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MannLabs / alphapeptdeep

Deep learning framework for proteomics
Apache License 2.0
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Error in installing by Developer installer #132

Closed hxxhust163 closed 3 months ago

hxxhust163 commented 6 months ago

Hi

Thanks for your work in alphapeptdeep!

I followed the instruction in Developer installer section to install alphapeptdeep in my linux server. Because the size of the /home folder is very small, so I intend to install in the /tools folder. Following is my cmd:

(peptdeep) user@linux:/tools/alphapeptdeep/project/alphapeptdeep$ sudo pip install -e ".[development]" -t /tools/anaconda3/envs/peptdeep/bin

then I got an error like this: Screenshot from 2024-01-19 22-29-27

Please help how to fix this problem. Thanks very much!

Best Xiaoxiang

jalew188 commented 6 months ago

Do not use sudo, as sudo may have its own python env

hxxhust163 commented 6 months ago

Thanks for your help ! very appreciated.

I removed the virtual environment created by conda and redo by

conda create --name peptdeep python=3.9 -y conda activate peptdeep

(peptdeep) user@linux:/tools/alphapeptdeep/project/alphapeptdeep$ pip install -e ".[development]"

after that, I got an error like this:

Screenshot from 2024-01-20 16-41-33

following is the entire info:

Obtaining file:///tools/alphapeptdeep/project/alphapeptdeep Preparing metadata (setup.py) ... done Collecting click Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Collecting pandas Using cached pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB) Collecting numpy Using cached numpy-1.26.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB) Collecting torch Using cached torch-2.1.2-cp39-cp39-manylinux1_x86_64.whl.metadata (25 kB) Collecting tqdm Using cached tqdm-4.66.1-py3-none-any.whl.metadata (57 kB) Collecting numba Using cached numba-0.58.1-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.7 kB) Collecting psutil Using cached psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB) Collecting biopython Using cached biopython-1.83-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB) Collecting transformers Using cached transformers-4.36.2-py3-none-any.whl.metadata (126 kB) Collecting scikit-learn Using cached scikit_learn-1.4.0-1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB) Collecting streamlit Using cached streamlit-1.30.0-py2.py3-none-any.whl.metadata (8.2 kB) Collecting streamlit-aggrid Using cached streamlit_aggrid-0.3.4.post3-py3-none-any.whl (3.4 MB) Collecting lxml Using cached lxml-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.5 kB) Collecting pyteomics Using cached pyteomics-4.6.3-py2.py3-none-any.whl.metadata (6.5 kB) Collecting alphabase Using cached alphabase-1.2.0-py3-none-any.whl.metadata (13 kB) Collecting alpharaw Using cached alpharaw-0.4.2-py3-none-any.whl.metadata (13 kB) Collecting jupyter Using cached jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB) Collecting twine Using cached twine-4.0.2-py3-none-any.whl (36 kB) Collecting bumpversion Using cached bumpversion-0.6.0-py2.py3-none-any.whl (8.4 kB) Collecting pipdeptree Using cached pipdeptree-2.13.2-py3-none-any.whl.metadata (15 kB) Collecting ipykernel Using cached ipykernel-6.29.0-py3-none-any.whl.metadata (6.0 kB) Collecting wget Using cached wget-3.2-py3-none-any.whl Collecting nbdev Using cached nbdev-2.3.13-py3-none-any.whl.metadata (10 kB) Collecting pyinstaller Using cached pyinstaller-6.3.0-py3-none-manylinux2014_x86_64.whl.metadata (8.3 kB) Collecting seaborn Using cached seaborn-0.13.1-py3-none-any.whl.metadata (5.4 kB) Collecting matplotlib Using cached matplotlib-3.8.