devxy/r-builds
Watch
2
0
Fork
You've already forked r-builds
 0
Code Issues 1 Pull requests Releases Activity

CI

Browse source
This commit is contained in:
Patrick Schratz 2024-06-05 14:32:08 +02:00
commit 6cd0047006
Signed by: pat-s
GPG key ID: 3C6318841EF78925
5 changed files with 151 additions and 410 deletions
Download patch file Download diff file Expand all files Collapse all files

123
.woodpecker/build.yaml
View file

@ -1,13 +1,126 @@
when: when:
event: push event: [push, cron]
matrix:
include:
- PLATFORM: rhel-9
PLATFORM_ID: el9
- PLATFORM: centos-8
PLATFORM_ID: el8
- PLATFORM: ubuntu-2204
PLATFORM_ID: 2204
- PLATFORM: ubuntu-2404
PLATFORM_ID: 2404
# - PLATFORM: opensuse-155
# PLATFORM_ID: suse155
steps: steps:
# - name: Check if files already exist # Ensures that we're always using the latest available upstream build chain
# - name: Pull upstream
# image: alpine:3.20
# commands:
# - apk add -q --no-cache git
# - git remote add upstream https://github.com/cynkra/r-builds.git
# - git config --global user.email "you@example.com"
# - git config --global user.name "Your Name"
# - git config pull.ff only
# - git fetch upstream
# - git merge upstream/main --allow-unrelated-histories
- name: Get latest R version
image: alpine:3.20
commands:
- apk add -q --no-cache curl
- curl -s https://raw.githubusercontent.com/Homebrew/homebrew-core/master/Formula/r/r.rb | grep -o 'R-[0-9]*\.[0-9]*\.[0-9]*' | tr -d 'R-' | tr -d '"' > r-release-version.txt
- cat r-release-version.txt
- name: Check if files for R version already exist in s3
secrets: [aws_access_key_id_cynkra, aws_secret_access_key_cynkra]
environment:
# AWS_ACCESS_KEY_ID:
# from_secret: aws_access_key_id_cynkra
# AWS_SECRET_ACCESS_KEY:
# from_secret: aws_secret_access_key_cynkra
AWS_ACCESS_KEY_ID:
from_secret: b2_application_key
AWS_SECRET_ACCESS_KEY:
from_secret: b2_application_key_id
AWS_ENDPOINT_URL: s3.eu-central-003.backblazeb2.com
image: alpine:3.20
commands:
- apk add -q --no-cache aws-cli
- aws s3 ls s3://devxy-r-builds/${PLATFORM_ID}/ | tail -1 | awk '{print $NF}' | cut -c 3-7 > r_build_latest.txt
- cat r_build_latest.txt
- name: Build - name: Build
image: alpine:3.20 image: alpine:3.20
commands: commands: |
- apk add --no-cache make just aws-cli docker-compose if [ ! -s r_build_latest.txt ] || [ ! "$(cat r-release-version.txt)" = "$(cat r_build_latest.txt)" ]; then
- just build-r-rhel-9 4.3.3 apk add -q --no-cache py3-pip make just aws-cli docker-compose
pip3 install -q b2 --break-system-packages
just build-r-${PLATFORM} $(cat r-release-version.txt)
fi
volumes: volumes:
- /var/run/docker.sock:/var/run/docker.sock - /var/run/docker.sock:/var/run/docker.sock
- /tmp:/tmp
- name: Upload
image: woodpeckerci/plugin-s3:1.1.3
secrets:
[
aws_access_key_id_cynkra,
aws_secret_access_key_cynkra,
b2_application_key,
b2_application_key_id,
]
environment:
# AWS_ACCESS_KEY_ID:
# from_secret: aws_access_key_id_cynkra
# AWS_SECRET_ACCESS_KEY:
# from_secret: aws_secret_access_key_cynkra
AWS_ACCESS_KEY_ID:
from_secret: b2_application_key
AWS_SECRET_ACCESS_KEY:
from_secret: b2_application_key_id
AWS_ENDPOINT_URL: s3.eu-central-003.backblazeb2.com
settings:
bucket: devxy-r-builds
source: /tmp/${PLATFORM}/*
target: ${PLATFORM_ID}/
path_style: true
acl: public-read
endpoint: s3.eu-central-003.backblazeb2.com
volumes:
- /tmp:/tmp
# - name: Upload to S3
# image: alpine:3.20
# secrets:
# [
# aws_access_key_id_cynkra,
# aws_secret_access_key_cynkra,
# b2_application_key,
# b2_application_key_id,
# ]
# environment:
# # AWS_ACCESS_KEY_ID:
# # from_secret: aws_access_key_id_cynkra
# # AWS_SECRET_ACCESS_KEY:
# # from_secret: aws_secret_access_key_cynkra
# AWS_ACCESS_KEY_ID:
# from_secret: b2_application_key
# AWS_SECRET_ACCESS_KEY:
# from_secret: b2_application_key_id
# AWS_ENDPOINT_URL: s3.eu-central-003.backblazeb2.com
# commands: |
# apk add -q --no-cache bash aws-cli
# if [ "$(ls -A /tmp/${PLATFORM}/)" ]; then
# for file in /tmp/${PLATFORM}/*; do
# aws s3 cp --acl public-read --no-progress "$file" "s3://devxy-r-builds/${PLATFORM_ID}/"
# done
# rm -f /tmp/${PLATFORM}/*
# else
# echo "No files to upload."
# fi
# volumes:
# - /tmp:/tmp

