Run CRAN check with `r-devel` when releasing a new version & daily #5777

harupy · 2022-04-26T06:58:32Z

Signed-off-by: harupy hkawamura0130@gmail.com

What changes are proposed in this pull request?

Run the CRAN check with r-devel when releasing a new version.
Run the CRAN check with r-devel daily to catch issues as early as possible.

How is this patch tested?

By manually confirming r-devel is used on a release branch, and not used on a non-release branch.

Does this PR change the documentation?

No. You can skip the rest of this section.
Yes. Make sure the changed pages / sections render correctly by following the steps below.

Check the status of the ci/circleci: build_doc check. If it's successful, proceed to the
next step, otherwise fix it.
Click Details on the right to open the job page of CircleCI.
Click the Artifacts tab.
Click docs/build/html/index.html.
Find the changed pages / sections and make sure they render correctly.

Release Notes

Is this a user-facing change?

No. You can skip the rest of this section.
Yes. Give a description of this change to be included in the release notes for MLflow users.

(Details in 1-2 sentences. You can just refer to another PR with a description if this PR is part of a larger change.)

What component(s), interfaces, languages, and integrations does this PR affect?

Components

Interface

area/uiux: Front-end, user experience, plotting, JavaScript, JavaScript dev server
area/docker: Docker use across MLflow's components, such as MLflow Projects and MLflow Models
area/sqlalchemy: Use of SQLAlchemy in the Tracking Service or Model Registry
area/windows: Windows support

Language

language/r: R APIs and clients
language/java: Java APIs and clients
language/new: Proposals for new client languages

Integrations

integrations/azure: Azure and Azure ML integrations
integrations/sagemaker: SageMaker integrations
integrations/databricks: Databricks integrations

How should the PR be classified in the release notes? Choose one:

rn/breaking-change - The PR will be mentioned in the "Breaking Changes" section
rn/none - No description will be included. The PR will be mentioned only by the PR number in the "Small Bugfixes and Documentation Updates" section
rn/feature - A new user-facing feature worth mentioning in the release notes
rn/bug-fix - A user-facing bug fix worth mentioning in the release notes
rn/documentation - A user-facing documentation change worth mentioning in the release notes

Signed-off-by: harupy <hkawamura0130@gmail.com>

dbczumar · 2022-04-27T02:21:53Z

.github/workflows/master.yml

@@ -106,6 +107,9 @@ jobs:
        Rscript -e 'install.packages("h2o", repos="http://cran.r-project.org")'
    - name: Build package
      run: |
+        # Use r-devel on a release branch to run the same submission checks as CRAN.


If we need rocker in order to test development versions of R, then we need to update r-devel to use rocker. However, our internal CI is incompatible with rocker, so we would then have to update internal CI to use another image. But, Dockerfile.dev also uses rocker, so we'd need to change Dockerfile.dev to use r-base, right?

@dbczumar Thanks for the comment!

our internal CI is incompatible with rocker.

Yep, can we do the following?

In our internal CI, use rocker/r-ver:4.2.0 (which uses ubuntu 20.04) and just build the package without running submission checks. We should be able to build the package as long as devtools works. We don't need ubuntu 22.04 or the latest version of R.

In GitHub Actions, run submission checks using rocker/r-ver:devel. We can add a stage for confirmation in our Spinnaker pipeline.

Will rocker/r-ver:4.2.0 switch to ubuntu 22.04 in the future? rocker-org/rocker-versioned2#282 (comment) says:

Base images for R versions released before 2022-07-19 (i.e. 4.1.3, 4.2.0) will remain ubuntu:focal and will not switch.

Hi, I am a member of the Rocker project.
I found this issue because there was a link to the issue I was looking at.

Note that if you want to try a development version of R (R 4.3.0 now), you can also use rocker/r-ver:devel, which is built daily using the same script as rocker/r-ver:4.2.0.
https://github.com/rocker-org/rocker-versioned2#tags
https://github.com/rocker-org/rocker-versioned2/blob/6c11d8486b83bf3d0be0cbc32a176716891d299a/.github/workflows/devel.yml

Will rocker/r-ver:4.2.0 switch to ubuntu 22.04 in the future?

Due to compatibility, the base image of rocker/r-ver:4.2.0 will not be upgraded.
However, as noted in that comment, the base image will switch to ubuntu:jammy for R 4.2.X images released after 2022-07-20.
Also, the base image for rocker/r-ver:devel is already Ubuntu 22.04 because ubuntu:latest is specified.
https://github.com/rocker-org/rocker-versioned2/blob/6c11d8486b83bf3d0be0cbc32a176716891d299a/dockerfiles/r-ver_devel.Dockerfile

@eitsupi Thanks for the comment! Is there any other image than rocker/r-ver:devel that provides a development version of R?

