ERROR: Could not build wheels for pybedtools, which is required to install pyproject.toml-based projects

[lili03080317]

Hi，when I tried to install the lastest version of oimcverse in conda env in Ubuntu-18.04，I got the errors. bash: conda create -n omicverse_new python=3.8 conda activate omicverse_new conda install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia sudo apt update sudo apt install build-essential pip install -U omicverse

when I run "pip install -U omicverse",I got the errors.

errors: building 'pybedtools.cbedtools' extension creating build/temp.linux-x86_64-cpython-38 creating build/temp.linux-x86_64-cpython-38/pybedtools creating build/temp.linux-x86_64-cpython-38/pybedtools/include gcc -pthread -B /opt/miniconda3/envs/omicverse_new/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipybedtools/include/ -I/opt/miniconda3/envs/omicverse_new/include/python3.8 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-cpython-38/pybedtools/cbedtools.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from pybedtools/include/bedFile.h:16:0, from pybedtools/cbedtools.cpp:802: pybedtools/include/gzstream.h:35:10: fatal error: zlib.h: 没有那个文件或目录

include

            ^~~~~~~~
  compilation terminated.
  error: command '/usr/bin/gcc' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pybedtools Running setup.py clean for pybedtools error: subprocess-exited-with-error

× python setup.py clean did not run successfully. │ exit code: 1 ╰─> [10 lines of output] /tmp/pip-install-65leg3pu/pybedtools_60ac1bf154314fc59d0a104b76734273/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /opt/miniconda3/envs/omicverse_new/lib/python3.8/site-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: setup.py --help [cmd1 cmd2 ...] or: setup.py --help-commands or: setup.py cmd --help

  error: option --all not recognized
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed cleaning build dir for pybedtools Building wheel for autograd-gamma (setup.py) ... done Created wheel for autograd-gamma: filename=autograd_gamma-0.5.0-py3-none-any.whl size=4031 sha256=987885d07be77dea446448292ad3a7c61a5b2c300571fe91760468c1dd20acd7 Stored in directory: /root/.cache/pip/wheels/16/a2/b6/582cfdfbeeccd469504a01af3bb952fd9e7eccba40995eafea Building wheel for future (setup.py) ... done Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492024 sha256=44fcac4f59af5d9a2a10ba42b74b587285216018ca7159c6028b9a7c560c6423 Stored in directory: /root/.cache/pip/wheels/a0/0b/ee/e6994fadb42c1354dcccb139b0bf2795271bddfe6253ccdf11 Building wheel for umap-learn (setup.py) ... done Created wheel for umap-learn: filename=umap_learn-0.5.4-py3-none-any.whl size=86770 sha256=5928e68469d0e466a2c3b32a00a4c1bd1840e630ad3d158ee0d61379c71aae45 Stored in directory: /root/.cache/pip/wheels/b0/b0/fa/673b574ab0d1ca1b9d6000d87258c23bb6c0c5e2aae5ba73f5 Building wheel for annoy (setup.py) ... done Created wheel for annoy: filename=annoy-1.17.3-cp38-cp38-linux_x86_64.whl size=396758 sha256=6e27d004a85cec92f1fae9cd6a4d4c0b92ed50c8a232501a36ed1f7cb9b2ad20 Stored in directory: /root/.cache/pip/wheels/55/2b/62/d6b83c564671d3cea4eb393ffdfc3ed9b9f2482fc79e8b4c35 Building wheel for bioservices (setup.py) ... done Created wheel for bioservices: filename=bioservices-1.11.2-py3-none-any.whl size=223233 sha256=d687a96794ab2726d8a41c95dd73647fc03486fed2050ef7e9d8f26eb4498500 Stored in directory: /root/.cache/pip/wheels/5a/58/4b/6191111a90451294dcc49e3483b4bb7638fa3ff0c2198c52d6 Building wheel for datashape (setup.py) ... done Created wheel for datashape: filename=datashape-0.5.2-py3-none-any.whl size=59413 sha256=43c2218ffebf500dc0618a2cb25a1fe244eb0621e42d345eb4323235d46630a0 Stored in directory: /root/.cache/pip/wheels/6d/79/c4/c425774559165f472d32e5ef592ff9a71179abb31f05dbc98b Building wheel for session-info (setup.py) ... done Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8026 sha256=c110150f65c5b8e003b0000a3bcfd21f0563a0d1714134dda29b53ba8e2e5162 Stored in directory: /root/.cache/pip/wheels/5c/1b/4d/111d73980c5c6a8e5e5905a19eccc34296cb359cac54c6c5b9 Building wheel for upsetplot (setup.py) ... done Created wheel for upsetplot: filename=UpSetPlot-0.8.0-py3-none-any.whl size=23527 sha256=4e334d3f224e0c326f7cf012909f7d103994ce9758400b618b8577c39f9b2e9a Stored in directory: /root/.cache/pip/wheels/ab/1c/20/a07c46f87040c01039dfaf8728b281ae4053c1d3d89d61930c Building wheel for easydev (setup.py) ... done Created wheel for easydev: filename=easydev-0.12.1-py3-none-any.whl size=64213 sha256=f2e84a56ef23e52a3774611dec253f782f11bd42ffcc599954c987ecf3f21515 Stored in directory: /root/.cache/pip/wheels/ed/f7/20/2b6bbee53a7f66bb264ad2bd1416f37285afab73dcec851feb Building wheel for pynndescent (setup.py) ... done Created wheel for pynndescent: filename=pynndescent-0.5.10-py3-none-any.whl size=55615 sha256=2d0717da4c66bb10f00800a04409e9d83e88b2ae02069e3716bd0f5e4f37deb3 Stored in directory: /root/.cache/pip/wheels/f8/32/54/fa1fd0454e0441eaa32550ea2a86da3f64eb7c8e5a82436770 Successfully built hnswlib autograd-gamma future umap-learn annoy bioservices datashape session-info upsetplot easydev pynndescent Failed to build pybedtools ERROR: Could not build wheels for pybedtools, which is required to install pyproject.toml-based projects.

I tried to install pybedtools only,but I got some errors. How to fix it?Thank you.