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Update r_ubuntu.yaml
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@davidycliao
davidycliao committed Dec 28, 2024
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282 changes: 199 additions & 83 deletions .github/workflows/r_ubuntu.yaml
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# R CMD check *tar.gz --no-build-vignettes --no-manual --no-examples
# shell: bash
#
# #
# name: R-ubuntu
#
# on:
# push:
# branches:
# - main
# pull_request:
# branches:
# - main
#
# jobs:
# R-CMD-check:
# runs-on: ubuntu-20.04
# strategy:
# matrix:
# r-version: ['4.3.2', '4.2.0', '4.2.1']
#
# env:
# R_LIBS_USER: /home/runner/work/_temp/Library
# TZ: UTC
# _R_CHECK_SYSTEM_CLOCK_: FALSE
# NOT_CRAN: true
# RSPM: https://packagemanager.posit.co/cran/__linux__/focal/latest
# RENV_CONFIG_REPOS_OVERRIDE: https://packagemanager.posit.co/cran/__linux__/focal/latest
#
# steps:
# - uses: actions/checkout@v3
#
# - name: Cache R dependencies
# uses: actions/cache@v2
# with:
# path: ~/R/x86_64-pc-linux-gnu-library/
# key: ${{ runner.os }}-r-${{ matrix.r-version }}-${{ hashFiles('**/renv.lock') }}
# restore-keys: ${{ runner.os }}-r-${{ matrix.r-version }}-
#
# - name: Setup R
# uses: r-lib/actions/setup-r@v2
# with:
# use-public-rspm: true
# r-version: ${{ matrix.r-version }}
#
# - name: Restore R environment
# run: |
# if (!requireNamespace('renv', quietly = TRUE)) install.packages('renv')
# renv::restore()
# shell: Rscript {0}
#
# - name: Install additional R packages
# env:
# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Use the default GitHub token for authentication
# run: |
# install.packages(c("knitr", "rmarkdown", "lsa", "purrr", "ggplot2"))
# install.packages('remotes')
# remotes::install_github("davidycliao/flaiR", auth_token = Sys.getenv("GITHUB_TOKEN"), force = TRUE)
# shell: Rscript {0}
#
# - name: Set up Python
# uses: actions/setup-python@v2
# with:
# python-version: '3.10.x'
#
# - name: Install Python virtualenv
# run: pip install virtualenv
#
# - name: Create Python virtual environment
# run: virtualenv flair_env
#
# - name: Install Python dependencies in virtual environment
# run: |
# source flair_env/bin/activate
# pip install --upgrade pip
# pip install scipy==1.12.0
# pip install flair
# pip install gensim
#
# - name: Remove Python cache files
# run: find . -name '*.pyc' -delete
#
# - name: Check R environment status
# run: renv::status()
# shell: Rscript {0}
#
# # - name: Check R package (with virtual environment)
# # run: |
# # source flair_env/bin/activate
# # R CMD build . --no-build-vignettes
# # R CMD check *tar.gz --no-build-vignettes --no-manual --no-tests --no-examples
# # shell: bash


name: R-ubuntu

on:
push:
branches:
- main
pull_request:
branches:
- main
push:
branches:
- main
pull_request:
branches:
- main

jobs:
R-CMD-check:
runs-on: ubuntu-20.04
strategy:
matrix:
r-version: ['4.3.2', '4.2.0', '4.2.1']

env:
R_LIBS_USER: /home/runner/work/_temp/Library
TZ: UTC
_R_CHECK_SYSTEM_CLOCK_: FALSE
NOT_CRAN: true
RSPM: https://packagemanager.posit.co/cran/__linux__/focal/latest
RENV_CONFIG_REPOS_OVERRIDE: https://packagemanager.posit.co/cran/__linux__/focal/latest

steps:
- uses: actions/checkout@v3

- name: Cache R dependencies
uses: actions/cache@v2
with:
path: ~/R/x86_64-pc-linux-gnu-library/
key: ${{ runner.os }}-r-${{ matrix.r-version }}-${{ hashFiles('**/renv.lock') }}
restore-keys: ${{ runner.os }}-r-${{ matrix.r-version }}-