8
Justfile
View file

@ -1,10 +1,10 @@
build-r-ubuntu-2004 R_VERSION: build-r-ubuntu-2204 R_VERSION:
export PLATFORM=ubuntu-2004; \ export PLATFORM=ubuntu-2204; \
export R_VERSION={{R_VERSION}}; \ export R_VERSION={{R_VERSION}}; \
make build-r-$PLATFORM make build-r-$PLATFORM
build-r-ubuntu-2204 R_VERSION: build-r-ubuntu-2404 R_VERSION:
export PLATFORM=ubuntu-2204; \ export PLATFORM=ubuntu-2404; \
export R_VERSION={{R_VERSION}}; \ export R_VERSION={{R_VERSION}}; \
make build-r-$PLATFORM make build-r-$PLATFORM

400
README.md
View file

@ -1,400 +1,6 @@
# r-builds # r-builds
This repository orchestrates tools to produce R binaries. The binaries are available as a Builds R interpreter binaries for Linux.
community resource, **they are not professionally supported by Posit**.
The R language is open source, please see the official documentation at https://www.r-project.org/.
These binaries are not a replacement to existing binary distributions for R. - No changes to upstream code ([rstudio/r-builds](https://github.com/rstudio/r-builds)) is made
The binaries were built with the following considerations: - Binaries are only built if they do not yet exist in the S3 bucket
- They use a minimal set of [build and runtime dependencies](builder).
- They are designed to be used side-by-side, e.g., on [Posit Workbench](https://docs.posit.co/ide/server-pro/r_versions/using_multiple_versions_of_r.html).
- They give users a consistent option for accessing R across different Linux distributions.
These binaries have been extensively tested, and are used in production everyday
on [Posit Cloud](https://posit.cloud) and
[shinyapps.io](https://shinyapps.io). Please open an issue to report a specific
bug, or ask questions on [Posit Community](https://community.rstudio.com).
## Supported Platforms
R binaries are built for the following Linux operating systems:
- Ubuntu 20.04, 22.04, 24.04
- Debian 10, 11, 12
- CentOS 7
- Red Hat Enterprise Linux 7, 8, 9
- openSUSE 15.5
- SUSE Linux Enterprise 15 SP5
- Fedora 39, 40
Operating systems are supported until their vendor end-of-support dates, which
can be found on the [Posit Platform Support](https://posit.co/about/platform-support/)
page. When an operating system has reached its end of support, builds for it
will be discontinued, but existing binaries will continue to be available.
## Quick Installation
To use our quick install script to install R, simply run the following
command. To use the quick installer, you must have root or sudo privileges,
and `curl` must be installed.
```sh
bash -c "$(curl -L https://rstd.io/r-install)"
```
## Manual Installation
### Specify R version
Define the version of R that you want to install. Available versions
of R can be found here: https://cdn.posit.co/r/versions.json
```bash
R_VERSION=4.3.3
```
### Download and install R
#### Ubuntu/Debian Linux
Download the deb package:
```bash
# Ubuntu 20.04
curl -O https://cdn.posit.co/r/ubuntu-2004/pkgs/r-${R_VERSION}_1_amd64.deb
# Ubuntu 22.04
curl -O https://cdn.posit.co/r/ubuntu-2204/pkgs/r-${R_VERSION}_1_amd64.deb
# Ubuntu 24.04
curl -O https://cdn.posit.co/r/ubuntu-2404/pkgs/r-${R_VERSION}_1_amd64.deb
# Debian 10
curl -O https://cdn.posit.co/r/debian-10/pkgs/r-${R_VERSION}_1_amd64.deb
# Debian 11
curl -O https://cdn.posit.co/r/debian-11/pkgs/r-${R_VERSION}_1_amd64.deb
# Debian 12
curl -O https://cdn.posit.co/r/debian-12/pkgs/r-${R_VERSION}_1_amd64.deb
```
Then install the package:
```bash
sudo apt-get install gdebi-core
sudo gdebi r-${R_VERSION}_1_amd64.deb
```
#### RHEL/CentOS Linux
Enable the [Extra Packages for Enterprise Linux](https://fedoraproject.org/wiki/EPEL)
repository (RHEL/CentOS 7 and RHEL 9 only):
```bash
# CentOS / RHEL 7
sudo yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
# Rocky Linux 9 / AlmaLinux 9
sudo dnf install dnf-plugins-core
sudo dnf config-manager --set-enabled crb
sudo dnf install epel-release
# RHEL 9
sudo dnf install https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm
```
> On RHEL 7, you may also need to enable the Optional repository:
> ```bash
> sudo subscription-manager repos --enable "rhel-*-optional-rpms"
>
> # If running RHEL 7 in a public cloud, such as Amazon EC2, enable the
> # Optional repository from Red Hat Update Infrastructure (RHUI) instead
> sudo yum install yum-utils
