Permission denied: '/usr/local/tests'

[daducci]

Hi guys,
while installing SPAMS (pip install spams, I get the following error:

ERROR: Could not install packages due to an OSError: [Errno 13] Permission denied: '/usr/local/tests'
Consider using the --user option or check the permissions.

I know I can use the PIP option --user, but this happens only for SPAMS and, what is really weird, is that if I run twice pip install spams, I get the error only the first time, the second one no error shows up.

I am not very familiar with the build system; any clue?

[samuelstjean]

Might be caused by the setup.py trying to install the doc, I remember I axes that part. Since the manifest already puts them in the zip, I guess that part could be deleted, since absolutely no one will go look for the doc inside system folders (and it's in the zip, it just will not get installed).

[gdurif]

I'll look into the doc setup (and remove the copy at install which is indeed useless).

[gdurif]

The doc issue should be fixed by #14

@daducci could you tell me if pip install git+https://github.com/getspams/spams-python.git@remove_doc_copy works for you?

[daducci]

No, it doesn't, I still get the error:

ERROR: Could not install packages due to an OSError: [Errno 13] Permission denied: '/usr/local/tests'
Consider using the `--user` option or check the permissions.

[gdurif]

Note: not fixed by #14

@daducci could you give more details on the environment (OS, Python version, etc.) on which you are encountering this issue ?

And if you try installing previous version from PyPI like pip install spams==2.6.3.3 (here is the history of version available on PyPI), all fail or some can be installed ?

Thanks

[daducci]

I'm on the new Macbook M1 with OSX 12.2.1 (Monterey) and python 3.9.10 (installed via howebrew), and this error happens with all spams versions. Whats is weird is that the first time I run pip install spams I get this error (and, in turn, our dmri-amico package is not installed), whereas if I run pip install spams a second time, the installation runs fine and also dmri-amico is properly installed without any error. Weird and I don't know why this happens...

[gdurif]

Do you have an example of a package that you can install without any issue (beside spams or dmri-amico)?

[daducci]

I install all other packages, e.g. numpy, scipy, nibabel, networkx etc, via pip install <name> (i.e., without flag --user) and they are installed properly. May this be due to a different settings which installs the tests in a wrong folder?

[gdurif]

Is pip install spams-bin working ?

[daducci]

Yes, indeed it does, without that error! :-)

[gdurif]

Ok, I think I understand the problem. Package with pre-built wheels do not cause any problem, but when you need some local build from source, it causes the issue.

[samuelstjean]

any modern local install should try to make wheels and install that, so I'd still point the culprit to the rest of the doc and test folder from the setup.py part. I'd guess the setup tries to install the files somehow (just like with the data folder) for important stuff, while the manifest only puts them in the source zip and discards everything from the real build.

Assuming nobody would ever read or run tests from the installed files and that we only want them in the zip (since people can easily refer to those instead), then this would be doable by removing all of those references from the setup.py and only using the manifest.in file. More details here https://packaging.python.org/en/latest/guides/using-manifest-in/

If you want to put here the wheel files before install (probably under /dist in your local folder), they likely contains references to those doc and tests files.

[gdurif]

@samuelstjean I agree. I will add all the non-standard include to the MANIFEST.in and remove them from the setup.py.