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Blosc / python-blosc2

https://www.blosc.org/python-blosc2
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pip install failure on ubuntu/popos 20 #9

Closed bkmartinjr closed 3 years ago

bkmartinjr commented 3 years ago

Using:

$ pip -V
pip 21.1.1 from /home/bruce/projects/diffexp-playground/venv/lib/python3.8/site-packages/pip (python 3.8)

An error is generated when attempting to install blosc2 from pypi:

$ pip install blosc2
Collecting blosc2
  Downloading blosc2-0.1.1.tar.gz (1.8 MB)
     |████████████████████████████████| 1.8 MB 3.6 MB/s 
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  ERROR: Command errored out with exit status 1:
   command: /home/bruce/projects/diffexp-playground/venv/bin/python /home/bruce/projects/diffexp-playground/venv/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py get_requires_for_build_wheel /tmp/tmp0h_a5ln5
       cwd: /tmp/pip-install-67g0rfgf/blosc2_2a32b130b04a48ad9981054e6619d174
  Complete output (18 lines):
  Traceback (most recent call last):
    File "/home/bruce/projects/diffexp-playground/venv/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 280, in <module>
      main()
    File "/home/bruce/projects/diffexp-playground/venv/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 263, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/home/bruce/projects/diffexp-playground/venv/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 114, in get_requires_for_build_wheel
      return hook(config_settings)
    File "/tmp/pip-build-env-qkyfpmft/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 154, in get_requires_for_build_wheel
      return self._get_build_requires(
    File "/tmp/pip-build-env-qkyfpmft/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 135, in _get_build_requires
      self.run_setup()
    File "/tmp/pip-build-env-qkyfpmft/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 258, in run_setup
      super(_BuildMetaLegacyBackend,
    File "/tmp/pip-build-env-qkyfpmft/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 150, in run_setup
      exec(compile(code, __file__, 'exec'), locals())
    File "setup.py", line 14, in <module>
      from skbuild import setup
  ModuleNotFoundError: No module named 'skbuild'
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/85/8b/c9e9a49d1c79b22455847899b7699ad87154a09eabcd0cd900f0bbc9f5af/blosc2-0.1.1.tar.gz#sha256=3f405c610c43c940e5e819f6f6a5e31158e18f24f14adf9ba2ea9d4ad94a5301 (from https://pypi.org/simple/blosc2/). Command errored out with exit status 1: /home/bruce/projects/diffexp-playground/venv/bin/python /home/bruce/projects/diffexp-playground/venv/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py get_requires_for_build_wheel /tmp/tmp0h_a5ln5 Check the logs for full command output.
ERROR: Could not find a version that satisfies the requirement blosc2 (from versions: 0.1.1)
ERROR: No matching distribution found for blosc2

skbuild is installed (I did it manually):

$ pip freeze | grep scikit-build
scikit-build==0.11.1
bkmartinjr commented 3 years ago

I just tried the latest (v0.1.2) from pipy. It progresses further, but fails while trying to run cmake, with the error:

Could NOT find NumPy (missing: NumPy_INCLUDE_DIR) (found version "")

system info:

$ pip --version
pip 21.1.1 from /home/bruce/projects/diffexp-playground/venv/lib/python3.8/site-packages/pip (python 3.8)
$ cmake --version
cmake version 3.16.3
$ pip freeze | grep numpy
numpy==1.20.3

Full pip output:

$ pip install -U blosc2
Collecting blosc2
  Downloading blosc2-0.1.2.tar.gz (1.8 MB)
     |████████████████████████████████| 1.8 MB 3.8 MB/s 
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
    Preparing wheel metadata ... done
Building wheels for collected packages: blosc2
  Building wheel for blosc2 (PEP 517) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/bruce/projects/diffexp-playground/venv/bin/python /home/bruce/projects/diffexp-playground/venv/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpocat5bj1
       cwd: /tmp/pip-install-2n0nu5gx/blosc2_1a0bfcf1fdae46369ffdba6b1c9f525c
  Complete output (82 lines):
  Not searching for unused variables given on the command line.
  -- The C compiler identification is GNU 10.2.0
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Check for working C compiler: /usr/bin/cc - skipped
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- The CXX compiler identification is GNU 10.2.0
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /usr/bin/c++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /tmp/pip-install-2n0nu5gx/blosc2_1a0bfcf1fdae46369ffdba6b1c9f525c/_cmake_test_compile/build
  -- The C compiler identification is GNU 10.2.0
  -- The CXX compiler identification is GNU 10.2.0
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Check for working C compiler: /usr/bin/cc - skipped
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /usr/bin/c++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- Found PythonInterp: /home/bruce/projects/diffexp-playground/venv/bin/python (found version "3.8.6")
  -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.8.so (found version "3.8.6")
  -- Found Cython: /tmp/pip-build-env-xcski9e4/normal/bin/cython
  CMake Error at /tmp/pip-build-env-xcski9e4/overlay/lib/python3.8/site-packages/cmake/data/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:165 (message):
    Could NOT find NumPy (missing: NumPy_INCLUDE_DIR) (found version "")
  Call Stack (most recent call first):
    /tmp/pip-build-env-xcski9e4/overlay/lib/python3.8/site-packages/cmake/data/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:458 (_FPHSA_FAILURE_MESSAGE)
    /tmp/pip-build-env-xcski9e4/overlay/lib/python3.8/site-packages/skbuild/resources/cmake/FindNumPy.cmake:98 (find_package_handle_standard_args)
    CMakeLists.txt:5 (find_package)