> sudo yum-config-manager --enable "rhel-*-optional-rpms"
> ```
> On RHEL 9, you may also need to enable the CodeReady Linux Builder repository:
> ```bash
> sudo subscription-manager repos --enable codeready-builder-for-rhel-9-$(arch)-rpms
>
> # If running RHEL 9 in a public cloud, such as Amazon EC2, enable the CodeReady
> # Linux Builder repository from Red Hat Update Infrastructure (RHUI) instead
> sudo dnf install dnf-plugins-core
> sudo dnf config-manager --enable codeready-builder-for-rhel-9-*-rpms
> ```
Download the rpm package:
```bash
# CentOS / RHEL 7
curl -O https://cdn.posit.co/r/centos-7/pkgs/R-${R_VERSION}-1-1.x86_64.rpm
# RHEL 8 / Rocky Linux 8 / AlmaLinux 8
curl -O https://cdn.posit.co/r/centos-8/pkgs/R-${R_VERSION}-1-1.x86_64.rpm
# RHEL 9 / Rocky Linux 9 / AlmaLinux 9
curl -O https://cdn.posit.co/r/rhel-9/pkgs/R-${R_VERSION}-1-1.x86_64.rpm
```
Then install the package:
```bash
sudo yum install R-${R_VERSION}-1-1.x86_64.rpm
```
#### SUSE Linux
Download the rpm package:
```bash
# openSUSE 15.5 / SLES 15 SP5
curl -O https://cdn.posit.co/r/opensuse-155/pkgs/R-${R_VERSION}-1-1.x86_64.rpm
```
Then install the package:
```bash
sudo zypper --no-gpg-checks install R-${R_VERSION}-1-1.x86_64.rpm
```
#### Fedora Linux
Download the rpm package:
```bash
# Fedora 39
curl -O https://cdn.posit.co/r/fedora-39/pkgs/R-${R_VERSION}-1-1.x86_64.rpm
# Fedora 40
curl -O https://cdn.posit.co/r/fedora-40/pkgs/R-${R_VERSION}-1-1.x86_64.rpm
```
Then install the package:
```bash
sudo dnf install r-${R_VERSION}_1_amd64.rpm
```
### Verify R installation
Test that R was successfully installed by running:
```bash
/opt/R/${R_VERSION}/bin/R --version
```
### Add R to the system path
To ensure that R is available on the system path, create symbolic links to
the version of R that you installed:
```bash
sudo ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R
sudo ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript
```
### Optional post-installation steps
You may want to install additional system dependencies for R packages.
We recommend installing a TeX distribution (such as [TinyTeX](https://yihui.name/tinytex/)
or TeX Live) and Pandoc. For more information on system dependencies, see
[system requirements for R packages](https://github.com/rstudio/r-system-requirements).
If you want to install multiple versions of R on the same system, you can
repeat these steps to install a different version of R alongside existing versions.
---
# Developer Documentation
This repository orchestrates builds using a variety of tools. The
instructions below outline the components in the stack and describe how to add a
new platform or inspect an existing platform.
## Building from source
To build the R binaries from source, you will need to have [Git](https://git-scm.com/),
[Docker](https://docs.docker.com/get-docker/), and `make` installed.
First, clone the Git repository locally and navigate to it.
```bash
git clone https://github.com/rstudio/R-builds
cd R-builds
```
Then, run the `build-r-$PLATFORM` Make target with the `R_VERSION` environment variable
set to your desired R version, where `$PLATFORM` is one of the supported platform
identifiers, such as `ubuntu-2204` or `rhel-9`.
```bash
export PLATFORM=ubuntu-2204
export R_VERSION=4.1.3
make build-r-$PLATFORM
```
The built DEB or RPM package will be available in the `builder/integration/tmp/$PLATFORM`
directory.
```bash
$ ls builder/integration/tmp/$PLATFORM
r-4.1.3_1_amd64.deb
```
### Custom installation path
R is installed to `/opt/R/${R_VERSION}` by default. If you want to customize the
installation path, set the optional `R_INSTALL_PATH` environment variable to a
custom location such as `/opt/custom/R-4.1.3`.
```bash
export PLATFORM=rhel-9
export R_VERSION=4.1.3
export R_INSTALL_PATH=/opt/custom/R-4.1.3
make build-r-$PLATFORM
```
## Adding a new platform.
### README
1. Add the new platform to the `Supported Platforms` list.
2. Add rpm package download instructions for the new platform.
### Dockerfile
Create a `builder/Dockerfile.platform-version` (where `platform-version` is `ubuntu-2204` or `centos-7`, etc.) This file must contain four major tasks:
1. an `OS_IDENTIFIER` env with the `platform-version`.
2. a step which ensures the R source build dependencies are installed
3. The `awscli`, 1.17.10+ if installed via `pip`, for uploading tarballs to S3
