Generating documentation gives errors and warnings

Issue #559 open
Gijs Molenaar created an issue
$ make html
[...]
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/robjects/lib/ggplot2.py:69: UserWarning: This was designed againt ggplot2 version 3.1.0 but you have
 3.1.1
  'have %s' % (TARGET_VERSION, ggplot2.__version__))
reading sources... [100%] vector
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:402: WARNING: Content block expected for the "note" directive; none found.
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:428: WARNING: Content block expected for the "warning" directive; none found.
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:449: WARNING: Content block expected for the "note" directive; none found.
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:490: WARNING: Include file '/Users/gijs/Work/alliander/rpy2/doc/generated_rst/\\_static/demos/graphics.p
y :start-after: #--' not found or reading it failed
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:491: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:495: WARNING: Include file '/Users/gijs/Work/alliander/rpy2/doc/generated_rst/\\_static/demos/graphics.p
y :start-after: #--' not found or reading it failed
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:496: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:498: WARNING: Include file '/Users/gijs/Work/alliander/rpy2/doc/generated_rst/\\_static/demos/graphics.p
y :start-after: #--' not found or reading it failed
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:499: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:503: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:508: WARNING: Content block expected for the "warning" directive; none found.
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:645: WARNING: Include file '/Users/gijs/Work/alliander/rpy2/doc/generated_rst/\\_static/demos/example01.
py' not found or reading it failed
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst:502: WARNING: image file not readable: generated_rst/_static/graphics_ggplot2_smoothbycylwithcolours.png
WARNING: autodoc: failed to import class '_rpy_device.GraphicalDevice' from module 'rpy2.rinterface'; the following exception was raised:
No module named 'rpy2.rinterface._rpy_device'; 'rpy2.rinterface' is not a package
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/ipython/rmagic.py:docstring of rpy2.ipython.rmagic:21: WARNING: Literal block expected; none found.
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/ipython/rmagic.py:docstring of rpy2.ipython.rmagic:151: WARNING: Option list ends without a blank li
ne; unexpected unindent.
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/ipython/rmagic.py:docstring of rpy2.ipython.rmagic:180: WARNING: Literal block expected; none found.
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/ipython/rmagic.py:docstring of rpy2.ipython.rmagic:218: WARNING: Literal block expected; none found.
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/ipython/rmagic.py:docstring of rpy2.ipython.rmagic.RMagics.R:133: WARNING: Option list ends without
a blank line; unexpected unindent.
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/ipython/rmagic.py:docstring of rpy2.ipython.rmagic.RMagics.Rpull:28: WARNING: Unexpected section tit
le.

Notes
-----
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/ipython/rmagic.py:docstring of rpy2.ipython.rmagic.RMagics.set_R_plotting_device:7: WARNING: Unexpec
ted section title.

Parameters
----------
WARNING: autodoc: failed to import function 'interactive.process_revents.process_revents' from module 'rpy2'; the following exception was raised:
cannot import name 'process_revents' from 'rpy2.rinterface' (/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/rinterface.py)
/Users/gijs/Work/alliander/rpy2/doc/pandas.rst:12: WARNING: Problems with "include" directive path:
InputError: [Errno 2] No such file or directory: 'generated_rst/pandas.rst'.
/Users/gijs/Work/alliander/rpy2/doc/performances.rst:: WARNING: image file not readable: _static/benchmark_sum.png
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/robjects/robject.py:docstring of rpy2.robjects.robject.RObjectMixin.rclass:6: WARNING: Bullet list ends without a blank line; unexpected unindent.
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/robjects/packages.py:docstring of rpy2.robjects.packages.reval:5: WARNING: Unexpected indentation.
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/robjects/vectors.py:docstring of rpy2.robjects.vectors.DataFrame.from_csvfile:8: WARNING: Unexpected indentation.
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/robjects/vectors.py:docstring of rpy2.robjects.vectors.DataFrame.from_csvfile:9: WARNING: Block quote ends without a blank line; unexpected unindent.
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/robjects/vectors.py:docstring of rpy2.robjects.vectors.DataFrame.from_csvfile:13: WARNING: Unexpected indentation.
/Users/gijs/Work/alliander/rpy2/.venv/lib/python3.7/site-packages/rpy2/robjects/vectors.py:docstring of rpy2.robjects.vectors.DataFrame.to_csvfile:13: WARNING: Unexpected indentation.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /Users/gijs/Work/alliander/rpy2/doc/generated_rst/introduction.rst: WARNING: document isn't included in any toctree
/Users/gijs/Work/alliander/rpy2/doc/generated_rst/tutorial.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] vector
/Users/gijs/Work/alliander/rpy2/doc/performances.rst:: WARNING: Could not obtain image size. :scale: option is ignored.
generating indices... genindex py-modindex
highlighting module code... [100%] rpy2.robjects.vectors
writing additional pages... search
copying images... [100%] _static/rpy2_logo.png
copying static files... WARNING: logo file 'rpy2_logo_64x64.png' does not exist

Comments (7)

  1. Laurent Gautier

    Clicking on “create issue” will show a brief description of what an issue and what are the information that will frequently be needed.

    Here for example, there is a copy paste a terminal operation without a description of what is the context (the version, and operating system in the list shown when clicking on “create issue” for example)

    I am adding a comment recommending an issue reporter to consider adding an outline of the difficulties the issue creates for a user of the project, and to read a last time the issue report before sending it to self-assess whether the report is believed one’s best effort to help improve the project at the time of filing.

  2. Gijs Molenaar reporter

    The OS is OS X and the version is the latest master.

    I understand you are frustrated, but i’m trying to help. I’m willing to spend time and effort on improving the project. I believe warnings are a indication of a potential future problem, hence i report them. Fixing a problem starts by reporting them. I thought the warnings was enough to start the investigation.

    I’m a maintainer of various open source projects myself. The fact that someone reports an issue doesn’t mean you need to solve them yourself, but you could point me in the right direction on how to solve the issue. This would be the most effective way of using our time, while improving the quality of the project. Something we both want.

  3. Laurent Gautier
    • changed status to open

    By the time I got to this one, the other issues about warnings that have nothing to rpy2 had made me too quick to close issues just opened because there is a warning. Happy to hear you want to help.

    Here the error is because make html is not sufficient to build the documentation. That’s definitely a problem and the fact that this is missing from the documentation is certainly an issue.

    The documentation contains jupyter notebooks dynamically evaluated, and turned in .rst files for Sphinx. Run make notebooks before make make html.

  4. Gijs Molenaar reporter

    that could be an easy fix, we can add the notebook make target as a dependency to the html target.

    I’ve opened up 2 PR’s on github, since I can’t open PR’s on bitbucket. did you see those?

    What is the preferred way to issue PR’s?

  5. Laurent Gautier

    I just checked and the following appears to just build the documentation (given the required R packages are installed):

    make notebooks html
    

    There are few warnings from Sphinx, but it builds nevertheless. Feel feel to submit PRs to fix this, otherwise they may be addressed over time.

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