Symbol not found: __PyCodecInfo_GetIncrementalDecoder

Question

Since updating from Homebrew Python 2.7.11 (from 2.7.10) I'm suddenly unable to test register my package on PyPi from the PyCharm IDE console.

Running (as an "External Tool")

python -B setup.py register -r pypitest

I now get

Traceback (most recent call last):
  File "setup.py", line 22, in <module>
    from setuptools import setup
  File "/usr/local/lib/python2.7/site-packages/setuptools/__init__.py", line 12, in <module>
    from setuptools.extension import Extension
  File "/usr/local/lib/python2.7/site-packages/setuptools/extension.py", line 8, in <module>
    from .dist import _get_unpatched
  File "/usr/local/lib/python2.7/site-packages/setuptools/dist.py", line 16, in <module>
    from setuptools.depends import Require
  File "/usr/local/lib/python2.7/site-packages/setuptools/depends.py", line 6, in <module>
    from setuptools import compat
  File "/usr/local/lib/python2.7/site-packages/setuptools/compat.py", line 17, in <module>
    import httplib
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py", line 80, in <module>
    import mimetools
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/mimetools.py", line 6, in <module>
    import tempfile
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tempfile.py", line 32, in <module>
    import io as _io
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/io.py", line 51, in <module>
    import _io
ImportError: dlopen(/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so, 2): Symbol not found: __PyCodecInfo_GetIncrementalDecoder
  Referenced from: /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so
  Expected in: flat namespace
 in /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so

Process finished with exit code 1

I'm not sure how to proceed. I only get this issue if I execute from within my IDE's console. If I do it directly at the system command line (Terminal on OS X) I have no problems.

---

OS X 10.11.3; Homebrew Python 2.7.11; PyCharm 5.0.3

Solution 1

tl;dr: Fix this issue by doing one of the following:

• type hash -r python, OR
• log out and log in.

EDIT: An answer to my related question makes it clear what's happening here. When you install a new version of python, you may need to run hash -r python to tell bash to reset the "cached" location to the python executable.

In my case, I was typing python, which was on my $PATH at /usr/local/bin/python. But bash was still using the old cache location /usr/bin/python. So, the old executable was called, but the new path was provided to python in sys.argv[0]. This means that the old executable was running, but the new sys.executable value caused all the wrong modules to get loaded (including the io module).

---

I'm having the same problem. I installed python 2.7.11 via an installer from Python.org. Strangely, the issue seems to be related to some subtle difference between how OSX launches python when I invoke it from the shell using the full path vs. using just the word python.

So, for me, this works (invoking python via the full path /usr/local/bin/python):

$ which python
/usr/local/bin/python
$ /usr/local/bin/python -c "import io"
$

... but this doesn't:

$ python -c "import io"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/io.py", line 51, in <module>
    import _io
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so, 2): Symbol not found: __PyCodecInfo_GetIncrementalDecoder
  Referenced from: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so
  Expected in: flat namespace
 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so

So, as a workaround, you can try doing the same thing.

Elsewhere, I've posted a separate question about this puzzling behavior. Maybe somehow merely calling python invokes some strange mix of the 2.7.11 executable with the 2.7.10 dylibs??

Solution 2

According to https://github.com/klen/python-mode/issues/634:

I had the same issue, but successfully fixed. In my case I compiled python and vim with homebrew, when PYTHON_PATH has been specified and set to one of my dev environments, where I also had some libraries, including io. Workaround was simple: open new terminal, make sure that you do not have custom PYTHON_PATH, uninstall python, uninstall vim. Reinstall both of them.

and

Problem solved.

Culprit is the update from python 2.7.10 to 2.7.11.

If you are using conda package control, simply run "conda install python=2.7.10" will solve this problem.

This doesn't give the root cause though. Since this happens with _io, this looks like a bug in python 2.7.11 (unlikely, there would be a world-scale outcry and a prompt fix if it was) or some packaging bug or version mismatch specifically with the homebrew version (and maybe some related ones, too).

Try to import _io in the console and if it succeeds, check if it was loaded from the same path.

