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[R-package] [ci] switch vignettes from 'rmarkdown' to 'markdown' #6258

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Jan 9, 2024
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[R-package] [ci] switch vignettes from 'rmarkdown' to 'markdown' #6258

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99cf0d7
[R-package] [ci] switch vignettes from 'rmarkdown' to 'markdown'
jameslamb Jan 6, 2024
f3ac92a
remove pandoc too
jameslamb Jan 7, 2024
813f8bc
Revert "remove pandoc too"
jameslamb Jan 7, 2024
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6 changes: 3 additions & 3 deletions .ci/test_r_package.sh
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Expand Up @@ -127,13 +127,13 @@ if [[ "${R_MAJOR_VERSION}" == "3" ]]; then
Rscript --vanilla -e "install.packages('https://cran.r-project.org/src/contrib/Archive/lattice/lattice_0.20-41.tar.gz', repos = NULL, lib = '${R_LIB_PATH}')"
fi

# Manually install Depends and Imports libraries + 'knitr', 'RhpcBLASctl', 'rmarkdown', 'testthat'
# Manually install Depends and Imports libraries + 'knitr', 'markdown', 'RhpcBLASctl', 'testthat'
# to avoid a CI-time dependency on devtools (for devtools::install_deps())
# NOTE: testthat is not required when running rchk
if [[ "${TASK}" == "r-rchk" ]]; then
packages="c('data.table', 'jsonlite', 'knitr', 'Matrix', 'R6', 'RhpcBLASctl', 'rmarkdown')"
packages="c('data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'R6', 'RhpcBLASctl')"
else
packages="c('data.table', 'jsonlite', 'knitr', 'Matrix', 'R6', 'RhpcBLASctl', 'rmarkdown', 'testthat')"
packages="c('data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'R6', 'RhpcBLASctl', 'testthat')"
fi
compile_from_source="both"
if [[ $OS_NAME == "macos" ]]; then
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2 changes: 1 addition & 1 deletion .ci/test_r_package_windows.ps1
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Expand Up @@ -124,7 +124,7 @@ Start-Process -FilePath Rtools.exe -NoNewWindow -Wait -ArgumentList "/VERYSILENT
Write-Output "Done installing Rtools"

Write-Output "Installing dependencies"
$packages = "c('data.table', 'jsonlite', 'knitr', 'Matrix', 'processx', 'R6', 'RhpcBLASctl', 'rmarkdown', 'testthat'), dependencies = c('Imports', 'Depends', 'LinkingTo')"
$packages = "c('data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'processx', 'R6', 'RhpcBLASctl', 'testthat'), dependencies = c('Imports', 'Depends', 'LinkingTo')"
Run-R-Code-Redirect-Stderr "options(install.packages.check.source = 'no'); install.packages($packages, repos = '$env:CRAN_MIRROR', type = 'binary', lib = '$env:R_LIB_PATH', Ncpus = parallel::detectCores())" ; Check-Output $?

