Closed ChaoXianSen closed 6 months ago
zachflam
commented
6 months ago Thank you for reporting this error. There was a new release of Miniconda that resulted in an issue with environment creation. I changed the version and it appears to be working. Please let me know if you can use the colab now.
ChaoXianSen
commented
6 months ago Thank you for reporting this error. There was a new release of Miniconda that resulted in an issue with environment creation. I changed the version and it appears to be working. Please let me know if you can use the colab now.
colab has already running smoothly~ thanks for your help !
Hi, I predict viral sequence on Google Colab :
PREFIX=/opt/conda Unpacking payload ...
Installing base environment...
Preparing transaction: ...working... done Executing transaction: ...working... done installation finished. WARNING: You currently have a PYTHONPATH environment variable set. This may cause unexpected behavior when running the Python interpreter in Miniconda3. For best results, please verify that your PYTHONPATH only points to directories of packages that are compatible with the Python interpreter in Miniconda3: /opt/conda env: PATH=/opt/conda/bin:/opt/conda/bin:/opt/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/tools/node/bin:/tools/google-cloud-sdk/bin Channels:
Downloading and Extracting Packages: python-3.7.16 | 44.8 MB | : 0% 0/1 [00:00<?, ?it/s] openssl-1.1.1w | 3.7 MB | : 0% 0/1 [00:00<?, ?it/s]
pip-22.3.1 | 2.7 MB | : 0% 0/1 [00:00<?, ?it/s]
setuptools-65.6.3 | 1.1 MB | : 0% 0/1 [00:00<?, ?it/s]
certifi-2022.12.7 | 150 KB | : 0% 0/1 [00:00<?, ?it/s]
wheel-0.38.4 | 63 KB | : 0% 0/1 [00:00<?, ?it/s] openssl-1.1.1w | 3.7 MB | : 0% 0.004187193943698291/1 [00:00<00:44, 44.28s/it]
certifi-2022.12.7 | 150 KB | : 11% 0.10679390158848107/1 [00:00<00:01, 1.88s/it]
setuptools-65.6.3 | 1.1 MB | : 1% 0.01372742712122012/1 [00:00<00:14, 14.92s/it]
python-3.7.16 | 44.8 MB | : 0% 0.00034843833210413685/1 [00:00<11:43, 704.02s/it]
wheel-0.38.4 | 63 KB | : 25% 0.25267963171450164/1 [00:00<00:00, 1.04it/s] openssl-1.1.1w | 3.7 MB | : 98% 0.9756161888817018/1 [00:00<00:00, 4.24it/s]
certifi-2022.12.7 | 150 KB | : 100% 1.0/1 [00:00<00:00, 1.88s/it]
python-3.7.16 | 44.8 MB | : 8% 0.07979237805184734/1 [00:00<00:03, 3.41s/it]
wheel-0.38.4 | 63 KB | : 100% 1.0/1 [00:00<00:00, 3.29it/s]
python-3.7.16 | 44.8 MB | : 30% 0.30000540394166186/1 [00:00<00:00, 1.27s/it] python-3.7.16 | 44.8 MB | : 62% 0.6184780394848429/1 [00:00<00:00, 1.20it/s]
setuptools-65.6.3 | 1.1 MB | : 100% 1.0/1 [00:00<00:00, 1.32it/s]
python-3.7.16 | 44.8 MB | : 81% 0.8104675604742223/1 [00:00<00:00, 1.42it/s]
Preparing transaction: done Verifying transaction: done Executing transaction: done Installing pip dependencies: | Ran pip subprocess with arguments: ['/opt/conda/envs/plm_vpf_embed/bin/python', '-m', 'pip', 'install', '-U', '-r', '/content/viral-protein-function-plm/condaenv.ffwdoebv.requirements.txt', '--exists-action=b'] Pip subprocess output: Collecting bio-transformers==0.1.17 Using cached bio_transformers-0.1.17-py3-none-any.whl (48 kB) Collecting tqdm==4.65.0 Using cached tqdm-4.65.0-py3-none-any.whl (77 kB) Collecting biopython<2,>=1.78 Using cached biopython-1.81-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.0 MB) Collecting torchmetrics<0.5,>=0.3.2 Using cached torchmetrics-0.4.1-py3-none-any.whl (234 kB) Collecting transformers<4.9,>=4.8 Using cached transformers-4.8.2-py3-none-any.whl (2.5 MB) Collecting fair-esm==0.4.0 Using cached fair_esm-0.4.0-py3-none-any.whl (37 kB) Collecting torch<1.9,>=1.7.0 Using cached torch-1.8.1-cp37-cp37m-manylinux1_x86_64.whl (804.1 MB) Collecting pytorch-lightning>=1.3.3 Using cached