No such file or directory: '/opt/anaconda3/lib/python3.8/site-packages/rtree/lib'

Question

I am trying to build an app from a python file (Mac OS) using the py2app extension. I have a folder with the python file and the "setup.py" file.

• I first tested the app by running python setup.py py2app -A in the terminal and the dist and build folder are successfully created and the app works when launched.
• Now when I try to build it non-locally by running the command python setup.py py2app in the terminal, there are various "WARNING: ImportERROR" messages while building and finally a error: [Errno 2] No such file or directory: '/opt/anaconda3/lib/python3.8/site-packages/rtree/lib' error.
  
  How can I fix this? I've tried to delete anaconda fully as I don't use it but it seems to still want to run through it. Additionally, I have tried to run the build command using a virtual environment but I end up having even more import errors.
  *I Left out a lot of the "skipping" and "warning" lines using "..." for space

(base) keshavshankar@Keshavs-MacBook-Pro IEEE Citation Creator % python setup.py py2app
running py2app
creating /Users/keshavshankar/Desktop/IEEE Citation Creator/build/bdist.macosx-10.9-x86_64/python3.8-standalone
creating /Users/keshavshankar/Desktop/IEEE Citation Creator/build/bdist.macosx-10.9-x86_64/python3.8-standalone/app
creating /Users/keshavshankar/Desktop/IEEE Citation Creator/build/bdist.macosx-10.9-x86_64/python3.8-standalone/app/collect
creating /Users/keshavshankar/Desktop/IEEE Citation Creator/build/bdist.macosx-10.9-x86_64/python3.8-standalone/app/temp
creating build/bdist.macosx-10.9-x86_64/python3.8-standalone/app/lib-dynload
creating build/bdist.macosx-10.9-x86_64/python3.8-standalone/app/Frameworks
--- Skipping recipe PIL ---
*** using recipe: automissing *** {'expected_missing_imports': {'winreg', '_frozen_importlib_external', 'sys.getwindowsversion', '_winapi', 'nt'}}
--- Skipping recipe PIL ---
--- Skipping recipe autopackages ---
CTYPES USERS [SourceModule('ctypes._endian', '/opt/anaconda3/lib/python3.8/ctypes/_endian.py'), Package('test.support', '/opt/anaconda3/lib/python3.8/test/support/__init__.py', ['/opt/anaconda3/lib/python3.8/test/support']), SourceModule('ctypes.wintypes', '/opt/anaconda3/lib/python3.8/ctypes/wintypes.py'), Package('ctypes.macholib', '/opt/anaconda3/lib/python3.8/ctypes/macholib/__init__.py', ['/opt/anaconda3/lib/python3.8/ctypes/macholib']), SourceModule('ctypes._aix', '/opt/anaconda3/lib/python3.8/ctypes/_aix.py'), SourceModule('ctypes.util', '/opt/anaconda3/lib/python3.8/ctypes/util.py'), SourceModule('multiprocessing.sharedctypes', '/opt/anaconda3/lib/python3.8/multiprocessing/sharedctypes.py'), Script('/Users/keshavshankar/Desktop/IEEE Citation Creator/.eggs/py2app-0.27-py3.8.egg/py2app/bootstrap/argv_emulation.py',)]
*** using recipe: ctypes *** {'prescripts': ['py2app.bootstrap.ctypes_setup']}
--- Skipping recipe PIL ---
--- Skipping recipe autopackages ---
*** using recipe: detect_dunder_file *** {'packages': {'certifi'}}
--- Skipping recipe PIL ---
--- Skipping recipe autopackages ---
*** using recipe: ftplib *** {}
--- Skipping recipe PIL ---
--- Skipping recipe autopackages ---
--- Skipping recipe gcloud ---
--- Skipping recipe lxml ---
--- Skipping recipe matplotlib ---
*** using recipe: multiprocessing *** {'prescripts': [<_io.StringIO object at 0x7f9221c91ca0>]}
--- Skipping recipe PIL ---
--- Skipping recipe autopackages ---
--- Skipping recipe gcloud ---
--- Skipping recipe lxml ---
--- Skipping recipe matplotlib ---
--- Skipping recipe opencv ---
--- Skipping recipe pandas ---
--- Skipping recipe platformdirs ---
--- Skipping recipe pydantic ---
*** using recipe: pydoc *** {}
--- Skipping recipe PIL ---
--- Skipping recipe autopackages ---
--- Skipping recipe gcloud ---
--- Skipping recipe lxml ---
--- Skipping recipe matplotlib ---
--- Skipping recipe opencv ---
--- Skipping recipe pandas ---
--- Skipping recipe platformdirs ---
--- Skipping recipe pydantic ---
--- Skipping recipe pyenchant ---
--- Skipping recipe pygame ---
--- Skipping recipe pylsp ---
--- Skipping recipe pyopengl ---
--- Skipping recipe pyside ---
--- Skipping recipe pyside2 ---
--- Skipping recipe pyside6 ---
--- Skipping recipe qt5 ---
--- Skipping recipe qt6 ---
--- Skipping recipe rtree ---
*** using recipe: setuptools *** {'expected_missing_imports': {'pkg_resources.extern.packaging', '__main__.__requires__', '__builtin__', 'pkg_resources.extern.pyp', 'pkg_resources.extern.app'}}
--- Skipping recipe PIL ---
...
--- Skipping recipe shiboken6 ---
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WARNING: ImportError in sip recipe ignored: No module named cytoolz-0
WARNING: ImportError in sip recipe ignored: No module named unicodecsv-0
WARNING: ImportError in sip recipe ignored: No module named mypy_extensions-0
WARNING: ImportError in sip recipe ignored: No module named anaconda_project-0
WARNING: ImportError in sip recipe ignored: No module named imageio-2
-:1114: SyntaxWarning: "is" with a literal. Did you mean "=="?
/opt/anaconda3/lib/python3.8/site-packages/boto/iam/connection.py:1114: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if tld is 'default':
WARNING: ImportError in sip recipe ignored: No module named isort-5
WARNING: ImportError in sip recipe ignored: No module named Markdown-3
...
WARNING: ImportError in sip recipe ignored: No module named sniffio-1
WARNING: ImportError in sip recipe ignored: No module named soupsieve-2
-:124: SyntaxWarning: "is" with a literal. Did you mean "=="?
-:130: SyntaxWarning: "is" with a literal. Did you mean "=="?
/opt/anaconda3/lib/python3.8/site-packages/binstar_client/requests_ext.py:124: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if mode is 0:
/opt/anaconda3/lib/python3.8/site-packages/binstar_client/requests_ext.py:130: SyntaxWarning: "is" with a literal. Did you mean "=="?
  elif mode is 2:
WARNING: ImportError in sip recipe ignored: No module named Rtree-0
WARNING: ImportError in sip recipe ignored: No module named glob2-0
...
WARNING: ImportError in sip recipe ignored: No module named backcall-0
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-:478: SyntaxWarning: "is not" with a literal. Did you mean "!="?
/opt/anaconda3/lib/python3.8/site-packages/bkcharts/utils.py:478: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if lev is not '' and row_text == '':
-:615: SyntaxWarning: "is not" with a literal. Did you mean "!="?
-:615: SyntaxWarning: "is not" with a literal. Did you mean "!="?
/opt/anaconda3/lib/python3.8/site-packages/bkcharts/data_source.py:615: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  k is not 'dims' and k is not 'required_dims']
/opt/anaconda3/lib/python3.8/site-packages/bkcharts/data_source.py:615: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  k is not 'dims' and k is not 'required_dims']
-:452: SyntaxWarning: "is" with a literal. Did you mean "=="?
/opt/anaconda3/lib/python3.8/site-packages/bkcharts/builder.py:452: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if attr is 'label':
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*** using recipe: sip *** {'resources': ['/Users/keshavshankar/Desktop/IEEE Citation Creator/.eggs/py2app-0.27-py3.8.egg/py2app/recipes/qt.conf']}
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*** using recipe: autopackages *** {'packages': ['docutils', 'pylint', 'h5py', 'numpy', 'scipy', 'tensorflow']}
-:142: SyntaxWarning: "is" with a literal. Did you mean "=="?
-:144: SyntaxWarning: "is" with a literal. Did you mean "=="?
-:146: SyntaxWarning: "is" with a literal. Did you mean "=="?
/opt/anaconda3/lib/python3.8/site-packages/tensorflow/python/keras/benchmarks/benchmark_util.py:142: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if 'x' is None:
/opt/anaconda3/lib/python3.8/site-packages/tensorflow/python/keras/benchmarks/benchmark_util.py:144: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if 'optimizer' is None:
/opt/anaconda3/lib/python3.8/site-packages/tensorflow/python/keras/benchmarks/benchmark_util.py:146: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if 'loss' is None:
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*** using recipe: lxml *** {}
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*** using recipe: opencv *** {'includes': ['numpy']}
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error: [Errno 2] No such file or directory: '/opt/anaconda3/lib/python3.8/site-packages/rtree/lib'

