Pinning R 4.0 with runtime.txt on mybinder.org not working as expected #1077
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Thank you for opening your first issue in this project! Engagement like this is essential for open source projects! 🤗 |
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Hi, unfortunately using Overall our support for R is a bit basic. This has a few reasons, but the most important one is that we lack people who really use and know R. It would be great to find someone who has more experience in that area and wants to help out. If I recall correctly the |
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I get the same problem as reported above. Another issue with the R 4.0.2 support (or 4.1.0) is that Rstudio is too old (from 2019) compared to R 4.1.0 and so plots are not visible. For an example, see: https://github.com/sje30/rescience-hor and hit the binder button. (it takes a few mins to spin up) after running CC: @nuest |
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@betatim Hi, My guess is that the step |
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I've transferred this issue to the repo2docker repo which is the tool that handles the builds behind BinderHub. This is an excerpt of the internal generated ...
COPY --chown=1000:1000 src/environment.yml ${REPO_DIR}/environment.yml
USER ${NB_USER}
RUN TIMEFORMAT='time: %3R' \
bash -c 'time mamba env update -p ${NB_PYTHON_PREFIX} -f "environment.yml" && \
time mamba clean --all -f -y && \
mamba list -p ${NB_PYTHON_PREFIX} \
'
RUN mamba install -p ${NB_PYTHON_PREFIX} r-base r-irkernel=1.1 r-devtools -y && \
mamba clean --all -f -y && \
mamba list -p ${NB_PYTHON_PREFIX}
...
repo2docker/repo2docker/buildpacks/_r_base.py Lines 19 to 20 in 6e2a6af repo2docker/repo2docker/buildpacks/conda/__init__.py Lines 347 to 353 in 6e2a6af |
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A first step can be to improve the tests: to check also the minor version and add more tests. To check the minor version, e.g. ! startsWith(paste(version$major,version$minor,sep="."),"4.0")Is this something that would add value and that I can suggest in a pull request? |
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@aplamada More tests are always welcome! I think a long term fix for this bug may require one of:
I'm not sure what's best though. |
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@manics Thanks for your feedback! Also it is not very clear to me why R with install.R is not following Python with requirements.txt . So either install.R can happen always in the conda env of R, or Python can be installed with |
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This issue has been mentioned on Jupyter Community Forum. There might be relevant details there: |
5 tasks
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@yuvipanda This is great news! |
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Unfortunately, the repository does not build at all anymore: Build logsMaybe related: #1116 |
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It works now, maybe because of #1114. Not sure though. |
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Bug description
Pinning the R version to 4.0 using
runtime.txtonmybinder.orgdoes not work – I get R 4.1 instead.Expected behaviour
I expect R version 4.0.5 ("Shake and Throw"):
Actual behaviour
I get R version 4.1.0 ("Camp Pontanezen"):
How to reproduce
runtime.txt:Your personal set up
I am using the
mybinder.orgservice.Versions:
jupyterhub --version:1.3.0python --version:Python 3.7.10Full environment
Related information
Explicitly demanding R 4.1 using the following
runtime.txt……does not work (which makes sense):
Try here:
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