  -- Configuring incomplete, errors occurred!
  See also "/tmp/pip-install-2n0nu5gx/blosc2_1a0bfcf1fdae46369ffdba6b1c9f525c/_skbuild/linux-x86_64-3.8/cmake-build/CMakeFiles/CMakeOutput.log".
    File "/tmp/pip-build-env-xcski9e4/overlay/lib/python3.8/site-packages/skbuild/setuptools_wrap.py", line 582, in setup
      env = cmkr.configure(cmake_args,
    File "/tmp/pip-build-env-xcski9e4/overlay/lib/python3.8/site-packages/skbuild/cmaker.py", line 229, in configure
      raise SKBuildError(

  --------------------------------------------------------------------------------
  -- Trying "Ninja" generator
  --------------------------------
  ---------------------------
  ----------------------
  -----------------
  ------------
  -------
  --
  --
  -------
  ------------
  -----------------
  ----------------------
  ---------------------------
  --------------------------------
  -- Trying "Ninja" generator - success
  --------------------------------------------------------------------------------

  Configuring Project
    Working directory:
      /tmp/pip-install-2n0nu5gx/blosc2_1a0bfcf1fdae46369ffdba6b1c9f525c/_skbuild/linux-x86_64-3.8/cmake-build
    Command:
      cmake /tmp/pip-install-2n0nu5gx/blosc2_1a0bfcf1fdae46369ffdba6b1c9f525c -G Ninja -DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-install-2n0nu5gx/blosc2_1a0bfcf1fdae46369ffdba6b1c9f525c/_skbuild/linux-x86_64-3.8/cmake-install -DPYTHON_EXECUTABLE:FILEPATH=/home/bruce/projects/diffexp-playground/venv/bin/python -DPYTHON_VERSION_STRING:STRING=3.8.6 -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.8 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython3.8.so -DSKBUILD:BOOL=TRUE -DCMAKE_MODULE_PATH:PATH=/tmp/pip-build-env-xcski9e4/overlay/lib/python3.8/site-packages/skbuild/resources/cmake -DDEACTIVATE_SSE2:BOOL=OFF -DDEACTIVATE_AVX2:BOOL=OFF -DDEACTIVATE_LZ4:BOOL=OFF -DDEACTIVATE_ZLIB:BOOL=OFF -DDEACTIVATE_ZSTD:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release

  Traceback (most recent call last):

  An error occurred while configuring with CMake.
    Command:
      cmake /tmp/pip-install-2n0nu5gx/blosc2_1a0bfcf1fdae46369ffdba6b1c9f525c -G Ninja -DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-install-2n0nu5gx/blosc2_1a0bfcf1fdae46369ffdba6b1c9f525c/_skbuild/linux-x86_64-3.8/cmake-install -DPYTHON_EXECUTABLE:FILEPATH=/home/bruce/projects/diffexp-playground/venv/bin/python -DPYTHON_VERSION_STRING:STRING=3.8.6 -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.8 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython3.8.so -DSKBUILD:BOOL=TRUE -DCMAKE_MODULE_PATH:PATH=/tmp/pip-build-env-xcski9e4/overlay/lib/python3.8/site-packages/skbuild/resources/cmake -DDEACTIVATE_SSE2:BOOL=OFF -DDEACTIVATE_AVX2:BOOL=OFF -DDEACTIVATE_LZ4:BOOL=OFF -DDEACTIVATE_ZLIB:BOOL=OFF -DDEACTIVATE_ZSTD:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release
    Source directory:
      /tmp/pip-install-2n0nu5gx/blosc2_1a0bfcf1fdae46369ffdba6b1c9f525c
    Working directory:
      /tmp/pip-install-2n0nu5gx/blosc2_1a0bfcf1fdae46369ffdba6b1c9f525c/_skbuild/linux-x86_64-3.8/cmake-build
  Please see CMake's output for more information.
  ----------------------------------------
  ERROR: Failed building wheel for blosc2
Failed to build blosc2
ERROR: Could not build wheels for blosc2 which use PEP 517 and cannot be installed directly
FrancescAlted commented 3 years ago

Yup, thanks for reporting back. If you try now, this should be fixed in latest 0.1.5. Bonus: wheels are available :-)

bkmartinjr commented 3 years ago

Fantastic! Thanks so much for this incredibly useful package.