pytorch_lightning-1.9.5-py3-none-any.whl (829 kB) Collecting pandas>=1.2.3 Using cached pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB) Collecting scikit-learn>=0.22.2 Using cached scikit_learn-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.8 MB) Collecting numpy<1.19,>=1.16 Using cached numpy-1.18.5-cp37-cp37m-manylinux1_x86_64.whl (20.1 MB) Collecting ray>=1.4.0 Using cached ray-2.7.2-cp37-cp37m-manylinux2014_x86_64.whl (62.8 MB) Collecting python-dateutil>=2.7.3 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) Collecting pytz>=2017.3 Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB) Collecting packaging>=17.1 Using cached packaging-24.0-py3-none-any.whl (53 kB) Collecting pytorch-lightning>=1.3.3 Using cached pytorch_lightning-1.9.4-py3-none-any.whl (827 kB) Using cached pytorch_lightning-1.9.3-py3-none-any.whl (826 kB) Using cached pytorch_lightning-1.9.2-py3-none-any.whl (826 kB) Using cached pytorch_lightning-1.9.1-py3-none-any.whl (825 kB) Using cached pytorch_lightning-1.9.0-py3-none-any.whl (825 kB) Using cached pytorch_lightning-1.8.6-py3-none-any.whl (800 kB) Collecting tensorboardX>=2.2 Downloading tensorboardX-2.6.2.2-py2.py3-none-any.whl (101 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 101.7/101.7 kB 5.6 MB/s eta 0:00:00 Collecting pytorch-lightning>=1.3.3 Using cached pytorch_lightning-1.8.5.post0-py3-none-any.whl (800 kB) Using cached pytorch_lightning-1.8.5-py3-none-any.whl (800 kB) Using cached pytorch_lightning-1.8.4.post0-py3-none-any.whl (800 kB) Using cached pytorch_lightning-1.8.4-py3-none-any.whl (799 kB) Using cached pytorch_lightning-1.8.3.post2-py3-none-any.whl (798 kB) Using cached pytorch_lightning-1.8.3.post1-py3-none-any.whl (798 kB) Using cached pytorch_lightning-1.8.3.post0-py3-none-any.whl (798 kB) Using cached pytorch_lightning-1.8.3-py3-none-any.whl (798 kB) Using cached pytorch_lightning-1.8.2-py3-none-any.whl (798 kB) Using cached pytorch_lightning-1.8.1-py3-none-any.whl (798 kB) Using cached pytorch_lightning-1.8.0.post1-py3-none-any.whl (796 kB) Using cached pytorch_lightning-1.8.0-py3-none-any.whl (795 kB) Using cached pytorch_lightning-1.7.7-py3-none-any.whl (708 kB) Using cached pytorch_lightning-1.7.6-py3-none-any.whl (707 kB) Using cached pytorch_lightning-1.7.5-py3-none-any.whl (706 kB) Using cached pytorch_lightning-1.7.4-py3-none-any.whl (706 kB) Using cached pytorch_lightning-1.7.3-py3-none-any.whl (705 kB) Using cached pytorch_lightning-1.7.2-py3-none-any.whl (705 kB) Using cached pytorch_lightning-1.7.1-py3-none-any.whl (701 kB) Using cached pytorch_lightning-1.7.0-py3-none-any.whl (700 kB) Using cached pytorch_lightning-1.6.5-py3-none-any.whl (585 kB) Collecting fsspec[http]!=2021.06.0,>=2021.05.0 Using cached fsspec-2023.1.0-py3-none-any.whl (143 kB) Collecting tensorboard>=2.2.0 Using cached tensorboard-2.11.2-py3-none-any.whl (6.0 MB) Collecting PyYAML>=5.4 Using cached PyYAML-6.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (670 kB) Collecting typing-extensions>=4.0.0 Using cached typing_extensions-4.7.1-py3-none-any.whl (33 kB) Collecting protobuf<=3.20.1 Using cached protobuf-3.20.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.0 MB) Collecting pyDeprecate>=0.3.1 Using cached pyDeprecate-0.3.2-py3-none-any.whl (10 kB) Collecting frozenlist Using cached frozenlist-1.3.3-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (148 kB) Collecting jsonschema Using cached jsonschema-4.17.3-py3-none-any.whl (90 kB) Collecting aiosignal Using cached aiosignal-1.3.1-py3-none-any.whl (7.6 kB) Collecting filelock Using cached filelock-3.12.2-py3-none-any.whl (10 kB) Collecting requests Using cached requests-2.31.0-py3-none-any.whl (62 kB) Collecting click>=7.0 Using cached click-8.1.7-py3-none-any.whl (97 kB) Collecting msgpack<2.0.0,>=1.0.0 Using cached msgpack-1.0.