisfied: python-dateutil>=2.1 in /opt/anaconda3/lib/python3.8/site-packages (from 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pyasn1<0.5.0,>=0.4.6 in /opt/anaconda3/lib/python3.8/site-packages (from pyasn1-modules>=0.2.1->google-auth<2,>=1.6.3->tensorboard!=2.5.0,>=2.2.0->pytorch-lightning>=0.8.1->bio-embeddings-deepblast==0.1.0->bio-embeddings[all]) (0.4.8) Requirement already satisfied: oauthlib>=3.0.0 in /opt/anaconda3/lib/python3.8/site-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard!=2.5.0,>=2.2.0->pytorch-lightning>=0.8.1->bio-embeddings-deepblast==0.1.0->bio-embeddings[all]) (3.1.0) Requirement already satisfied: typing-extensions in /opt/anaconda3/lib/python3.8/site-packages (from torch<1.9.0,>=1.7.0->bio-embeddings[all]) (3.7.4.3) Collecting huggingface-hub==0.0.8 Using cached huggingface_hub-0.0.8-py3-none-any.whl (34 kB) Collecting sacremoses Using cached sacremoses-0.0.45-py3-none-any.whl (895 kB) Collecting tokenizers<0.11,>=0.10.1 Using cached tokenizers-0.10.3-cp38-cp38-macosx_10_11_x86_64.whl (2.2 MB) Collecting pynndescent>=0.5 Using cached pynndescent-0.5.2-py3-none-any.whl Requirement already satisfied: llvmlite<0.36,>=0.35.0 in /opt/anaconda3/lib/python3.8/site-packages (from numba->bio-embeddings-deepblast==0.1.0->bio-embeddings[all]) (0.35.0) Collecting async-timeout<4.0,>=3.0 Using cached async_timeout-3.0.1-py3-none-any.whl (8.2 kB) Requirement already satisfied: attrs>=17.3.0 in /opt/anaconda3/lib/python3.8/site-packages (from aiohttp->fsspec[http]>=2021.4.0->pytorch-lightning>=0.8.1->bio-embeddings-deepblast==0.1.0->bio-embeddings[all]) (20.3.0) Collecting multidict<7.0,>=4.5 Using cached multidict-5.1.0-cp38-cp38-macosx_10_14_x86_64.whl (49 kB) Collecting yarl<2.0,>=1.0 Using cached yarl-1.6.3-cp38-cp38-macosx_10_14_x86_64.whl (124 kB) Collecting jmespath<1.0.0,>=0.7.1 Using cached jmespath-0.10.0-py2.py3-none-any.whl (24 kB) Collecting s3transfer<0.5.0,>=0.4.0 Using cached s3transfer-0.4.2-py2.py3-none-any.whl (79 kB) Collecting botocore<1.21.0,>=1.20.84 Using cached botocore-1.20.84-py2.py3-none-any.whl (7.6 MB) Requirement already satisfied: wcwidth in /opt/anaconda3/lib/python3.8/site-packages (from ftfy->bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (0.2.5) Collecting flatbuffers<3.0,>=1.12 Using cached flatbuffers-2.0-py2.py3-none-any.whl (26 kB) Collecting colorlog Using cached colorlog-5.0.1-py2.py3-none-any.whl (10 kB) Collecting cmaes>=0.8.2 Using cached cmaes-0.8.2-py3-none-any.whl (15 kB) Collecting alembic Using cached alembic-1.6.5-py2.py3-none-any.whl (164 kB) Collecting cliff Using cached cliff-3.8.0-py3-none-any.whl (80 kB) Requirement already satisfied: sqlalchemy>=1.1.0 in /opt/anaconda3/lib/python3.8/site-packages (from optuna->jax-unirep<2.0.0,>=1.0.0->bio-embeddings[all]) (1.3.23) Collecting python-editor>=0.3 Using cached python_editor-1.0.4-py3-none-any.whl (4.9 kB) Collecting Mako Using cached Mako-1.1.4-py2.py3-none-any.whl (75 kB) Collecting pbr!=2.1.0,>=2.0.0 Using cached pbr-5.6.0-py2.py3-none-any.whl (111 kB) Collecting stevedore>=2.0.1 Using cached stevedore-3.3.0-py3-none-any.whl (49 kB) Collecting PrettyTable>=0.7.2 Using cached prettytable-2.1.0-py3-none-any.whl (22 kB) Collecting cmd2>=1.0.0 Using cached cmd2-1.5.0-py3-none-any.whl (133 kB) Collecting pyperclip>=1.6 Using cached pyperclip-1.8.2-py3-none-any.whl Requirement already satisfied: colorama>=0.3.7 in /opt/anaconda3/lib/python3.8/site-packages (from cmd2>=1.0.0->cliff->optuna->jax-unirep<2.0.0,>=1.0.0->bio-embeddings[all]) (0.4.4) Requirement already satisfied: iniconfig in /opt/anaconda3/lib/python3.8/site-packages (from pytest->bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (1.1.1) Requirement already satisfied: pluggy<1.0.0a1,>=0.12 in /opt/anaconda3/lib/python3.8/site-packages (from pytest->bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (0.13.1) Requirement already satisfied: py>=1.8.2 in /opt/anaconda3/lib/python3.8/site-packages (from pytest->bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (1.10.0) Requirement already satisfied: toml in /opt/anaconda3/lib/python3.8/site-packages (from pytest->bio-embeddings-allennlp==0.9.2->bio-embeddings[all]) (0.10.1) Building wheels for collected packages: bio-embeddings-bepler, jsonnet, editdistance Building wheel for bio-embeddings-bepler (PEP 517) ... error ERROR: Command errored out with exit status 1: command: /opt/anaconda3/bin/python /opt/anaconda3/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/tmpgxxuthgo cwd: /private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-install-d4jqy96f/bio-embeddings-bepler_8e5648e9bac44ef194d2c40dd56b2f5a Complete output (28 lines): running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.9-x86_64-3.8 creating build/lib.macosx-10.9-x86_64-3.8/bepler copying bepler/transmembrane.py -> build/lib.macosx-10.9-x86_64-3.8/bepler copying bepler/parse_utils.py -> build/lib.macosx-10.9-x86_64-3.8/bepler copying bepler/init.py -> build/lib.macosx-10.9-x86_64-3.8/bepler copying bepler/pdb.py -> build/lib.macosx-10.9-x86_64-3.8/bepler copying bepler/scop.py -> build/lib.macosx-10.9-x86_64-3.8/bepler copying bepler/utils.py -> build/lib.macosx-10.9-x86_64-3.8/bepler copying bepler/pfam.py -> build/lib.macosx-10.9-x86_64-3.8/bepler copying bepler/alphabets.py -> build/lib.macosx-10.9-x86_64-3.8/bepler copying bepler/fasta.py -> build/lib.macosx-10.9-x86_64-3.8/bepler creating build/lib.macosx-10.9-x86_64-3.8/bepler/models copying bepler/models/embedding.py -> build/lib.macosx-10.9-x86_64-3.8/bepler/models copying bepler/models/sequence.py -> build/lib.macosx-10.9-x86_64-3.8/bepler/models copying bepler/models/init.py -> build/lib.macosx-10.9-x86_64-3.8/bepler/models copying bepler/models/comparison.py -> build/lib.macosx-10.9-x86_64-3.8/bepler/models copying bepler/models/multitask.py -> build/lib.macosx-10.9-x86_64-3.8/bepler/models running build_ext building 'bepler.metrics' extension creating build/temp.macosx-10.9-x86_64-3.8 creating build/temp.macosx-10.9-x86_64-3.8/bepler gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/include -arch x86_64 -I/private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-build-env-1x0kaqtn/overlay/lib/python3.8/site-packages/numpy/core/include -I/opt/anaconda3/include/python3.8 -c bepler/metrics.c -o build/temp.macosx-10.9-x86_64-3.8/bepler/metrics.o xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command 'gcc' failed with exit status 1

