h5py: pip install fails on Cython dependency

This is on Debian wheezy.

For some reason, the Cython dependency doesn’t work as it should. I see that there has been quite some refactoring in setup.py and Cython is listed in both requires and install_requires, so I really don’t know why that doesn’t work.

As you can see, pip correctly fetches h5py, numpy and Cython and then proceeds to install them in that order.

martijn@hue:~$ virtualenv /tmp/h5py
New python executable in /tmp/h5py/bin/python
Installing setuptools, pip...done.
martijn@hue:~$ /tmp/h5py/bin/pip install h5py
Downloading/unpacking h5py
  Downloading h5py-2.4.0.tar.gz (172kB): 172kB downloaded
  Running setup.py (path:/tmp/h5py/build/h5py/setup.py) egg_info for package h5py

    warning: no previously-included files found matching 'h5py/defs.pyx'
    warning: no previously-included files found matching 'h5py/defs.pxd'
    warning: no previously-included files found matching 'h5py/config.pxi'
Downloading/unpacking numpy>=1.6.1 (from h5py)
  Downloading numpy-1.9.1.tar.gz (4.0MB): 4.0MB downloaded
  Running setup.py (path:/tmp/h5py/build/numpy/setup.py) egg_info for package numpy
    Running from numpy source directory.

    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '*.pyo' found anywhere in distribution
    warning: no previously-included files matching '*.pyd' found anywhere in distribution
Downloading/unpacking Cython>=0.17 (from h5py)
  Downloading Cython-0.21.2.tar.gz (1.5MB): 1.5MB downloaded
  Running setup.py (path:/tmp/h5py/build/Cython/setup.py) egg_info for package Cython
    Compiling module Cython.Plex.Scanners ...
    Compiling module Cython.Plex.Actions ...
    Compiling module Cython.Compiler.Lexicon ...
    Compiling module Cython.Compiler.Scanning ...
    Compiling module Cython.Compiler.Parsing ...
    Compiling module Cython.Compiler.Visitor ...
    Compiling module Cython.Compiler.FlowControl ...
    Compiling module Cython.Compiler.Code ...
    Compiling module Cython.Runtime.refnanny ...
    Compiling module Cython.Tempita._tempita ...

    warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests'
    warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests'
    warning: no files found matching '*.h' under directory 'Cython/Debugger/Tests'
    warning: no files found matching '*.pxd' under directory 'Cython/Utility'
Installing collected packages: h5py, numpy, Cython
  Running setup.py install for h5py
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/h5py/build/h5py/setup.py", line 147, in <module>
        cmdclass = CMDCLASS,
      File "/usr/lib/python2.7/distutils/core.py", line 152, in setup
        dist.run_commands()
      File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "build/bdist.linux-x86_64/egg/setuptools/command/install.py", line 61, in run
      File "/usr/lib/python2.7/distutils/command/install.py", line 601, in run
        self.run_command('build')
      File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
        self.distribution.run_command(command)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/usr/lib/python2.7/distutils/command/build.py", line 128, in run
        self.run_command(cmd_name)
      File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
        self.distribution.run_command(command)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "setup_build.py", line 99, in run
        from Cython.Build import cythonize
    ImportError: No module named Cython.Build
    Complete output from command /tmp/h5py/bin/python -c "import setuptools, tokenize;__file__='/tmp/h5py/build/h5py/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-nyKOEl-record/install-record.txt --single-version-externally-managed --compile --install-headers /tmp/h5py/include/site/python2.7:
    running install

running build

running build_py

creating build

creating build/lib.linux-x86_64-2.7

creating build/lib.linux-x86_64-2.7/h5py

copying h5py/version.py -> build/lib.linux-x86_64-2.7/h5py

copying h5py/__init__.py -> build/lib.linux-x86_64-2.7/h5py

copying h5py/highlevel.py -> build/lib.linux-x86_64-2.7/h5py

copying h5py/ipy_completer.py -> build/lib.linux-x86_64-2.7/h5py

creating build/lib.linux-x86_64-2.7/h5py/_hl

copying h5py/_hl/selections2.py -> build/lib.linux-x86_64-2.7/h5py/_hl

copying h5py/_hl/__init__.py -> build/lib.linux-x86_64-2.7/h5py/_hl

copying h5py/_hl/attrs.py -> build/lib.linux-x86_64-2.7/h5py/_hl

copying h5py/_hl/dataset.py -> build/lib.linux-x86_64-2.7/h5py/_hl

copying h5py/_hl/base.py -> build/lib.linux-x86_64-2.7/h5py/_hl

copying h5py/_hl/dims.py -> build/lib.linux-x86_64-2.7/h5py/_hl

copying h5py/_hl/group.py -> build/lib.linux-x86_64-2.7/h5py/_hl

copying h5py/_hl/files.py -> build/lib.linux-x86_64-2.7/h5py/_hl

copying h5py/_hl/selections.py -> build/lib.linux-x86_64-2.7/h5py/_hl

copying h5py/_hl/datatype.py -> build/lib.linux-x86_64-2.7/h5py/_hl

copying h5py/_hl/filters.py -> build/lib.linux-x86_64-2.7/h5py/_hl

creating build/lib.linux-x86_64-2.7/h5py/tests

copying h5py/tests/__init__.py -> build/lib.linux-x86_64-2.7/h5py/tests

copying h5py/tests/common.py -> build/lib.linux-x86_64-2.7/h5py/tests

creating build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_dataset.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_h5.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/__init__.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_slicing.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_dimension_scales.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_selections.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_attrs.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_h5p.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_h5t.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_group.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_file.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_h5f.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/common.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_objects.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_datatype.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_base.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

