JupyterHub pip install permission denied error

[Michael Gilbert]

Hi,

I'm trying to install JupiterHub for the first time on my school's CentOS 6.6 cluster and I'm running into problems when I run "pip install . ". My environment is somewhat complex due to the cluster having a module system setup. I have created a python virtual environment where I installed ipython 3.2 and the dependencies in "requirements.txt" successfully. I also have node0.12.6 and npm2.11.2 binaries in my PATH, which was done by loading our "node" module. But when I run "pip install ." in the jupyterhub folder, I get the following errors:

Exception:

Traceback (most recent call last):

  File "/home/mkg52/.conda/envs/jupyter/lib/python3.4/site-packages/pip/basecommand.py", line 223, in main

    status = self.run(options, args)

  File "/home/mkg52/.conda/envs/jupyter/lib/python3.4/site-packages/pip/commands/install.py", line 282, in run

    requirement_set.prepare_files(finder)

  File "/home/mkg52/.conda/envs/jupyter/lib/python3.4/site-packages/pip/req/req_set.py", line 334, in prepare_files

    functools.partial(self._prepare_file, finder))

  File "/home/mkg52/.conda/envs/jupyter/lib/python3.4/site-packages/pip/req/req_set.py", line 321, in _walk_req_to_install

    more_reqs = handler(req_to_install)

  File "/home/mkg52/.conda/envs/jupyter/lib/python3.4/site-packages/pip/req/req_set.py", line 491, in _prepare_file

    session=self.session)

  File "/home/mkg52/.conda/envs/jupyter/lib/python3.4/site-packages/pip/download.py", line 814, in unpack_url

    unpack_file_url(link, location, download_dir)

  File "/home/mkg52/.conda/envs/jupyter/lib/python3.4/site-packages/pip/download.py", line 699, in unpack_file_url

    shutil.copytree(link_path, location, symlinks=True)

  File "/home/mkg52/.conda/envs/jupyter/lib/python3.4/shutil.py", line 343, in copytree

    raise Error(errors)

shutil.Error: [('/scratch/mkg52/_MONSOON_SOFTWARE/Jupyter/jupyterhub/.git/objects/pack/pack-394d2b981c172bce5c3140038765705ca8349ec4.idx', '/tmp/pip-nnhtq5eq-build/.git/objects/pack/pack-394d2b981c172bce5c3140038765705ca8349ec4.idx', "[Errno 13] Permission denied: '/tmp/pip-nnhtq5eq-build/.git/objects/pack/pack-394d2b981c172bce5c3140038765705ca8349ec4.idx'"), ('/scratch/mkg52/_MONSOON_SOFTWARE/Jupyter/jupyterhub/.git/objects/pack/pack-394d2b981c172bce5c3140038765705ca8349ec4.pack', '/tmp/pip-nnhtq5eq-build/.git/objects/pack/pack-394d2b981c172bce5c3140038765705ca8349ec4.pack', "[Errno 13] Permission denied: '/tmp/pip-nnhtq5eq-build/.git/objects/pack/pack-394d2b981c172bce5c3140038765705ca8349ec4.pack'")]

I'm at a complete loss as to why this is happening. I checked that my versions of python and pip and they are both python3. The interesting thing is I was able to successfully install jupyterhub in a test virtual machine that doesn't use a module system, so I'm wondering if this is the problem. 

Something else to note is that I downloaded the node source and built it with configure, make, make install. I wasn't able to use yum to install nodejs-legacy due to a lack of root privileges.

Any help would be greatly appreciated!

Thank you,

Mike

[Jess Hamrick]

Hi Mike,

It loks like the error is permission denied — is it possible that you don’t have write permissions to /tmp, which is where pip is attempting to copy the JupyterHub files to?

Cheers,

Jess

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[Michael Gilbert]

Thank you for the reply, Jess. I just double-checked and yes I do have write access to /tmp.

[Douglas La Rocca]

What's the filesystem and kernel version?

Someone has posted an identical-looking bug report here https://github.com/pypa/pip/issues/2941 suggesting it has something to do with the filesystem and extended attributes.

In the meanwhile you *might* be able to get away with moving the .git folder entirely for the moment. Permissions on files in .git/objects should be read only 444, so no user write permission, but the stuff you actually need to run will probably copy just fine.

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Douglas La Rocca

[Douglas La Rocca]

For reference, it looks like the exception is being raised here: https://github.com/python/cpython/blob/master/Lib/shutil.py#L159

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Douglas La Rocca

[Douglas La Rocca]

https://bugs.python.org/issue24538

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Douglas La Rocca

[Jess Hamrick]

Sigh. If your issue is in fact the one that Douglas posted, then it is the same as an issue I just recently ran into as well: https://bugs.python.org/issue24564

I was able to work around mine for the moment by not using Python 3, but that’s not going to work if you’re installing JupyterHub.

Since it looks like you’re installing from source anyway, if you do “pip install -e .” then I *think* it won’t try to copy the .git folder to /tmp, though I am not entirey sure. Or, the workaround Douglas suggested (removing the .git folder) may work too, it just means you’ll have to re-clone JuptyerHub if you want to update it in the future.

Cheers,

Jess

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[Douglas La Rocca]

Looks like you're in good hands... Jess's suggestion of "pip install -e ." is definitely much better than my idea to move the whole .git folder. If that still doesn't work, a slight improvement on the workaround could be chmod -R u+w .git/objects.

To view this discussion on the web visit https://groups.google.com/d/msgid/jupyter/BF79DBCC-79F6-475F-B0CF-5840270566F4%40gmail.com.

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Douglas La Rocca

[Michael Gilbert]

"pip install -e ." resolved my problem. I was able to complete the install with no errors. Thank you guys so much!