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DOC: rpy2 examples started failing #20648
Description
The rpy2 examples in the documentation started failing recently (http://pandas-docs.github.io/pandas-docs-travis/r_interface.html) with:
In [1]: from rpy2.robjects import r, pandas2ri
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-79b90b86f23f> in <module>()
----> 1 from rpy2.robjects import r, pandas2ri
~/miniconda3/envs/pandas/lib/python3.6/site-packages/rpy2/robjects/__init__.py in <module>()
14 import itertools
15 from datetime import datetime
---> 16 import rpy2.rinterface as rinterface
17 import rpy2.rlike.container as rlc
18
~/miniconda3/envs/pandas/lib/python3.6/site-packages/rpy2/rinterface/__init__.py in <module>()
48 del(os)
49
---> 50 from rpy2.rinterface._rinterface import (baseenv,
51 emptyenv,
52 endr,
ImportError: dlopen: cannot load any more object with static TLS
However, I don't see any change in version between a recent working build and the current failing (this working one uses rpy2 2.9.1-py36mro343h14c3975_0, and this failing one 2.9.1-py36mro343h14c3975_0, so the same)
Could this be caused by installing another library?
cc @lgautier
Activity
WillAyd commentedon Apr 18, 2018
Hmm this has been inconsistent right? Googling the error I saw a few other issues for other projects but none seemed to have a definite resolution. Here's something similar from Tensorflow:
tensorflow/models#523
A lot of the answers seemed to be doing things that "fixed" the issue without any explanation (ex: changing import order) or just restarting the system...
jorisvandenbossche commentedon Apr 19, 2018
I think is has been rather consistently failing since some time.
But indeed, I also googled and only found such not very helpful issues as you describe ..
TomAugspurger commentedon Apr 30, 2018
Reproduced locally from docker's base image.
Haven't narrowed things down yet. Pushing to the next release.
datapythonista commentedon Nov 16, 2018
Looks like this is failing even more than when the issue was created. We don't even have the required modules in the dependencies we use to build the docs:
https://pandas.pydata.org/pandas-docs/stable/r_interface.html
As the functionality being documented is not on pandas but on
rpy2, and nobody complained about the page giving errors everywhere, what I'd do is simply remove the page from the docs. One of the reasons I think it's better to delete the page instead of fixing the problem, is that fixing the problem implies installing more than 50 additional dependencies (required by rpy2) in the builds and in our local development environments.Does this sound reasonable?
jorisvandenbossche commentedon Nov 16, 2018
The error you see in the stable docs is "fixed" by #22424 (and this was also backported to the 0.23.x branch, but we never released again). So in the dev build it is back to the above error: http://pandas-docs.github.io/pandas-docs-travis/r_interface.html), and @TomAugspurger has a working environment locally to built them correctly, but I suppose he never uploaded updated docs: #22777 (comment)
So I think it is possible to have correctly built docs online (the doc were also correct up to 0.23.3, only started failing from 0.23.4).
That said, I am certainly not against removing it from our doc build (whether it is removing completely, or just removing the fact that the examples are run during the doc build)
datapythonista commentedon Nov 16, 2018
I opened the PR #23737 removing it, so we can see what's the impact while we make a decision. I think moving the examples from
ipythonblocks to regular code blocks is a good idea too. But personally I think that page is documentingrpy2(another package) and not pandas, and feels to me like if we start addingdaskexamples to our documentation. So my preferred option is still delete the page.To give more context, these are the additional dependencies that we need for
rpy2:jorisvandenbossche commentedon Nov 16, 2018
Simply converting it to plain code-blocks and removing the packages from the doc build environment is certainly good for me.
Historically, the reason that I wanted to keep this page and put some effort in it to update it when we removed the interface included in pandas, is because the rpy2 docs itself don't really mention it (I would personally think that the pandas <-> R interaction should be one of their selling points, but that is clearly not the case at this point).
For example, if we remove the page, I think it would be good in the beginning to still keep the url working but redirect / point to a page in the rpy2 docs, but I didn't find such a page (and I am not going to do a PR to rpy2 myself, as I don't use it personally).
TomAugspurger commentedon Nov 16, 2018
datapythonista commentedon Nov 16, 2018
Ok, let's close this then.