copying h5py/tests/old/test_attrs_data.py -> build/lib.linux-x86_64-2.7/h5py/tests/old

creating build/lib.linux-x86_64-2.7/h5py/tests/hl

copying h5py/tests/hl/__init__.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl

copying h5py/tests/hl/test_dataset_getitem.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl

copying h5py/tests/hl/test_dims_dimensionproxy.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl

copying h5py/tests/hl/test_file.py -> build/lib.linux-x86_64-2.7/h5py/tests/hl

running build_ext

Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/tmp/h5py/build/h5py/setup.py", line 147, in <module>

    cmdclass = CMDCLASS,

  File "/usr/lib/python2.7/distutils/core.py", line 152, in setup

    dist.run_commands()

  File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands

    self.run_command(cmd)

  File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command

    cmd_obj.run()

  File "build/bdist.linux-x86_64/egg/setuptools/command/install.py", line 61, in run

  File "/usr/lib/python2.7/distutils/command/install.py", line 601, in run

    self.run_command('build')

  File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command

    self.distribution.run_command(command)

  File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command

    cmd_obj.run()

  File "/usr/lib/python2.7/distutils/command/build.py", line 128, in run

    self.run_command(cmd_name)

  File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command

    self.distribution.run_command(command)

  File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command

    cmd_obj.run()

  File "setup_build.py", line 99, in run

    from Cython.Build import cythonize

ImportError: No module named Cython.Build

----------------------------------------
Cleaning up...
Command /tmp/h5py/bin/python -c "import setuptools, tokenize;__file__='/tmp/h5py/build/h5py/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-nyKOEl-record/install-record.txt --single-version-externally-managed --compile --install-headers /tmp/h5py/include/site/python2.7 failed with error code 1 in /tmp/h5py/build/h5py
Storing debug log for failure in /home/martijn/.pip/pip.log
martijn@hue:~$

About this issue

Original URL
State: closed
Created 9 years ago
Reactions: 8
Comments: 25 (4 by maintainers)

Commits related to this issue

Fixed numpy and Cython dependencies Added numpy and Cython to setup_requires as recommended in https://github.com/numpy/numpy/issues/2434#issuecomment-65252402 and https://github.com/h5py/h5py/issues... — committed to jarthurgross/bloch_distribution by jarthurgross 9 years ago
hoping tip from h5py/h5py#535 will help — committed to bmorris3/shampoo by bmorris3 8 years ago
Pip install Cython before h5py See this bug regarding pip dependency ordering: https://github.com/h5py/h5py/issues/535 — committed to ChrisCummins/clgen by ChrisCummins 8 years ago
added setup_requires Added setup_requires, like they describe in this general pip issue: https://github.com/h5py/h5py/issues/535#issuecomment-79158166 — committed to chriamue/libMR by chriamue 6 years ago
Pip install Cython before h5py See this bug regarding pip dependency ordering: https://github.com/h5py/h5py/issues/535 [Exported from ffc86d3540cdee14e100d75d48db6c14e500e669] — committed to ChrisCummins/bazel_subtree_github_export by ChrisCummins 8 years ago
Pip install Cython before h5py See this bug regarding pip dependency ordering: https://github.com/h5py/h5py/issues/535 [Exported from ffc86d3540cdee14e100d75d48db6c14e500e669] — committed to ChrisCummins/photolib by ChrisCummins 8 years ago
Pip install Cython before h5py See this bug regarding pip dependency ordering: https://github.com/h5py/h5py/issues/535 [Exported from ffc86d3540cdee14e100d75d48db6c14e500e669] — committed to ChrisCummins/format by ChrisCummins 8 years ago
Pip install Cython before h5py See this bug regarding pip dependency ordering: https://github.com/h5py/h5py/issues/535 [Exported from ffc86d3540cdee14e100d75d48db6c14e500e669] — committed to ChrisCummins/cldrive by ChrisCummins 8 years ago
Pip install Cython before h5py See this bug regarding pip dependency ordering: https://github.com/h5py/h5py/issues/535 [Exported from ffc86d3540cdee14e100d75d48db6c14e500e669] — committed to ChrisCummins/cldrive by ChrisCummins 8 years ago

Most upvoted comments

This is some ridiculous pip bug. In a clean virtualenv, if I do:

pip install --no-use-wheel --no-cache-dir h5py

pip does the right thing and installs Cython first. However, if I do:

pip install --no-use-wheel --no-cache-dir Cython h5py

then pip does the wrong thing and tries to build h5py before installing Cython.

+45

taion on Mar 4, 2015

I worked around this by:

pip install Cython
pip install h5py

+34

skorokithakis on Jun 12, 2015

👍

Looks like pip is being a bit stupid here. If you try to install both Cython and h5py simultaneously from e.g. a requirements.txt file, Cython will not be available for building h5py, and h5py will fail to install.

taion on Feb 18, 2015

If someone is having this issue even after trying all above suggestions, it may be because of difference in pip and python versions. If you are running python2, try: pip2 install Cython pip2 install h5py For python3, use pip3.

parulm on Feb 28, 2018