Install R-Packages with version lock #405

dibryant · 2024-02-06T15:51:34Z

fixes for https://issues.redhat.com/browse/RHOAIENG-2799

Description

Added R packages with fixed version lock

How Has This Been Tested?

Use either the image build in the PR or built from this commit:

git checkout dibryant:rs-packages

cd rstudio/c9s-python-3.9/
podman build -t rstudio . --build-arg BASE_IMAGE=quay.io/opendatahub/workbench-images:base-c9s-python-3.9-20240124

And the run the image in local or directly in cluster

podman run -p 8787:8787 quay.io/opendatahub/workbench-images:rstudio-c9s-python-3.9-pr-405

Merge criteria:

The commits are squashed in a cohesive manner and have meaningful messages.
Testing instructions have been added in the PR body (for PRs involving changes that are not immediately obvious).
The developer has manually tested the changes and verified that the changes work

dibryant · 2024-02-06T20:23:17Z

/retest

rstudio/c9s-python-3.9/Dockerfile

harshad16

Missed this PR for review.
Took a quick look.
this is missing the ARG
which this the variable $NEEDPACKAGE cant be used.
please include it .

will look thoroughly over this.

rstudio/c9s-python-3.9/Dockerfile

dibryant · 2024-03-05T18:53:53Z

/retest-required

rstudio/c9s-python-3.9/Dockerfile

atheo89

I was able to build with or without the extra packages.
Added some minor enhancements, about the dockerfile syntax

atheo89 · 2024-03-29T15:27:42Z

I've noticed that during the image building process, you can observe the packages being installed. However, upon completion, when you spin up the notebook, the installed packages are mysteriously absent.

atheo89 · 2024-03-29T16:16:11Z

rstudio/c9s-python-3.9/Dockerfile

@@ -50,9 +50,12 @@ COPY rsession.conf /etc/rstudio/rsession.conf
 # package installation 
 RUN dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" \
    && dnf clean all && rm -rf /var/cache/yum
-RUN R -e "install.packages('Rcpp')"


Why this line is been deleted?

We have decided to add it to the install.versions to be able to version lock this package.

Have in mind this should be installed before any other package

jiridanek · 2024-03-29T18:52:52Z

'

@@ -0,0 +1,24 @@
+# This is a combination of 2 commits.


this file was probably added (and also created) by some mistake; it should be removed from PR?

harshad16

Following changes are needed:

rstudio/c9s-python-3.9/Dockerfile

harshad16 · 2024-04-01T18:17:01Z

I've noticed that during the image building process, you can observe the packages being installed. However, upon completion, when you spin up the notebook, the installed packages are mysteriously absent.

This is happening due the R_LIBS_USER is set to /opt/app-root/src/Rpackages/4.3
https://github.com/opendatahub-io/notebooks/blob/c0355fcd489a87c2293ea9adf1c73f8bfc4c2aa5/rstudio/c9s-python-3.9/Dockerfile#L35C17-L35C48

as the /opt/app-root/src is overwritten during the runtime, by the PVC that is attached to the Workbenches
all the present content is overwritten.

@dibryant please make this change
we should move this to a new path:
/opt/app-root/src/Rpackages/4.3 -> /opt/app-root/bin/Rpackages/4.3
https://github.com/opendatahub-io/notebooks/blob/main/rstudio/c9s-python-3.9/Dockerfile#L34-L35

dibryant · 2024-04-01T21:59:16Z

/retest-required

harshad16 · 2024-04-02T03:28:16Z

Seems like following additional changes are required at this:

notebooks/rstudio/c9s-python-3.9/run-rstudio.sh

Line 19 in c0355fc

cp -r /opt/app-root/bin/Rpackages/4.3/* /opt/app-root/src/Rpackages/4.3/

as the during the runtime R_LIBS_USER is set to: /opt/app-root/src/Rpackages/4.3

atheo89 · 2024-04-02T07:22:47Z

as the /opt/app-root/src is overwritten during the runtime, by the PVC that is attached to the Workbenches all the present content is overwritten.

Right, the same situation occurred with code-server extensions, leading us to include their installation in the startup .sh script.

openshift-ci · 2024-04-03T15:58:45Z

@dibryant: The following tests failed, say /retest to rerun all failed tests or /retest-required to rerun all mandatory failed tests:

Test name	Commit	Details	Required	Rerun command
ci/prow/notebook-jupyter-intel-pyt-ubi9-python-3-9-pr-image-mirror	`a294343`	link	true	`/test notebook-jupyter-intel-pyt-ubi9-python-3-9-pr-image-mirror`
ci/prow/runtime-intel-pyt-ubi9-python-3-9-pr-image-mirror	`a294343`	link	true	`/test runtime-intel-pyt-ubi9-python-3-9-pr-image-mirror`
ci/prow/runtime-intel-tf-ubi9-python-3-9-pr-image-mirror	`a294343`	link	true	`/test runtime-intel-tf-ubi9-python-3-9-pr-image-mirror`
ci/prow/notebook-jupyter-intel-tf-ubi9-python-3-9-pr-image-mirror	`a294343`	link	true	`/test notebook-jupyter-intel-tf-ubi9-python-3-9-pr-image-mirror`
ci/prow/runtime-intel-ml-ubi9-python-3-9-pr-image-mirror	`a294343`	link	true	`/test runtime-intel-ml-ubi9-python-3-9-pr-image-mirror`
ci/prow/notebook-jupyter-intel-ml-ubi9-python-3-9-pr-image-mirror	`a294343`	link	true	`/test notebook-jupyter-intel-ml-ubi9-python-3-9-pr-image-mirror`
ci/prow/notebooks-e2e-tests	`8a403d6`	link	true	`/test notebooks-e2e-tests`

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harshad16 · 2024-04-03T16:35:58Z

Test this in a cluster.
Seems like it works as expected 💯
Thanks for the awesome.

/lgtm
/approve
🎖️

openshift-ci · 2024-04-03T16:36:08Z

[APPROVALNOTIFIER] This PR is APPROVED

This pull-request has been approved by: harshad16

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openshift-ci bot requested review from atheo89 and harshad16 February 6, 2024 15:51

openshift-merge-robot added the needs-rebase label Feb 6, 2024

dibryant force-pushed the rs-packages branch 3 times, most recently from b7a0875 to 1b0ae09 Compare February 6, 2024 20:22

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dibryant changed the title ~~Option to install R core package in R-Studio Build~~ Install R-Packages Feb 29, 2024

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dibryant force-pushed the rs-packages branch from 9d60772 to 8b4d6b8 Compare April 1, 2024 18:29

Install R-Package with version locks

8a403d6

dibryant force-pushed the rs-packages branch from 8b4d6b8 to 8a403d6 Compare April 3, 2024 13:26

openshift-ci bot added the lgtm label Apr 3, 2024

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harshad16 merged commit 1efd888 into opendatahub-io:main Apr 3, 2024
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Install R-Packages with version lock #405

Install R-Packages with version lock #405

dibryant commented Feb 6, 2024 •

edited by harshad16

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Install R-Packages with version lock #405

Install R-Packages with version lock #405

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dibryant commented Feb 6, 2024 • edited by harshad16 Loading

Description

How Has This Been Tested?

Merge criteria:

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