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB) Collecting autodocsumm Using cached autodocsumm-0.2.12-py3-none-any.whl.metadata (5.5 kB) Collecting myst_parser Using cached myst_parser-2.0.0-py3-none-any.whl.metadata (5.4 kB) Collecting sphinx Using cached sphinx-7.2.6-py3-none-any.whl.metadata (5.9 kB) Collecting nbsphinx Using cached nbsphinx-0.9.3-py3-none-any.whl.metadata (2.1 kB) Collecting jinja2 Using cached Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB) Collecting contextfilter Using cached contextfilter-0.3.0-py3-none-any.whl (3.7 kB) Collecting furo Using cached furo-2023.9.10-py3-none-any.whl.metadata (5.9 kB) Collecting pyyaml (from alphabase) Using cached PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) Collecting h5py (from alphabase) Using cached h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) Collecting contextlib2 (from alphabase) Using cached contextlib2-21.6.0-py2.py3-none-any.whl (13 kB) Collecting xxhash (from alphabase) Using cached xxhash-3.4.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB) Collecting regex (from alphabase) Using cached regex-2023.12.25-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (40 kB) Collecting dask (from alphabase) Using cached dask-2024.1.0-py3-none-any.whl.metadata (3.7 kB) Collecting pyahocorasick (from alphabase) Using cached pyahocorasick-2.0.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (103 kB) Collecting sqlalchemy (from alpharaw) Using cached SQLAlchemy-2.0.25-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.6 kB) Collecting alphatims (from alpharaw) Using cached alphatims-1.0.8-py3-none-any.whl.metadata (39 kB) Collecting sphinxcontrib-applehelp (from sphinx) Using cached sphinxcontrib_applehelp-1.0.8-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-devhelp (from sphinx) Using cached sphinxcontrib_devhelp-1.0.6-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-jsmath (from sphinx) Using cached sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-htmlhelp>=2.0.0 (from sphinx) Using cached sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx) Using cached sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl.metadata (2.4 kB) Collecting sphinxcontrib-qthelp (from sphinx) Using cached sphinxcontrib_qthelp-1.0.7-py3-none-any.whl.metadata (2.2 kB) Collecting Pygments>=2.14 (from sphinx) Using cached pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB) Collecting docutils<0.21,>=0.18.1 (from sphinx) Using cached docutils-0.20.1-py3-none-any.whl.metadata (2.8 kB) Collecting snowballstemmer>=2.0 (from sphinx) Using cached snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) Collecting babel>=2.9 (from sphinx) Using cached Babel-2.14.0-py3-none-any.whl.metadata (1.6 kB) Collecting alabaster<0.8,>=0.7 (from sphinx) Using cached alabaster-0.7.16-py3-none-any.whl.metadata (2.9 kB) Collecting imagesize>=1.3 (from sphinx) Using cached imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting requests>=2.25.0 (from sphinx) Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting packaging>=21.0 (from sphinx) Using cached packaging-23.2-py3-none-any.whl.metadata (3.2 kB) Collecting importlib-metadata>=4.8 (from sphinx) Using cached importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB) Collecting MarkupSafe>=2.0 (from jinja2) Using cached MarkupSafe-2.1.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB) Collecting bump2version (from bumpversion) Using cached bump2version-1.0.1-py2.py3-none-any.whl (22 kB) Collecting beautifulsoup4 (from furo) Using cached beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB) Collecting sphinx-basic-ng (from furo) Using cached sphinx_basic_ng-1.0.0b2-py3-none-any.whl.metadata (1.5 kB) Collecting comm>=0.1.1 (from ipykernel) Using cached comm-0.2.1-py3-none-any.whl.metadata (3.7 kB) Collecting debugpy>=1.6.5 (from ipykernel) Using cached debugpy-1.8.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.0 kB) Collecting ipython>=7.23.1 (from ipykernel) Using cached ipython-8.18.1-py3-none-any.whl.metadata (6.0 kB) Collecting jupyter-client>=6.1.12 (from ipykernel) Using cached jupyter_client-8.6.0-py3-none-any.whl.metadata (8.3 kB) Collecting jupyter-core!