Solution 3

Reinstall python.

brew unlink python && brew reinstall python

Secure the path

export PYTHONPATH=$PYTHONPATH:/usr/local/bin/

BACKUP and Change the order of "paths" file.

sudo nano /etc/paths

it seems, the order of paths, it is decisive to run python properly. In my case, the result was:

#sudo nano /etc/paths
  /usr/bin  
  /usr/local/bin
  /bin
  /usr/sbin
  /sbin

On my mac, path is like this.

$ which python
    /usr/local/bin/python

Now I can run both:

$ /usr/local/bin/python -c "import io"
$ python -c "import io"

Solution 4

I had the same issue, it is successfully fixed by just replacing the _io.so file.

sudo find / -name _io.so

copy the path of the _io.so file which DOES NOT belong to python-2.7.11. For example, copy the path of _io.so which is under python-2.7.5: /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so

Replace the /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_io.so file with the _io.so that you just found.

Solution 5

If your problem is caused by anaconda, it is unnecessary to remove //anaconda directory.

Just open your ~/.bash_profile, find the line

export PATH="//anaconda/bin:$PATH

and comment it out, then restart your terminal session.

View more solutions

Comments

[orome]

Weirdly, I only get this issue if I execute from within my IDE's console. If I do it directly at the system command line (Terminal on OS X) I have no problems. I suspect the path in my IDE.

[ivan_pozdeev]

@raxacoricofallapatorius check environments, executable paths and sys.path for differences.

[orome]

Also checking here, since it's IDE-specific.

[Codious-JR]

thank you @ivan_pozdeev. Downgrading from python 2.7.11 to 2.7.10 fixed the problem

[skybondsor]

@Codious-JR How did you downgrade? I am having the hardest time figuring that out (using homebrew, not conda)

[skybondsor]

I'm not using anaconda, tho at this point I'm starting to think installing it will be my easiest path forward since homebrew doesn't have previous versions of python "on tap"

[Codious-JR]

hey @skybondsor, i am using anaconda, so the command conda install python=2.7.10 worked for me. Is there any specific reason why you don't want to use anaconda? cause otherwise i really recommend using it.

[Codious-JR]

@skybondsor I found the previous releases page on python.org, here you can find the mac installer for the version 2.7.10. python version 2.7.10

[Stuart Berg]

The fundamental problem here is that bash's hash cache can become incorrect immediately after you install a new version of python. (Try type python to verify that's the problem.) The person you quoted may have accidentally fixed this via all the uninstalling/reinstalling they described, but the straightforward fix is to type hash -r python into the terminal.

[Tim Smith]

Mixing and matching extension modules from Python 2.7.11 and the system Python, which is 2.7.10 on recent systems, is a very crude way to resolve this issue. The root problem is that Python 2.7.10 is attempting to import a module that belongs to 2.7.11; the symbol is defined in 2.7.11 but not 2.7.10. A better solution is to understand why Python 2.7.10 is being invoked at all.

[Yanan]

Thanks Tim. I run into this problem when using Anaconda. Anaconda2.4.1 has scipy-0.16.0 as one of the dependencies, and scipy-0.16.0 requires python 2.7.11. The default python in Anaconda is 2.7.10 (as well as the rest of the dependent libs are using 2.7.10), so that after upgrading to the newest Anaconda, I was unable to use it. While I'm waiting for the official bug fix of Anaconda, I need to run several conda scripts. So I decided to use this crude way to resolve the issue temporarily.

[Tuxdude]

I had installed macvim using an older version of Python and after upgrading Python, my vim was giving me this error every time when a plugin wanted to use python modules. Running brew upgrade macvim upgraded my vim to be built using the updated python path. This fixed the issue for me. PS: At least for me, it was not a bash caching issue as mentioned in the above post.

[GiriB]

login and logout worked. Notably I had installed python using brew during the session.

[Sergey Orshanskiy]

Also see joernhees.de/blog/2014/02/25/…

[James McLaughlin]

This fixed it for me. Thanks!

[gogasca]

After installing Dato Launcher I had this issue. After trying many of the options above this helped.

[Srini]

Gotta love StackOverflow!!

[Sisyphus]

if hash -r python says too many args, you can use rehash command.