ERROR: Failed building wheel for bio-embeddings-bepler Building wheel for jsonnet (setup.py) ... error ERROR: Command errored out with exit status 1: command: /opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-install-d4jqy96f/jsonnet_d1837cd150e2440796e349b1b20691ca/setup.py'"'"'; file='"'"'/private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-install-d4jqy96f/jsonnet_d1837cd150e2440796e349b1b20691ca/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-wheel-6qx7ndfv cwd: /private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-install-d4jqy96f/jsonnet_d1837cd150e2440796e349b1b20691ca/ Complete output (31 lines): running bdist_wheel running build running build_ext xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Traceback (most recent call last): File "", line 1, in File "/private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-install-d4jqy96f/jsonnet_d1837cd150e2440796e349b1b20691ca/setup.py", line 65, in setup(name='jsonnet', File "/opt/anaconda3/lib/python3.8/site-packages/setuptools/init.py", line 153, in setup return distutils.core.setup(**attrs) File "/opt/anaconda3/lib/python3.8/distutils/core.py", line 148, in setup dist.run_commands() File "/opt/anaconda3/lib/python3.8/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/opt/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/opt/anaconda3/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 299, in run self.run_command('build') File "/opt/anaconda3/lib/python3.8/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/opt/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/opt/anaconda3/lib/python3.8/distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/opt/anaconda3/lib/python3.8/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/opt/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-install-d4jqy96f/jsonnet_d1837cd150e2440796e349b1b20691ca/setup.py", line 54, in run raise Exception('Could not build %s' % (', '.join(LIB_OBJECTS))) Exception: Could not build core/desugarer.o, core/formatter.o, core/libjsonnet.o, core/lexer.o, core/parser.o, core/pass.o, core/static_analysis.o, core/string_utils.o, core/vm.o, third_party/md5/md5.o