=5.0.*,>=4.12 (from ipykernel) Using cached jupyter_core-5.7.1-py3-none-any.whl.metadata (3.4 kB) Collecting matplotlib-inline>=0.1 (from ipykernel) Using cached matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB) Collecting nest-asyncio (from ipykernel) Using cached nest_asyncio-1.5.9-py3-none-any.whl.metadata (2.8 kB) Collecting pyzmq>=24 (from ipykernel) Using cached pyzmq-25.1.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (4.9 kB) Collecting tornado>=6.1 (from ipykernel) Using cached tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) Collecting traitlets>=5.4.0 (from ipykernel) Using cached traitlets-5.14.1-py3-none-any.whl.metadata (10 kB) Collecting notebook (from jupyter) Using cached notebook-7.0.7-py3-none-any.whl.metadata (10 kB) Collecting qtconsole (from jupyter) Using cached qtconsole-5.5.1-py3-none-any.whl.metadata (5.1 kB) Collecting jupyter-console (from jupyter) Using cached jupyter_console-6.6.3-py3-none-any.whl (24 kB) Collecting nbconvert (from jupyter) Using cached nbconvert-7.14.2-py3-none-any.whl.metadata (7.7 kB) Collecting ipywidgets (from jupyter) Using cached ipywidgets-8.1.1-py3-none-any.whl.metadata (2.4 kB) Collecting contourpy>=1.0.1 (from matplotlib) Using cached contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB) Collecting cycler>=0.10 (from matplotlib) Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) Collecting fonttools>=4.22.0 (from matplotlib) Using cached fonttools-4.47.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (157 kB) Collecting kiwisolver>=1.3.1 (from matplotlib) Using cached kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.4 kB) Collecting pillow>=8 (from matplotlib) Using cached pillow-10.2.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.7 kB) Collecting pyparsing>=2.3.1 (from matplotlib) Using cached pyparsing-3.1.1-py3-none-any.whl.metadata (5.1 kB) Collecting python-dateutil>=2.7 (from matplotlib) Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting importlib-resources>=3.2.0 (from matplotlib) Using cached importlib_resources-6.1.1-py3-none-any.whl.metadata (4.1 kB) Collecting markdown-it-py~=3.0 (from myst_parser) Using cached markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB) Collecting mdit-py-plugins~=0.4 (from myst_parser) Using cached mdit_py_plugins-0.4.0-py3-none-any.whl.metadata (2.7 kB) Collecting ipywidgets (from jupyter) Using cached ipywidgets-8.0.4-py3-none-any.whl (137 kB) Collecting fastcore>=1.5.27 (from nbdev) Using cached fastcore-1.5.29-py3-none-any.whl (67 kB) Collecting execnb>=0.1.4 (from nbdev) Using cached execnb-0.1.5-py3-none-any.whl (13 kB) Collecting astunparse (from nbdev) Using cached astunparse-1.6.3-py2.py3-none-any.whl (12 kB) Collecting ghapi>=1.0.3 (from nbdev) Using cached ghapi-1.0.4-py3-none-any.whl.metadata (13 kB) Collecting watchdog (from nbdev) Using cached watchdog-3.0.0-py3-none-manylinux2014_x86_64.whl (82 kB) Collecting asttokens (from nbdev) Using cached asttokens-2.4.1-py2.py3-none-any.whl.metadata (5.2 kB) Collecting nbformat (from nbsphinx) Using cached nbformat-5.9.2-py3-none-any.whl.metadata (3.4 kB) Collecting llvmlite<0.42,>=0.41.0dev0 (from numba) Using cached llvmlite-0.41.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.8 kB) Collecting pytz>=2020.1 (from pandas) Using cached pytz-2023.3.post1-py2.py3-none-any.whl.metadata (22 kB) Collecting tzdata>=2022.7 (from pandas) Using cached tzdata-2023.4-py2.py3-none-any.whl.metadata (1.4 kB) Requirement already satisfied: setuptools>=42.0.0 in /tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages (from pyinstaller) (68.2.2) Collecting altgraph (from pyinstaller) Using cached altgraph-0.17.4-py2.py3-none-any.whl.metadata (7.3 kB) Collecting pyinstaller-hooks-contrib>=2021.4 (from pyinstaller) Using cached pyinstaller_hooks_contrib-2024.0-py2.py3-none-any.whl.metadata (16 kB) Collecting scipy>=1.6.0 (from scikit-learn) Using cached scipy-1.11.