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (299 kB) Collecting scipy>=1.1.0 Using cached scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB) Collecting threadpoolctl>=2.0.0 Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Collecting joblib>=0.11 Using cached joblib-1.3.2-py3-none-any.whl (302 kB) Collecting importlib-metadata Using cached importlib_metadata-6.7.0-py3-none-any.whl (22 kB) Collecting sacremoses Using cached sacremoses-0.0.53-py3-none-any.whl Collecting tokenizers<0.11,>=0.10.1 Using cached tokenizers-0.10.3-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (3.3 MB) Collecting regex!=2019.12.17 Using cached regex-2024.4.16-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (761 kB) Collecting huggingface-hub==0.0.12 Using cached huggingface_hub-0.0.12-py3-none-any.whl (37 kB) Collecting aiohttp!=4.0.0a0,!=4.0.0a1 Using cached aiohttp-3.8.6-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (987 kB) Collecting six>=1.5 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting tensorboard-data-server<0.7.0,>=0.6.0 Using cached tensorboard_data_server-0.6.1-py3-none-manylinux2010_x86_64.whl (4.9 MB) Collecting google-auth-oauthlib<0.5,>=0.4.1 Using cached google_auth_oauthlib-0.4.6-py2.py3-none-any.whl (18 kB) Collecting google-auth<3,>=1.6.3 Using cached google_auth-2.29.0-py2.py3-none-any.whl (189 kB) Collecting absl-py>=0.4 Using cached absl_py-2.1.0-py3-none-any.whl (133 kB) Requirement already satisfied: setuptools>=41.0.0 in /opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.3->bio-transformers==0.1.17->-r /content/viral-protein-function-plm/condaenv.ffwdoebv.requirements.txt (line 1)) (65.6.3) Collecting werkzeug>=1.0.1 Using cached Werkzeug-2.2.3-py3-none-any.whl (233 kB) Collecting tensorboard-plugin-wit>=1.6.0 Using cached tensorboard_plugin_wit-1.8.1-py3-none-any.whl (781 kB) Collecting markdown>=2.6.8 Using cached Markdown-3.4.4-py3-none-any.whl (94 kB) Requirement already satisfied: wheel>=0.26 in /opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.3->bio-transformers==0.1.17->-r /content/viral-protein-function-plm/condaenv.ffwdoebv.requirements.txt (line 1)) (0.38.4) Collecting grpcio>=1.24.3 Using cached grpcio-1.62.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.6 MB) Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages (from requests->ray>=1.4.0->bio-transformers==0.1.17->-r /content/viral-protein-function-plm/condaenv.ffwdoebv.requirements.txt (line 1)) (2022.12.7) Collecting urllib3<3,>=1.21.1 Using cached urllib3-2.0.7-py3-none-any.whl (124 kB) Collecting charset-normalizer<4,>=2 Using cached charset_normalizer-3.3.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (136 kB) Collecting idna<4,>=2.5 Using cached idna-3.7-py3-none-any.whl (66 kB) Collecting zipp>=0.5 Using cached zipp-3.15.0-py3-none-any.whl (6.8 kB) Collecting pkgutil-resolve-name>=1.3.10 Using cached pkgutil_resolve_name-1.3.10-py3-none-any.whl (4.7 kB) Collecting pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 Using cached pyrsistent-0.19.3-py3-none-any.whl (57 kB) Collecting attrs>=17.4.0 Using cached attrs-23.2.0-py3-none-any.whl (60 kB) Collecting importlib-resources>=1.4.0 Using cached importlib_resources-5.12.0-py3-none-any.whl (36 kB) Collecting multidict<7.0,>=4.5 Using cached multidict-6.0.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (99 kB) Collecting yarl<2.0,>=1.0 Using cached yarl-1.9.