pip installation broken

[ABignaud]

Hi,

It seems that the pip installation is broken in the latest release (v0.3.19). Here is the error message:

pip install pyBigWig --upgrade

Requirement already satisfied: pyBigWig in /home/rsg/anaconda3/lib/python3.9/site-packages (0.3.18)
Collecting pyBigWig
  Using cached pyBigWig-0.3.19.tar.gz (51 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
    Preparing wheel metadata ... done
Building wheels for collected packages: pyBigWig
  Building wheel for pyBigWig (PEP 517) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/rsg/anaconda3/bin/python /home/rsg/anaconda3/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmp9wfcmz_4
       cwd: /tmp/pip-install-y5e3o1d1/pybigwig_60ef96ebcbe841f3b474835ccdbb6746
  Complete output (28 lines):
  /tmp/pip-build-env-km46od8t/overlay/lib/python3.9/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
    warnings.warn(msg, _BetaConfiguration)
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-cpython-39
  creating build/lib.linux-x86_64-cpython-39/pyBigWigTest
  copying pyBigWigTest/__init__.py -> build/lib.linux-x86_64-cpython-39/pyBigWigTest
  copying pyBigWigTest/test.py -> build/lib.linux-x86_64-cpython-39/pyBigWigTest
  running egg_info
  writing pyBigWig.egg-info/PKG-INFO
  writing dependency_links to pyBigWig.egg-info/dependency_links.txt
  writing top-level names to pyBigWig.egg-info/top_level.txt
  listing git files failed - pretending there aren't any
  reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
  adding license file 'LICENSE.txt'
  writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
  running build_ext
  building 'pyBigWig' extension
  creating build/temp.linux-x86_64-cpython-39
  creating build/temp.linux-x86_64-cpython-39/libBigWig
  gcc -pthread -B /home/rsg/anaconda3/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/rsg/anaconda3/include -fPIC -O2 -isystem /home/rsg/anaconda3/include -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/rsg/anaconda3/include/python3.9 -I/tmp/pip-build-env-km46od8t/overlay/lib/python3.9/site-packages/numpy/core/include -I/home/rsg/anaconda3/include/python3.9 -c libBigWig/bwRead.c -o build/temp.linux-x86_64-cpython-39/libBigWig/bwRead.o
  libBigWig/bwRead.c:1:10: fatal error: bigWig.h: No such file or directory
      1 | #include "bigWig.h"
        |          ^~~~~~~~~~
  compilation terminated.
  error: command '/usr/bin/gcc' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for pyBigWig
Failed to build pyBigWig
ERROR: Could not build wheels for pyBigWig which use PEP 517 and cannot be installed directly

Amaury

[dpryan79]

I just saw an email come in about this too. Apparently the change to using wheels resulting in missing files :( I'll look into this.

[dpryan79]

@ABignaud Can you see if 0.3.20 fixes this?

[ABignaud]

Yes it works !
Thanks for your quick answer.
Amaury

[dpryan79]

Perfect, thanks for pointing out the issue :)