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) Collecting joblib>=1.2.0 (from scikit-learn) Using cached joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB) Collecting threadpoolctl>=2.0.0 (from scikit-learn) Using cached threadpoolctl-3.2.0-py3-none-any.whl.metadata (10.0 kB) Collecting altair<6,>=4.0 (from streamlit) Using cached altair-5.2.0-py3-none-any.whl.metadata (8.7 kB) Collecting blinker<2,>=1.0.0 (from streamlit) Using cached blinker-1.7.0-py3-none-any.whl.metadata (1.9 kB) Collecting cachetools<6,>=4.0 (from streamlit) Using cached cachetools-5.3.2-py3-none-any.whl.metadata (5.2 kB) Collecting protobuf<5,>=3.20 (from streamlit) Using cached protobuf-4.25.2-cp37-abi3-manylinux2014_x86_64.whl.metadata (541 bytes) Collecting pyarrow>=6.0 (from streamlit) Using cached pyarrow-14.0.2-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (3.0 kB) Collecting rich<14,>=10.14.0 (from streamlit) Using cached rich-13.7.0-py3-none-any.whl.metadata (18 kB) Collecting tenacity<9,>=8.1.0 (from streamlit) Using cached tenacity-8.2.3-py3-none-any.whl.metadata (1.0 kB) Collecting toml<2,>=0.10.1 (from streamlit) Using cached toml-0.10.2-py2.py3-none-any.whl (16 kB) Collecting typing-extensions<5,>=4.3.0 (from streamlit) Using cached typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB) Collecting tzlocal<6,>=1.1 (from streamlit) Using cached tzlocal-5.2-py3-none-any.whl.metadata (7.8 kB) Collecting validators<1,>=0.2 (from streamlit) Using cached validators-0.22.0-py3-none-any.whl.metadata (4.7 kB) Collecting gitpython!=3.1.19,<4,>=3.0.7 (from streamlit) Using cached GitPython-3.1.41-py3-none-any.whl.metadata (14 kB) Collecting pydeck<1,>=0.8.0b4 (from streamlit) Using cached pydeck-0.8.1b0-py2.py3-none-any.whl (4.8 MB) Collecting python-decouple<4.0,>=3.6 (from streamlit-aggrid) Using cached python_decouple-3.8-py3-none-any.whl (9.9 kB) Collecting filelock (from torch) Using cached filelock-3.13.1-py3-none-any.whl.metadata (2.8 kB) Collecting sympy (from torch) Using cached sympy-1.12-py3-none-any.whl (5.7 MB) Collecting networkx (from torch) Using cached networkx-3.2.1-py3-none-any.whl.metadata (5.2 kB) Collecting fsspec (from torch) Using cached fsspec-2023.12.2-py3-none-any.whl.metadata (6.8 kB) Collecting nvidia-cuda-nvrtc-cu12==12.1.105 (from torch) Using cached nvidia_cuda_nvrtc_cu12-12.1.105-py3-none-manylinux1_x86_64.whl (23.7 MB) Collecting nvidia-cuda-runtime-cu12==12.1.105 (from torch) Using cached nvidia_cuda_runtime_cu12-12.1.105-py3-none-manylinux1_x86_64.whl (823 kB) Collecting nvidia-cuda-cupti-cu12==12.1.105 (from torch) Using cached nvidia_cuda_cupti_cu12-12.1.105-py3-none-manylinux1_x86_64.whl (14.1 MB) Collecting nvidia-cudnn-cu12==8.9.2.26 (from torch) Using cached nvidia_cudnn_cu12-8.9.2.26-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB) Collecting nvidia-cublas-cu12==12.1.3.1 (from torch) Using cached nvidia_cublas_cu12-12.1.3.1-py3-none-manylinux1_x86_64.whl (410.6 MB) Collecting nvidia-cufft-cu12==11.0.2.54 (from torch) Using cached nvidia_cufft_cu12-11.0.2.54-py3-none-manylinux1_x86_64.whl (121.6 MB) Collecting nvidia-curand-cu12==10.3.2.106 (from torch) Using cached nvidia_curand_cu12-10.3.2.106-py3-none-manylinux1_x86_64.whl (56.5 MB) Collecting nvidia-cusolver-cu12==11.4.5.107 (from torch) Using cached nvidia_cusolver_cu12-11.4.5.107-py3-none-manylinux1_x86_64.whl (124.2 MB) Collecting nvidia-cusparse-cu12==12.1.0.106 (from torch) Using cached nvidia_cusparse_cu12-12.1.0.106-py3-none-manylinux1_x86_64.whl (196.0 MB) Collecting nvidia-nccl-cu12==2.18.1 (from torch) Using cached 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nh3-0.2.15-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.7 kB) Collecting charset-normalizer<4,>=2 (from