4. `COPY` and `ENTRYPOINT` for the `build.sh` file in `builder/`.
### Packaging script
Create a `builder/package.platform-version` script (where `platform-version` is `ubuntu-2204` or `centos-7`, etc.).
### docker-compose.yml
A new service in the docker-compose file named according to the `platform-version` and containing the proper entries:
```
command: ./build.sh
environment:
- R_VERSION=${R_VERSION} # for testing out R builds locally
- LOCAL_STORE=/tmp/output # ensures that output tarballs are persisted locally
build:
context: .
dockerfile: Dockerfile.debian-11
image: r-builds:debian-11
volumes:
- ./integration/tmp:/tmp/output # path to output tarballs
```
### Job definition
IN `serverless-resources.yml` you'll need to add a job definition that points to the ECR image.
```
rBuildsBatchJobDefinitionDebian11:
Type: AWS::Batch::JobDefinition
Properties:
Type: container
ContainerProperties:
Command:
- ./build.sh
Vcpus: 4
Memory: 4096
JobRoleArn:
"Fn::GetAtt": [ rBuildsEcsTaskIamRole, Arn ]
Image: #{AWS::AccountId}.dkr.ecr.#{AWS::Region}.amazonaws.com/r-builds:debian-11
```
### Environment variables in the serverless.yml functions.
The serverless functions which trigger R builds need to be informed of new platforms.
1. Add a `JOB_DEFINITION_ARN_PlatformVersion` env variable with a ref to the Job definition above.
2. Append the `platform-version` to `SUPPORTED_PLATFORMS`.
```
environment:
# snip
JOB_DEFINITION_ARN_debian_11:
Ref: rBuildsBatchJobDefinitionDebian11
SUPPORTED_PLATFORMS: debian-10,centos-7,centos-8
```
### Makefile
In order for the makefile to push these new platforms to ECR, add them to the PLATFORMS variable near the top of the Makefile
### test/docker-compose.yml
A new service in the `test/docker-compose.yml` file named according to the `platform-version` and containing the proper entries:
```yaml
ubuntu-2204:
image: ubuntu:jammy
command: /r-builds/test/test-apt.sh
environment:
- OS_IDENTIFIER=ubuntu-2204
- R_VERSION=${R_VERSION}
volumes:
- ../:/r-builds
```
### Submit a Pull Request
Once you've followed the steps above, submit a pull request. On successful merge, builds for this platform will begin to be available from the CDN.
## "Break Glass"
Periodically, someone with access to these resources may need to re-trigger every R version/platform combination. This quite easy with the `serverless` tool installed.
```bash
# Rebuild all R versions
serverless invoke stepf -n rBuilds -d '{"force": true}'
# Rebuild specific R versions
serverless invoke stepf -n rBuilds -d '{"force": true, "versions": ["3.6.3", "4.0.2"]}'
```
## Testing
Tests are automatically run on each push that changes a file in `builder/`, `test/`, or the `Makefile`.
These tests validate that R was correctly configured, built, and packaged. By default, the tests run
for the last 5 minor R versions on each platform.
To run the tests manually, you can navigate to the [GitHub Actions workflow page](https://github.com/rstudio/r-builds/actions/workflows/test.yml)
and use "Run workflow" to run the tests from a custom branch, list of platforms, and list of R versions.
To skip the tests, add `[skip ci]` to your commit message. See [Skipping workflow runs](https://docs.github.com/en/actions/managing-workflow-runs/skipping-workflow-runs)
for more information.
To test the R builds locally, you can use the `build-r-$PLATFORM` and `test-r-$PLATFORM`
targets to build R and run the tests. The tests use the quick install script to install R,
using a locally built R if present, or otherwise a build from the CDN.
```bash
# Build R 4.1.3 for Ubuntu 22
R_VERSION=4.1.3 make build-r-ubuntu-2204
# Test R 4.1.3 for Ubuntu 22
R_VERSION=4.1.3 make test-r-ubuntu-2204
```
Alternatively, you can build an image using the `docker-build-$PLATFORM`
target, launch a bash session within a container using the `bash-$PLATFORM` target,
and interactively run the build script:
```bash
# Build the image for Ubuntu 22
make docker-build-ubuntu-2204
# Launch a bash session for Ubuntu 22
make bash-ubuntu-2204
# Build R 4.1.3
R_VERSION=4.1.3 ./build.sh
# Build R devel with parallel execution to speed up the build
MAKEFLAGS=-j4 R_VERSION=devel ./build.sh
# Build a prerelease version of R (e.g., alpha or beta)
R_VERSION=rc R_TARBALL_URL=https://cran.r-project.org/src/base-prerelease/R-latest.tar.gz ./build.sh
```

