PyNeb

Troubleshooting

Quick solutions to problems encountered occasionally

Could not fetch URL...

When trying to install pip, the following error is sometimes produced:

  Downloading/unpacking PyNeb
  Could not fetch URL https://pypi.python.org/simple/PyNeb/: There was a problem confirming the ssl certificate: 
  Will skip URL https://pypi.python.org/simple/PyNeb/ when looking for download links for PyNeb
  Could not fetch URL https://pypi.python.org/simple/: There was a problem confirming the ssl certificate: 
  Will skip URL https://pypi.python.org/simple/ when looking for download links for PyNeb
  Cannot fetch index base URL https://pypi.python.org/simple/
  Could not fetch URL https://pypi.python.org/simple/PyNeb/: There was a problem confirming the ssl certificate: 
  Will skip URL https://pypi.python.org/simple/PyNeb/ when looking for download links for PyNeb
  Could not find any downloads that satisfy the requirement PyNeb
  No distributions at all found for PyNeb
  Storing complete log in /Users/manund/.pip/pip.log

Solution:

 
sudo easy_install pip==1.2.1

Command python setup.py egg_info failed: numpy

When downloading/unpacking PyNeb with pip, the following error (abridged here) related to numpy is sometimes produced:

  Did find:
    /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/multiarray.so: no matching architecture in universal wrapper
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
  .
  .
  .

    File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in 
      import numpy.core.numeric as _nx
    File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in   
     import multiarray
   ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/multiarray.so, 2): no suitable image found.  Did find:
     /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/multiarray.so: no matching architecture in universal wrapper 

----------------------------------------
Command python setup.py egg_info failed with error code 1 in /private/tmp/pip-build-root/PyNeb

Solution:
Either upgrade numpy:

  pip install --upgrade --user numpy

or uninstall it and reinstall it again:

  pip uninstall numpy
  pip install --user numpy
  pip install --upgrade --user numpy

Command python setup.py egg_info failed...

When downloading/unpacking PyNeb with pip, the following error (abridged here) is sometimes produced:

   Command python setup.py egg_info failed with error code 1 in /private/tmp/pip-build-root/PyNeb

   Exception information:
   Traceback (most recent call last):
     File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/basecommand.py", 
       status = self.run(options, args)
     File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/commands/install.py", line 266, in run
        requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle)
     File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/req.py", line 1057, in prepare_files
       req_to_install.run_egg_info()
     File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/req.py", line 236, in run_egg_info
       command_desc='python setup.py egg_info')
     File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/util.py", line 662, in call_subprocess
       % (command_desc, proc.returncode, cwd))
   InstallationError: Command python setup.py egg_info failed with error code 1 in /private/tmp/pip-build-root/PyNeb

Solution:

TBD

Missing distribution spec...

When downloading/unpacking PyNeb with pip, the following error (abridged here) is sometimes produced:

  pip install ––user PyNeb 
  Exception:
  Traceback (most recent call last):
   File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/basecommand.py", line 139, in main
     status = self.run(options, args)
   File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/commands/install.py", line 235, in run
     InstallRequirement.from_line(name, None))
   File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/req.py", line 118, in from_line
     return cls(req, comes_from, url=url)
   File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/req.py", line 43, in __init__
     req = pkg_resources.Requirement.parse(req)
   File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/distribute-0.6.35-py2.7.egg/pkg_resources.py", line 2680, in parse
     reqs = list(parse_requirements(s))
   File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/distribute-0.6.35-py2.7.egg/pkg_resources.py", line 2593, in parse_requirements
     raise ValueError("Missing distribution spec", line)
  ValueError: ('Missing distribution spec', '\xe2\x80\x93\xe2\x80\x93user')

Solution:

 
The hyphens before "user" in the command are incorrectly encoded. Try writing them from the keyboard rather than copying and pasting from somewhere else.

No module named pyfits

When downloading/unpacking PyNeb with pip, the installation crashes because pyfits can't be found, although it is indeed installed:

Downloading/unpacking PyNeb
  Running setup.py egg_info for package PyNeb
    warng PyNeb: PyFITS package needed
    Traceback (most recent call last):
      File "", line 16, in 
      File "/var/folders/c5/190bsmr91l3c2tsmdtdlz3qm0000gn/T/pip-build/PyNeb/setup.py", line 4, in 
        import pyneb
      File "pyneb/__init__.py", line 34, in 
        from utils.fits import Hdr, writeAtom, writeColl
      File "pyneb/utils/fits.py", line 5, in 
        import pyfits
    ImportError: No module named pyfits
    Complete output from command python setup.py egg_info:
    warng PyNeb: PyFITS package needed

Traceback (most recent call last):
  File "", line 16, in 
  File "/var/folders/c5/190bsmr91l3c2tsmdtdlz3qm0000gn/T/pip-build/PyNeb/setup.py", line 4, in 
    import pyneb
  File "pyneb/__init__.py", line 34, in 
    from utils.fits import Hdr, writeAtom, writeColl
  File "pyneb/utils/fits.py", line 5, in 
    import pyfits

ImportError: No module named pyfits

----------------------------------------
Command python setup.py egg_info failed with error code 1 in /var/folders/c5/190bsmr91l3c2tsmdtdlz3qm0000gn/T/pip-build/PyNeb
Storing complete log in /Users/vale/Library/Logs/pip.log

Solution:

 
The new Enthought Python distribution (Enthought Canopy) apparently clashes with previously installed libraries. A quick fix is manually adding the pyfits directory to the shell profile:
In tcsh:
  setenv PYTHONPATH "directory_where_pyfits_is_installed"

In bash:
  export PYTHONPATH="directory_where_pyfits_is_installed"


The directory can be found under "File:" upon executing within python:
  import pyfits
  pyfits?



 

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