Installation error

[tonyhqanguyen]

Tonys-MBP:~ tonynguyen$ cd virtualenv-*; python2.7 virtualenv.py ../khmerEnv; cd ..
New python executable in ../khmerEnv/bin/python
Installing setuptools, pip...done.
Tonys-MBP:~ tonynguyen$ source khmerEnv/bin/activate
(khmerEnv)Tonys-MBP:~ tonynguyen$ pip2 install khmer
Downloading/unpacking khmer
  Downloading khmer-2.1.1.tar.gz (8.5MB): 8.5MB downloaded
  Running setup.py (path:/Users/tonynguyen/khmerEnv/build/khmer/setup.py) egg_info for package khmer
    /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'python_requires'
      warnings.warn(msg)
    Traceback (most recent call last):
      File "<string>", line 17, in <module>
      File "/Users/tonynguyen/khmerEnv/build/khmer/setup.py", line 304, in <module>
        setup(cmdclass=CMDCLASS, **SETUP_METADATA)
      File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 111, in setup
        _setup_distribution = dist = klass(attrs)
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/dist.py", line 260, in __init__
        self.fetch_build_eggs(attrs.pop('setup_requires'))
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/dist.py", line 285, in fetch_build_eggs
        replace_conflicting=True
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/pkg_resources.py", line 631, in resolve
        dist = best[req.key] = env.best_match(req, ws, installer)
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/pkg_resources.py", line 871, in best_match
        return self.obtain(req, installer)
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/pkg_resources.py", line 883, in obtain
        return installer(requirement)
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/dist.py", line 335, in fetch_build_egg
        return cmd.easy_install(req)
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 595, in easy_install
        return self.install_item(spec, dist.location, tmpdir, deps)
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 625, in install_item
        dists = self.install_eggs(spec, download, tmpdir)
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 822, in install_eggs
        return self.build_and_install(setup_script, setup_base)
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1028, in build_and_install
        self.run_setup(setup_script, setup_base, args)
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1013, in run_setup
        run_setup(setup_script, args)
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/sandbox.py", line 50, in run_setup
        lambda: execfile(
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/sandbox.py", line 100, in run
        return func()
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/sandbox.py", line 52, in <lambda>
        {'__file__':setup_script, '__name__':'__main__'}
      File "setup.py", line 73, in <module>
        # Checking for OpenMP support. Currently clang doesn't work with OpenMP,
      File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 111, in setup
        _setup_distribution = dist = klass(attrs)
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/dist.py", line 264, in __init__
        _Distribution.__init__(self,attrs)
      File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 287, in __init__
        self.finalize_options()
      File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/dist.py", line 298, in finalize_options
        ep.load()(self, ep.name, value)
      File "/private/var/folders/0w/9pfmj2b54hl6cplpkgb2slyw0000gn/T/easy_install-wIdsFC/pytest-runner-2.12.2/setuptools_scm-2.0.0-py2.7.egg/setuptools_scm/integration.py", line 10, in version_keyword
      File "/private/var/folders/0w/9pfmj2b54hl6cplpkgb2slyw0000gn/T/easy_install-wIdsFC/pytest-runner-2.12.2/setuptools_scm-2.0.0-py2.7.egg/setuptools_scm/version.py", line 44, in _warn_if_setuptools_outdated
    setuptools_scm.version.SetuptoolsOutdatedWarning: your setuptools is too old (<12)
    Complete output from command python setup.py egg_info:
    /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'python_requires'

  warnings.warn(msg)

Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/Users/tonynguyen/khmerEnv/build/khmer/setup.py", line 304, in <module>

    setup(cmdclass=CMDCLASS, **SETUP_METADATA)

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 111, in setup

    _setup_distribution = dist = klass(attrs)

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/dist.py", line 260, in __init__

    self.fetch_build_eggs(attrs.pop('setup_requires'))

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/dist.py", line 285, in fetch_build_eggs

    replace_conflicting=True

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/pkg_resources.py", line 631, in resolve

    dist = best[req.key] = env.best_match(req, ws, installer)

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/pkg_resources.py", line 871, in best_match

    return self.obtain(req, installer)

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/pkg_resources.py", line 883, in obtain

    return installer(requirement)

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/dist.py", line 335, in fetch_build_egg

    return cmd.easy_install(req)

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 595, in easy_install

    return self.install_item(spec, dist.location, tmpdir, deps)

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 625, in install_item

    dists = self.install_eggs(spec, download, tmpdir)

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 822, in install_eggs

    return self.build_and_install(setup_script, setup_base)

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1028, in build_and_install

    self.run_setup(setup_script, setup_base, args)

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1013, in run_setup

    run_setup(setup_script, args)

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/sandbox.py", line 50, in run_setup

    lambda: execfile(

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/sandbox.py", line 100, in run

    return func()

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/sandbox.py", line 52, in <lambda>

    {'__file__':setup_script, '__name__':'__main__'}

  File "setup.py", line 73, in <module>

    # Checking for OpenMP support. Currently clang doesn't work with OpenMP,

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 111, in setup

    _setup_distribution = dist = klass(attrs)

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/dist.py", line 264, in __init__

    _Distribution.__init__(self,attrs)

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 287, in __init__

    self.finalize_options()

  File "/Users/tonynguyen/khmerEnv/lib/python2.7/site-packages/setuptools/dist.py", line 298, in finalize_options

    ep.load()(self, ep.name, value)

  File "/private/var/folders/0w/9pfmj2b54hl6cplpkgb2slyw0000gn/T/easy_install-wIdsFC/pytest-runner-2.12.2/setuptools_scm-2.0.0-py2.7.egg/setuptools_scm/integration.py", line 10, in version_keyword

  File "/private/var/folders/0w/9pfmj2b54hl6cplpkgb2slyw0000gn/T/easy_install-wIdsFC/pytest-runner-2.12.2/setuptools_scm-2.0.0-py2.7.egg/setuptools_scm/version.py", line 44, in _warn_if_setuptools_outdated

setuptools_scm.version.SetuptoolsOutdatedWarning: your setuptools is too old (<12)

----------------------------------------
Cleaning up...
Command python setup.py egg_info failed with error code 1 in /Users/tonynguyen/khmerEnv/build/khmer
Storing debug log for failure in /Users/tonynguyen/.pip/pip.log
(khmerEnv)Tonys-MBP:~ tonynguyen$ 

I tried to install khmer but I keep getting this egg_info error. Any help?

[standage]

Hi @UltraSpecialException!

It looks like you're installing khmer in a python 2 environment. We recently stopped supporting Python 2, so khmer requires Python 3.4 or higher. Sorry the default installation instructions don't reflect this yet. Please try the latest version of the installation instructions and let us know if this solves your issue. Thanks!

[andrea-w]

Hi @standage

I'm encountering the same installation issue as the OP, but when I click your link to the latest installation instructions, I get a 404 error. Could you please check the link? Thanks!

[luizirber]

@standage I fixed the link in your comment, it works now

[luizirber]

@UltraSpecialException this error happens because you have a (very) old version of setuptools. Try to do pip2 install -U setuptools before running pip2 install khmer

(in this case you're still installing khmer 2.1.1, which does support Python 2. If you install from master, you need the new instructions that @standage posted)