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (289 kB) Collecting asynctest==0.13.0 Using cached asynctest-0.13.0-py3-none-any.whl (26 kB) Collecting async-timeout<5.0,>=4.0.0a3 Using cached async_timeout-4.0.3-py3-none-any.whl (5.7 kB) Collecting rsa<5,>=3.1.4 Using cached rsa-4.9-py3-none-any.whl (34 kB) Collecting cachetools<6.0,>=2.0.0 Using cached cachetools-5.3.3-py3-none-any.whl (9.3 kB) Collecting pyasn1-modules>=0.2.1 Using cached pyasn1_modules-0.3.0-py2.py3-none-any.whl (181 kB) Collecting requests-oauthlib>=0.7.0 Using cached requests_oauthlib-2.0.0-py2.py3-none-any.whl (24 kB) Collecting MarkupSafe>=2.1.1 Using cached MarkupSafe-2.1.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting pyasn1<0.6.0,>=0.4.6 Using cached pyasn1-0.5.1-py2.py3-none-any.whl (84 kB) Collecting oauthlib>=3.0.0 Using cached oauthlib-3.2.2-py3-none-any.whl (151 kB) Installing collected packages: tokenizers, tensorboard-plugin-wit, pytz, msgpack, fair-esm, zipp, urllib3, typing-extensions, tqdm, threadpoolctl, tensorboard-data-server, six, regex, PyYAML, pyrsistent, pyDeprecate, pyasn1, protobuf, pkgutil-resolve-name, packaging, oauthlib, numpy, multidict, MarkupSafe, joblib, idna, grpcio, fsspec, frozenlist, filelock, charset-normalizer, cachetools, asynctest, absl-py, yarl, werkzeug, torch, scipy, rsa, requests, python-dateutil, pyasn1-modules, importlib-resources, importlib-metadata, biopython, async-timeout, aiosignal, torchmetrics, scikit-learn, requests-oauthlib, pandas, markdown, huggingface-hub, google-auth, click, attrs, sacremoses, jsonschema, google-auth-oauthlib, aiohttp, transformers, tensorboard, ray, pytorch-lightning, bio-transformers Successfully installed MarkupSafe-2.1.5 PyYAML-6.0.1 absl-py-2.1.0 aiohttp-3.8.6 aiosignal-1.3.1 async-timeout-4.0.3 asynctest-0.13.0 attrs-23.2.0 bio-transformers-0.1.17 biopython-1.81 cachetools-5.3.3 charset-normalizer-3.3.2 click-8.1.7 fair-esm-0.4.0 filelock-3.12.2 frozenlist-1.3.3 fsspec-2023.1.0 google-auth-2.29.0 google-auth-oauthlib-0.4.6 grpcio-1.62.2 huggingface-hub-0.0.12 idna-3.7 importlib-metadata-6.7.0 importlib-resources-5.12.0 joblib-1.3.2 jsonschema-4.17.3 markdown-3.4.4 msgpack-1.0.5 multidict-6.0.5 numpy-1.18.5 oauthlib-3.2.2 packaging-24.0 pandas-1.3.5 pkgutil-resolve-name-1.3.10 protobuf-3.20.1 pyDeprecate-0.3.2 pyasn1-0.5.1 pyasn1-modules-0.3.0 pyrsistent-0.19.3 python-dateutil-2.9.0.post0 pytorch-lightning-1.6.5 pytz-2024.1 ray-2.7.2 regex-2024.4.16 requests-2.31.0 requests-oauthlib-2.0.0 rsa-4.9 sacremoses-0.0.53 scikit-learn-1.0.2 scipy-1.7.3 six-1.16.0 tensorboard-2.11.2 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.1 threadpoolctl-3.1.0 tokenizers-0.10.3 torch-1.8.1 torchmetrics-0.4.1 tqdm-4.65.0 transformers-4.8.2 typing-extensions-4.7.1 urllib3-2.0.7 werkzeug-2.2.3 yarl-1.9.4 zipp-3.15.0done #
To activate this environment, use
#
$ conda activate plm_vpf_embed
#
To deactivate an active environment, use
#
$ conda deactivate
Collecting tensorflow Using cached tensorflow-2.16.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.3 kB) Collecting seaborn Using cached seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB) Collecting scikit-learn==1.1.3 Using cached scikit-learn-1.1.3.tar.gz (7.0 MB) Installing build dependencies ... done 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. Getting requirements to build wheel ... error 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.
CalledProcessError Traceback (most recent call last)
2 frames /usr/local/lib/python3.10/dist-packages/google/colab/_system_commands.py in check_returncode(self) 135 def check_returncode(self): 136 if self.returncode: --> 137 raise subprocess.CalledProcessError( 138 returncode=self.returncode, cmd=self.args, output=self.output 139 )
CalledProcessError: Command 'pip install tensorflow seaborn scikit-learn==1.1.3 ipykernel' returned non-zero exit status 1