Write-Output "Building R package"
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4 changes: 2 additions & 2 deletions .github/workflows/r_package.yml
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Expand Up @@ -246,7 +246,7 @@ jobs:
- name: Install packages
shell: bash
run: |
RDscript${{ matrix.r_customization }} -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'Matrix', 'RhpcBLASctl', 'rmarkdown', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
RDscript${{ matrix.r_customization }} -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'RhpcBLASctl', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
sh build-cran-package.sh --r-executable=RD${{ matrix.r_customization }}
RD${{ matrix.r_customization }} CMD INSTALL lightgbm_*.tar.gz || exit -1
- name: Run tests with sanitizers
Expand Down Expand Up @@ -320,7 +320,7 @@ jobs:
shell: bash
run: |
export PATH=/opt/R-devel/bin/:${PATH}
Rscript -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'Matrix', 'RhpcBLASctl', 'rmarkdown', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
Rscript -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'RhpcBLASctl', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
sh build-cran-package.sh
R CMD check --as-cran --run-donttest lightgbm_*.tar.gz || exit -1
if grep -q -E "NOTE|WARNING|ERROR" lightgbm.Rcheck/00check.log; then
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2 changes: 1 addition & 1 deletion .github/workflows/static_analysis.yml
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Expand Up @@ -66,7 +66,7 @@ jobs:
- name: Install packages
shell: bash
run: |
Rscript -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'Matrix', 'RhpcBLASctl', 'rmarkdown', 'roxygen2', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
Rscript -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'RhpcBLASctl', 'roxygen2', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
sh build-cran-package.sh || exit -1
R CMD INSTALL --with-keep.source lightgbm_*.tar.gz || exit -1
- name: Test documentation
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2 changes: 1 addition & 1 deletion .vsts-ci.yml
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Expand Up @@ -309,7 +309,7 @@ jobs:
R_LIB_PATH=~/Rlib
export R_LIBS=${R_LIB_PATH}
mkdir -p ${R_LIB_PATH}
RDscript -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'Matrix', 'RhpcBLASctl', 'rmarkdown'), lib = '${R_LIB_PATH}', dependencies = c('Depends', 'Imports', 'LinkingTo'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())" || exit -1
RDscript -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'RhpcBLASctl'), lib = '${R_LIB_PATH}', dependencies = c('Depends', 'Imports', 'LinkingTo'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())" || exit -1
sh build-cran-package.sh --r-executable=RD || exit -1
mv lightgbm_${LGB_VER}.tar.gz $(Build.ArtifactStagingDirectory)/lightgbm-${LGB_VER}-r-cran.tar.gz
displayName: 'Build CRAN R-package'
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2 changes: 1 addition & 1 deletion R-package/DESCRIPTION
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Expand Up @@ -46,9 +46,9 @@ Biarch: true
VignetteBuilder: knitr
Suggests:
knitr,
markdown,
processx,
RhpcBLASctl,
rmarkdown,
testthat
Depends:
R (>= 3.5)
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4 changes: 2 additions & 2 deletions R-package/README.md
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Expand Up @@ -428,7 +428,7 @@ docker run \
# install dependencies
RDscript${R_CUSTOMIZATION} \
-e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'Matrix', 'RhpcBLASctl', 'rmarkdown', 'testthat'), repos = 'https://cran.r-project.org', Ncpus = parallel::detectCores())"
-e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'RhpcBLASctl', 'testthat'), repos = 'https://cran.r-project.org', Ncpus = parallel::detectCores())"
# install lightgbm
sh build-cran-package.sh --r-executable=RD${R_CUSTOMIZATION}
Expand Down Expand Up @@ -459,7 +459,7 @@ docker run \
-it \
wch1/r-debug
RDscriptvalgrind -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'Matrix', 'RhpcBLASctl', 'rmarkdown', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
RDscriptvalgrind -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'RhpcBLASctl', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
sh build-cran-package.sh \
--r-executable=RDvalgrind
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10 changes: 7 additions & 3 deletions R-package/vignettes/basic_walkthrough.Rmd
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Expand Up @@ -3,10 +3,14 @@ title:
"Basic Walkthrough"
description: >
This vignette describes how to train a LightGBM model for binary classification.
output: rmarkdown::html_vignette
output:
markdown::html_format:
options:
toc: true
number_sections: true
vignette: >
%\VignetteIndexEntry{Basic Walkthrough}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEngine{knitr::knitr}
%\VignetteEncoding{UTF-8}
---

Expand All @@ -23,7 +27,7 @@ knitr::opts_chunk$set(

Welcome to the world of [LightGBM](https://lightgbm.readthedocs.io/en/latest/), a highly efficient gradient boosting implementation (Ke et al. 2017).

```{r setup}
```{r}
library(lightgbm)
```

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2 changes: 1 addition & 1 deletion docs/env.yml
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Expand Up @@ -9,9 +9,9 @@ dependencies:
- r-data.table=1.14.2
- r-jsonlite=1.7.2
- r-knitr=1.37
- r-markdown
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I'm planning a follow-up PR updating the version constraints on all the conda packages we pull in in this project's CI. I'll put an constraint on r-markdown then.

For now, I think it's fine to let this float and have the conda solver figure out an appropriate version.

- r-matrix=1.4_0
- r-pkgdown=1.6.1
- r-rmarkdown=2.11
- r-roxygen2=7.2.1
- scikit-learn
- sphinx
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