The Rocker project have rocker/r-devel and rocker/drd.
https://github.com/rocker-org/r-devel
https://github.com/rocker-org/drd

However, these are only built once a week, so if you want to try a newer version, rocker/r-ver:devel, which is built daily, is a good choice, I think.

Signed-off-by: harupy <hkawamura0130@gmail.com>

harupy · 2022-04-28T04:45:40Z

.github/workflows/r.yml

+  schedule:
+    # Run this workflow daily at 7:00 UTC
+    - cron: "0 7 * * *"


I'll add a badge on README later in a follow-up PR.

Signed-off-by: harupy <hkawamura0130@gmail.com>

harupy · 2022-04-28T04:50:26Z

.github/workflows/r.yml

+        elif [ "$GITHUB_EVENT_NAME" = "pull_request" ]; then
+          # Use r-devel on a pull request targeted to a release branch
+          USE_R_DEVEL=$([[ $GITHUB_BASE_REF =~ branch-[0-9]+\.[0-9]+$ ]] && echo true || echo false)
+        else
+          # Use r-devel on a push to a release branch
+          USE_R_DEVEL=$([[ $GITHUB_REF_NAME =~ branch-[0-9]+\.[0-9]+$ ]] && echo true || echo false)
+        fi


Uses r-devel when releasing a new version. For example, a PR for bumping the package versions sets USE_R_DEVEL to true and runs the CRAN check with r-devel.

Do we still need a manual confirmation stage for the CRAN check with r-devel?

dbczumar

LGTM! Thanks @harupy !

Use r-devel on release branch

09e6bae

Signed-off-by: harupy <hkawamura0130@gmail.com>

harupy changed the base branch from master to branch-9.99 April 26, 2022 06:59

github-actions bot added area/build Build and test infrastructure for MLflow rn/none List under Small Changes in Changelogs. labels Apr 26, 2022

set shell

a6443b5

Signed-off-by: harupy <hkawamura0130@gmail.com>

harupy changed the base branch from branch-9.99 to master April 26, 2022 10:47

harupy closed this Apr 26, 2022

harupy reopened this Apr 26, 2022

dbczumar reviewed Apr 27, 2022

View reviewed changes

harupy added 9 commits April 28, 2022 11:37

pin to 4.2.0

ce5c9c2

Signed-off-by: harupy <hkawamura0130@gmail.com>

use rocker/r-ver:devel

859387e

Signed-off-by: harupy <hkawamura0130@gmail.com>

set USE_R_DEVEL

64f7508

Signed-off-by: harupy <hkawamura0130@gmail.com>

add workflow for R

5a40f0d

Signed-off-by: harupy <hkawamura0130@gmail.com>

use latest

e57ee03

Signed-off-by: harupy <hkawamura0130@gmail.com>

newline

3f3fa4f

Signed-off-by: harupy <hkawamura0130@gmail.com>

improve set USE_R_DEVEL step

3d19fee

Signed-off-by: harupy <hkawamura0130@gmail.com>

use v2

4496fa9

Signed-off-by: harupy <hkawamura0130@gmail.com>

comments

11a5d78

Signed-off-by: harupy <hkawamura0130@gmail.com>

harupy commented Apr 28, 2022

View reviewed changes

address todo

ea2e05e

Signed-off-by: harupy <hkawamura0130@gmail.com>

harupy commented Apr 28, 2022

View reviewed changes

harupy changed the title ~~Use r-devel on a release branch to run the same submission checks as CRAN~~ Run CRAN check with r-devel when releasing a new version & daily Apr 28, 2022

harupy requested a review from dbczumar April 28, 2022 05:03

dbczumar approved these changes Apr 28, 2022

View reviewed changes

harupy merged commit 7be6451 into mlflow:master Apr 28, 2022

harupy deleted the use-r-devel-on-release-branch branch April 28, 2022 06:46

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Run CRAN check with `r-devel` when releasing a new version & daily #5777

Run CRAN check with `r-devel` when releasing a new version & daily #5777

harupy commented Apr 26, 2022 •

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Run CRAN check with r-devel when releasing a new version & daily #5777

Run CRAN check with r-devel when releasing a new version & daily #5777

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harupy commented Apr 26, 2022 • edited Loading

What changes are proposed in this pull request?

How is this patch tested?

Does this PR change the documentation?

Release Notes

Is this a user-facing change?

What component(s), interfaces, languages, and integrations does this PR affect?

How should the PR be classified in the release notes? Choose one:

dbczumar Apr 27, 2022

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Run CRAN check with `r-devel` when releasing a new version & daily #5777

Run CRAN check with `r-devel` when releasing a new version & daily #5777

harupy commented Apr 26, 2022 •

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