swolock / scrublet

Detect doublets in single-cell RNA-seq data
MIT License
135 stars 73 forks source link

Rolling back uninstall of llvmlite #38

Open brianpenghe opened 2 years ago

brianpenghe commented 2 years ago

I was trying to install scrublet but got stuck at the last step:

~/tools/scrublet$ sudo pip3 install --upgrade .

  Running setup.py install for pillow ... done
  Found existing installation: kiwisolver 1.2.0
    Uninstalling kiwisolver-1.2.0:
      Successfully uninstalled kiwisolver-1.2.0
  Found existing installation: matplotlib 3.3.2
    Uninstalling matplotlib-3.3.2:
      Successfully uninstalled matplotlib-3.3.2
  Found existing installation: llvmlite 0.34.0
    Uninstalling llvmlite-0.34.0:
      Successfully uninstalled llvmlite-0.34.0
  Running setup.py install for llvmlite ... error
    Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-uknjr2ti/llvmlite/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-jd371i4f-record/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    got version from file /tmp/pip-build-uknjr2ti/llvmlite/llvmlite/_version.py {'version': '0.36.0', 'full': 'e6bb8d137d922bec8beeb01a237254778759becd'}
    running build_ext
    /usr/bin/python3 /tmp/pip-build-uknjr2ti/llvmlite/ffi/build.py
    LLVM version... Traceback (most recent call last):
      File "/tmp/pip-build-uknjr2ti/llvmlite/ffi/build.py", line 220, in <module>
        main()
      File "/tmp/pip-build-uknjr2ti/llvmlite/ffi/build.py", line 210, in main
        main_posix('linux', '.so')
      File "/tmp/pip-build-uknjr2ti/llvmlite/ffi/build.py", line 134, in main_posix
        raise RuntimeError(msg) from None
    RuntimeError: Could not find a `llvm-config` binary. There are a number of reasons this could occur, please see: https://llvmlite.readthedocs.io/en/latest/admin-guide/install.html#using-pip for help.
    error: command '/usr/bin/python3' failed with exit status 1

    ----------------------------------------
  Rolling back uninstall of llvmlite
Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-uknjr2ti/llvmlite/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-jd371i4f-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-uknjr2ti/llvmlite/

Any ideas?

jambler24 commented 2 years ago

Are you using an M1 Mac? Had a similar issue recently and had to switch to a non-M1 python

brianpenghe commented 2 years ago

I was using our linux server. And how do I check M1 vs non-M1 thing?