- name: Setup R
uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
r-version: ${{ matrix.r-version }}

- name: Restore R environment
run: |
if (!requireNamespace('renv', quietly = TRUE)) install.packages('renv')
renv::restore()
shell: Rscript {0}

- name: Install additional R packages
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Use the default GitHub token for authentication
run: |
install.packages(c("knitr", "rmarkdown", "lsa", "purrr", "ggplot2"))
install.packages('remotes')
remotes::install_github("davidycliao/flaiR", auth_token = Sys.getenv("GITHUB_TOKEN"), force = TRUE)
shell: Rscript {0}

- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: '3.10.x'

- name: Install Python virtualenv
run: pip install virtualenv

- name: Create Python virtual environment
run: virtualenv flair_env

- name: Install Python dependencies in virtual environment
run: |
source flair_env/bin/activate
pip install --upgrade pip
pip install scipy==1.12.0
pip install flair
pip install gensim
- name: Remove Python cache files
run: find . -name '*.pyc' -delete

- name: Check R environment status
run: renv::status()
shell: Rscript {0}

# - name: Check R package (with virtual environment)
# run: |
# source flair_env/bin/activate
# R CMD build . --no-build-vignettes
# R CMD check *tar.gz --no-build-vignettes --no-manual --no-tests --no-examples
# shell: bash
R-CMD-check:
runs-on: ubuntu-20.04
strategy:
matrix:
r-version: ['4.3.2', '4.2.0', '4.2.1']
fail-fast: false

env:
R_LIBS_USER: /home/runner/work/_temp/Library
TZ: UTC
R_CHECK_SYSTEM_CLOCK: FALSE
NOT_CRAN: true
RSPM: https://packagemanager.posit.co/cran/__linux__/focal/latest
RENV_CONFIG_REPOS_OVERRIDE: https://packagemanager.posit.co/cran/__linux__/focal/latest

steps:
- uses: actions/checkout@v3

- name: Cache R dependencies
uses: actions/cache@v3
with:
path: ~/R/x86_64-pc-linux-gnu-library/
key: ${{ runner.os }}-r-${{ matrix.r-version }}-${{ hashFiles('**/renv.lock') }}
restore-keys: ${{ runner.os }}-r-${{ matrix.r-version }}-

- name: Setup R
uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
r-version: ${{ matrix.r-version }}

- name: Install system dependencies
run: |
sudo apt-get update
sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
- name: Install R Matrix package
run: |
install.packages('remotes')
if (getRversion() >= "4.3.0") {
remotes::install_version("Matrix", version = "1.5-1")
} else {
remotes::install_version("Matrix", version = "1.4-1")
}
shell: Rscript {0}

- name: Restore R environment
run: |
if (!requireNamespace('renv', quietly = TRUE)) install.packages('renv')
renv::restore()
shell: Rscript {0}

- name: Install additional R packages
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
install.packages(c("knitr", "rmarkdown", "lsa", "purrr", "ggplot2"))
tryCatch({
remotes::install_github("davidycliao/flaiR",
auth_token = Sys.getenv("GITHUB_TOKEN"),
force = TRUE,
dependencies = TRUE)
}, error = function(e) {
message("Error installing flaiR: ", e$message)
quit(status = 1)
})
shell: Rscript {0}

- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.10.x'
cache: 'pip'

- name: Install Python virtualenv
run: pip install virtualenv

- name: Create Python virtual environment
run: virtualenv flair_env

- name: Install Python dependencies in virtual environment
run: |
source flair_env/bin/activate
pip install --upgrade pip
pip install scipy==1.12.0
pip install flair
pip install gensim
deactivate
- name: Remove Python cache files
run: find . -name '*.pyc' -delete

- name: Check R environment status
run: renv::status()
shell: Rscript {0}

- name: Check R package (with virtual environment)
run: |
source flair_env/bin/activate
set -e
R CMD build . --no-build-vignettes
R CMD check *tar.gz --no-build-vignettes --no-manual --no-tests --no-examples || true
shell: bash

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