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JaneliaSciComp / Neuroptikon

Neuroptikon
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System osg module overrides internal osg module on Mac #26

Open cmbruns-hhmi opened 9 years ago

cmbruns-hhmi commented 9 years ago

On Charlotte Weaver's Mac, there was an incompatible osg module installed under /Library/, causing Neuroptikon to fail to launch. It would be better if the internal osg module would take precedence. As a workaround, we renamed the system osg module, to hide it, so Neuroptikon could run correctly.

@csweaver

  1. Is your PYTHONPATH environment variable set? If so, to what? (launch Terminal -> "echo $PYTHONPATH")
  2. What does sys.path look like in Neuroptikon? (Run neuroptikon from 1.0.0rc2 installer->At python prompt type "import sys" then "sys.path". Mine is set to:
>>> sys.path
['/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7', 
'/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/lib-dynload', 
'/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/site-packages.zip', 
'/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python27.zip', 
'/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/plat-darwin', 
'/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/plat-mac',
'/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/plat-mac/lib-scriptpackages', 
'/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/lib-tk', 
'/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/lib-old', 
'/Library/Python/2.7/site-packages', 
'/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources', 
'/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources']

I don't see any osg.py[c] in there anywhere at all! But perhaps I have not searched hard enough. There may be some py2app magic going on here.

csweaver commented 9 years ago

Here you go

1.

/home/weaverc10/workspace/SageDjango/src::/home/weaverc10/workspace/Larval_Loader/sage-loader/src:/home/weaverc10/workspace/Larval_Loader/sage-loader/test

2.

import sys print sys.path ['/Library/Python/2.7/site-packages/Flask-0.9-py2.7.egg', '/Library/Python/2.7/site-packages/Jinja2-2.6-py2.7.egg', '/Library/Python/2.7/site-packages/Werkzeug-0.8.3-py2.7.egg', '/Library/Python/2.7/site-packages/distribute-0.6.28-py2.7.egg', '/Library/Python/2.7/site-packages/webdb3-0.0-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_ErrorMail-0.2.1-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_Script-0.4.0-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_SQLAlchemy-0.16-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_Principal-0.3.3-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_Login-0.1.3-py2.7.egg', '/Library/Python/2.7/site-packages/jinja2_hamlpy-0.1-py2.7.egg', '/Library/Python/2.7/site-packages/hamlpy-0.82.2-py2.7.egg', '/Library/Python/2.7/site-packages/decorator-3.3.3-py2.7.egg', '/Library/Python/2.7/site-packages/pyparsing-1.5.6-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_Mail-0.7.1-py2.7.egg', '/Library/Python/2.7/site-packages/argparse-1.2.1-py2.7.egg', '/Library/Python/2.7/site-packages/SQLAlchemy-0.7.8-py2.7-macosx-10.8-intel.egg', '/Library/Python/2.7/site-packages/blinker-1.2-py2.7.egg', '/Library/Python/2.7/site-packages/Pygments-1.5-py2.7.egg', '/Library/Python/2.7/site-packages/Markdown-2.2.0-py2.7.egg', '/Library/Python/2.7/site-packages/Django-1.4.1-py2.7.egg', '/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python', '/Library/Python/2.7/site-packages/nseqweb-0.0-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_Coffee-0.3-py2.7.egg', '/Library/Python/2.7/site-packages/flask_lesscss-0.9.1-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_FlatPages-0.3-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_Markdown-0.3-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_WTF-0.8-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_Uploads-0.1.3-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_Testing-0.4-py2.7.egg', '/Library/Python/2.7/site-packages/Flask_Restless-0.6-py2.7.egg', '/Library/Python/2.7/site-packages/python_ldap-2.4.10-py2.7-macosx-10.8-intel.egg', '/Library/Python/2.7/site-packages/closure_linter-2.3.13-py2.7.egg', '/Library/Python/2.7/site-packages/python_gflags-2.0-py2.7.egg', '/Library/Python/2.7/site-packages/pydvid-0.1-py2.7.egg', '/Library/Python/2.7/site-packages/jsonschema-2.4.0-py2.7.egg', '/Library/Python/2.7/site-packages/virtualenv-1.11.6-py2.7.egg', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/lib-dynload', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/site-packages.zip', '/usr/local/lib/wxPython-3.0.1.1/lib/python2.7/site-packages', '/usr/local/lib/wxPython-3.0.1.1/lib/python2.7/site-packages/wx-3.0-osx_cocoa', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python27.zip', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/plat-darwin', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/plat-mac', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/plat-mac/lib-scriptpackages', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/lib-tk', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/lib-old', '/Library/Python/2.7/site-packages', '/usr/local/lib/wxPython-3.0.1.1/lib/python2.7', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources']

On Dec 8, 2014, at 9:08 AM, Christopher Bruns notifications@github.com wrote:

On Charlotte Weaver's Mac, there was an incompatible osg module installed under /Library/, causing Neuroptikon to fail to launch. It would be better if the internal osg module would take precedence. As a workaround, we renamed the system osg module, to hide it, so Neuroptikon could run correctly. @csweaver

  1. Is your PYTHONPATH environment variable set? If so, to what? (launch Terminal -> "echo $PYTHONPATH")
  2. What does sys.path look like in Neuroptikon? (Run neuroptikon from 1.0.0rc2 installer->At python prompt type "import sys" then "sys.path". Mine is set to:

sys.path ['/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/lib-dynload', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/site-packages.zip', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python27.zip', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/plat-darwin', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/plat-mac', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/plat-mac/lib-scriptpackages', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/lib-tk', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources/lib/python2.7/lib-old', '/Library/Python/2.7/site-packages', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources', '/Volumes/Neuroptikon 1.0.0rc2/Neuroptikon.app/Contents/Resources']

I don't see any osg.py[c] in there anywhere at all! But perhaps I have not searched hard enough. There may be some py2app magic going on here. — Reply to this email directly or view it on GitHub.