Answer 1

The error error: [Errno 2] No such file or directory: '/opt/anaconda3/lib/python3.8/site-packages/rtree/lib' was caused by py2app trying to build the program bundle using a non-existent interpreter. This means that even if you try to uninstall a manager like Anaconda, it still has option logs somewhere on your mac.

The fix:

1. Open the terminal and type the command type -a python.

• You will see similar lines

python is /opt/anaconda3/bin/python
python is /usr/local/bin/python
python is /usr/bin/python

• In my case, anaconda has been deleted but not fully, thus building the app through it corrupts the process. We want to delete anaconda fully

2. To delete this, open the location of anaconda by typing open /opt/ in the terminal

• Doing this will display the different environments on your computer. Delete the entire folder of the environment you don't want

3. Now retype type -a python in the terminal and you should see the anaconda path gone

• After this, simply rebuild your app in alias mode to make sure it works, then progress with the full build.

Answer 2

I'm using Mac OS Big Sur, and I had a similar issue as you describe, except that the error said:

No such file or directory: /Users/[me]/opt/anaconda3/bin/python

I tried your solution, with no avail:

• I had only one result with type -a python
• It was not related to Anaconda.

In the end, I could solve my problem by installing ipython:

brew install ipython

The installation itself was not automatic. It requested me to delete plenty of files in different protected locations, which I did. Then I had to uninstall jupyter. Finally, I could install ipyhton, then jupyterlab, and the anaconda problem was no more.