requests>=2.25.0->sphinx) Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB) Collecting idna<4,>=2.5 (from requests>=2.25.0->sphinx) Using cached idna-3.6-py3-none-any.whl.metadata (9.9 kB) Collecting certifi>=2017.4.17 (from requests>=2.25.0->sphinx) Using cached certifi-2023.11.17-py3-none-any.whl.metadata (2.2 kB) Collecting pyzstd (from alphatims->alpharaw) Using cached pyzstd-0.15.9-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.5 kB) Requirement already satisfied: wheel<1.0,>=0.23.0 in /tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages (from astunparse->nbdev) (0.41.2) Collecting soupsieve>1.2 (from beautifulsoup4->furo) Using cached soupsieve-2.5-py3-none-any.whl.metadata (4.7 kB) Collecting cloudpickle>=1.5.0 (from dask->alphabase) Using cached 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send2trash>=1.8.2 (from jupyter-server<3,>=2.4.0->notebook->jupyter) Using cached Send2Trash-1.8.2-py3-none-any.whl (18 kB) Collecting terminado>=0.8.3 (from jupyter-server<3,>=2.4.0->notebook->jupyter) Using cached terminado-0.18.0-py3-none-any.whl.metadata (5.8 kB) Collecting websocket-client (from jupyter-server<3,>=2.4.0->notebook->jupyter) Using cached websocket_client-1.7.0-py3-none-any.whl.metadata (7.9 kB) Collecting async-lru>=1.0.0 (from jupyterlab<5,>=4.0.2->notebook->jupyter) Using cached async_lru-2.0.4-py3-none-any.whl.metadata (4.5 kB) Collecting jupyter-lsp>=2.0.0 (from jupyterlab<5,>=4.0.2->notebook->jupyter) Using cached jupyter_lsp-2.2.2-py3-none-any.whl.metadata (1.8 kB) Collecting tomli (from jupyterlab<5,>=4.0.2->notebook->jupyter) Using cached tomli-2.0.1-py3-none-any.whl (12 kB) Collecting json5>=0.9.0 (from jupyterlab-server<3,>=2.22.1->notebook->jupyter) Using cached json5-0.9.14-py2.py3-none-any.whl.metadata (10 kB) Collecting locket (from 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send2trash, safetensors, rpds-py, rfc3986-validator, rfc3986, regex, pyzstd, pyzmq, pyyaml, python-json-logger, pyparsing, Pygments, pycparser, pyahocorasick, psutil, protobuf, prompt-toolkit, prometheus-client, platformdirs, pkginfo, pipdeptree, pillow, pexpect, parso, pandocfilters, packaging, overrides, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, numpy, networkx, nest-asyncio, more-itertools, mistune, mdurl, MarkupSafe, lxml, locket, llvmlite, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, joblib, jeepney, imagesize, idna, greenlet, fsspec, fqdn, fonttools, filelock, executing, exceptiongroup, docutils, defusedxml, decorator, debugpy, cycler, contextlib2, contextfilter, cloudpickle, click, charset-normalizer, certifi, cachetools, bump2version, blinker, babel, attrs, alabaster, triton, terminado, sqlalchemy, scipy, rfc3339-validator, requests, referencing, readme-renderer, qtpy, python-dateutil, pyarrow, partd, nvidia-cusparse-cu12, nvidia-cudnn-cu12, numba, matplotlib-inline, markdown-it-py, jupyter-core, jinja2, jedi, jaraco.classes, importlib-resources, importlib-metadata, h5py, gitdb, fastcore, contourpy, comm, cffi, bumpversion, bleach, biopython, beautifulsoup4, async-lru, astunparse, asttokens, anyio, stack-data, sphinx, scikit-learn, rich, requests-toolbelt, pyinstaller-hooks-contrib, pydeck, pandas, nvidia-cusolver-cu12, mdit-py-plugins, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, huggingface-hub, gitpython, ghapi, dask, cryptography, arrow, argon2-cffi-bindings, torch, tokenizers, sphinx-basic-ng, SecretStorage, seaborn, pyinstaller, myst_parser, jsonschema, isoduration, ipython, autodocsumm, argon2-cffi, alphatims, alphabase, transformers, nbformat, keyring, ipykernel, furo, execnb, altair, alpharaw, twine, streamlit, qtconsole, nbclient, jupyter-events, jupyter-console, ipywidgets, streamlit-aggrid, nbdev, nbconvert, peptdeep, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, notebook, jupyter Running setup.py develop for peptdeep error: subprocess-exited-with-error

× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [29 lines of output]
    running develop
    /tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/command/develop.py:40: EasyInstallDeprecationWarning: easy_install command is deprecated.
    !!

            ********************************************************************************
            Please avoid running ``setup.py`` and ``easy_install``.
            Instead, use pypa/build, pypa/installer or other
            standards-based tools.

            See https://github.com/pypa/setuptools/issues/917 for details.
            ********************************************************************************

    !!
      easy_install.initialize_options(self)
    /tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
    !!

            ********************************************************************************
            Please avoid running ``setup.py`` directly.
            Instead, use pypa/build, pypa/installer or other
            standards-based tools.

            See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
            ********************************************************************************

    !!
      self.initialize_options()
    running egg_info
    error: Cannot update time stamp of directory 'peptdeep.egg-info'
    [end of output]

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

error: subprocess-exited-with-error

× python setup.py develop did not run successfully. │ exit code: 1 ╰─> [29 lines of output] running develop /tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/command/develop.py:40: EasyInstallDeprecationWarning: easy_install command is deprecated. !!

        ********************************************************************************
        Please avoid running ``setup.py`` and ``easy_install``.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://github.com/pypa/setuptools/issues/917 for details.
        ********************************************************************************

!!
  easy_install.initialize_options(self)
/tools/anaconda3/envs/peptdeep/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
running egg_info
error: Cannot update time stamp of directory 'peptdeep.egg-info'
[end of output]

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

hxxhust163 commented 6 months ago

Oh, I tried the installation described in the second installation section 'pip'. And finally success.

Thanks very much!

jalew188 commented 6 months ago

Does pip install -e . work? "development" just add some additional packages for developers, you can install them after pip install -e .

hxxhust163 commented 6 months ago

I followed you advice and tried the cmd 'pip install -e .' Unfortunately, it reported the same error as above.

jalew188 commented 6 months ago

Then how did you install it?

hxxhust163 commented 6 months ago

I firstly installed anaconda3 with python3.9. And then installed peptdeep in this existing python environment by 'pip install peptdeep'.

jalew188 commented 6 months ago

I see, just pip install -e . does not work, hmmm..