ERROR: Failed building wheel for jsonnet Running setup.py clean for jsonnet Building wheel for editdistance (setup.py) ... error ERROR: Command errored out with exit status 1: command: /opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-install-d4jqy96f/editdistance_43459ad6a5fb4b8d995c03e237bfb2c7/setup.py'"'"'; file='"'"'/private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-install-d4jqy96f/editdistance_43459ad6a5fb4b8d995c03e237bfb2c7/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-wheel-db50acac cwd: /private/var/folders/1k/1zyx6bn14j302n77wbw9bssw0000gn/T/pip-install-d4jqy96f/editdistance_43459ad6a5fb4b8d995c03e237bfb2c7/ Complete output (16 lines): running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.9-x86_64-3.8 creating build/lib.macosx-10.9-x86_64-3.8/editdistance copying editdistance/init.py -> build/lib.macosx-10.9-x86_64-3.8/editdistance copying editdistance/_editdistance.h -> build/lib.macosx-10.9-x86_64-3.8/editdistance copying editdistance/def.h -> build/lib.macosx-10.9-x86_64-3.8/editdistance running build_ext building 'editdistance.bycython' extension creating build/temp.macosx-10.9-x86_64-3.8 creating build/temp.macosx-10.9-x86_64-3.8/editdistance gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/include -arch x86_64 -I./editdistance -I/opt/anaconda3/include/python3.8 -c editdistance/_editdistance.cpp -o build/temp.macosx-10.9-x86_64-3.8/editdistance/_editdistance.o xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command 'gcc' failed with exit status 1

ERROR: Failed building wheel for editdistance Running setup.py clean for editdistance Failed to build bio-embeddings-bepler jsonnet editdistance ERROR: Could not build wheels for bio-embeddings-bepler which use PEP 517 and cannot be installed directly

konstin commented 3 years ago

Hi,

we (or rather the embedder we include) don't really support mac, so I'd recommend using a linux machine. You might also have success with pip install bio_embeddings[seqvec], which doesn't try to install bepler (see also https://github.com/sacdallago/bio_embeddings/issues/124#issuecomment-811812580).