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New key breaks r docker container build #322

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merged 3 commits into from
Mar 12, 2022

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danielStrobl
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A new key for the R repo (see https://cloud.r-project.org/) breaks building the R container.
This PR fixes that.

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  • This submission adds a new dataset
  • This submission adds a new method
  • This submission adds a new metric
  • This submission adds a new task
  • This submission adds a new Docker image
  • This submission fixes a bug (link to related issue: )
  • This submission adds a new feature not listed above

A new key for the R repo (see https://cloud.r-project.org/) breaks building the R container.
This PR fixes that.
@danielStrobl danielStrobl requested a review from LuckyMD March 1, 2022 16:26
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codecov-commenter commented Mar 9, 2022

Codecov Report

Merging #322 (3a9524f) into main (4394dbb) will decrease coverage by 0.18%.
The diff coverage is n/a.

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #322      +/-   ##
==========================================
- Coverage   89.30%   89.11%   -0.19%     
==========================================
  Files          73       73              
  Lines        1533     1498      -35     
  Branches       90       90              
==========================================
- Hits         1369     1335      -34     
+ Misses        135      134       -1     
  Partials       29       29              
Flag Coverage Δ
unittests 89.11% <ø> (-0.19%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
...s/tasks/multimodal_data_integration/metrics/mse.py 81.25% <0.00%> (-1.11%) ⬇️
openproblems/patch.py 96.87% <0.00%> (-0.19%) ⬇️
openproblems/data/utils.py 96.42% <0.00%> (-0.07%) ⬇️
openproblems/tools/normalize.py 100.00% <0.00%> (ø)
openproblems/tools/decorators.py 100.00% <0.00%> (ø)
openproblems/tasks/denoising/metrics/mse.py 100.00% <0.00%> (ø)
openproblems/tasks/denoising/methods/alra.py 0.00% <0.00%> (ø)
openproblems/tasks/denoising/methods/magic.py 100.00% <0.00%> (ø)
openproblems/tasks/denoising/metrics/poisson.py 100.00% <0.00%> (ø)
openproblems/tasks/label_projection/metrics/f1.py 100.00% <0.00%> (ø)
... and 11 more

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@scottgigante-immunai scottgigante-immunai left a comment

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LGTM, but why do we need to change the R version here?

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I couldn't find an official repository that still contains R 4.0, the old one is not available anymore. Not sure what the policy for additional packages was, should they be added to the r-extras container or to a new, separate container? The first case wouldn't work anymore as the old package does no longer exist.

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That makes sense. Thanks!

@scottgigante-immunai scottgigante-immunai merged commit c6bb854 into main Mar 12, 2022
lazappi added a commit to lazappi/openproblems that referenced this pull request Mar 24, 2022
* upstream/main:
  Convert normalizers to return anndata (openproblems-bio#329)
  require anndata<0.8 (openproblems-bio#336)
  Fix GPG key for R install (openproblems-bio#334)
  Fix R dependencies for docker build (openproblems-bio#331)
  Jamboree dimensionality reduction datasets (openproblems-bio#316)
  Jamboree dimensionality reduction metrics (openproblems-bio#317)
  use cmake==3.18.4 for multicoretsne build (openproblems-bio#328)
  Update 'master' to 'main' on CI (openproblems-bio#326)
  New key breaks r docker container build (openproblems-bio#322)
@scottgigante-immunai scottgigante-immunai deleted the danielStrobl-patch-1 branch April 14, 2022 17:41
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3 participants