22
build.sh Normal file
View file

@ -0,0 +1,22 @@
export PLATFORM=ubuntu-2004
export R_VERSION=4.3.3
make build-r-$PLATFORM
export PLATFORM=ubuntu-2204
export R_VERSION=4.3.3
make build-r-$PLATFORM
export PLATFORM=centos-8
export R_VERSION=4.3.3
make build-r-$PLATFORM
export PLATFORM=rhel-9
export R_VERSION=4.3.3
make build-r-$PLATFORM

8
builder/docker-compose.yml
View file

@ -22,7 +22,7 @@ services:
dockerfile: Dockerfile.ubuntu-2204 dockerfile: Dockerfile.ubuntu-2204
image: r-builds:ubuntu-2204 image: r-builds:ubuntu-2204
volumes: volumes:
- ./integration/tmp:/tmp/output - /tmp/ubuntu-2204:/tmp/output/ubuntu-2204
ubuntu-2404: ubuntu-2404:
command: ./build.sh command: ./build.sh
environment: environment:
@ -34,7 +34,7 @@ services:
dockerfile: Dockerfile.ubuntu-2404 dockerfile: Dockerfile.ubuntu-2404
image: r-builds:ubuntu-2404 image: r-builds:ubuntu-2404
volumes: volumes:
- ./integration/tmp:/tmp/output - /tmp/ubuntu-2404:/tmp/output/ubuntu-2404
debian-10: debian-10:
command: ./build.sh command: ./build.sh
environment: environment:
@ -94,7 +94,7 @@ services:
dockerfile: Dockerfile.centos-8 dockerfile: Dockerfile.centos-8
image: r-builds:centos-8 image: r-builds:centos-8
volumes: volumes:
- ./integration/tmp:/tmp/output - /tmp/centos-8:/tmp/output/centos-8
rhel-9: rhel-9:
command: ./build.sh command: ./build.sh
environment: environment:
@ -106,7 +106,7 @@ services:
dockerfile: Dockerfile.rhel-9 dockerfile: Dockerfile.rhel-9
image: r-builds:rhel-9 image: r-builds:rhel-9
volumes: volumes:
- ./integration/tmp:/tmp/output - /tmp/rhel-9:/tmp/output/rhel-9
opensuse-155: opensuse-155:
command: ./build.sh command: ./build.sh
environment: environment: