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

.ci/test_r_package.sh

@@ -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

.ci/test_r_package_windows.ps1

@@ -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"

.github/workflows/r_package.yml

@@ -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
@@ -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

.github/workflows/static_analysis.yml

@@ -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

.vsts-ci.yml

@@ -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'

R-package/DESCRIPTION

@@ -46,9 +46,9 @@ Biarch: true
 VignetteBuilder: knitr
 Suggests:
     knitr,
+    markdown,
     processx,
     RhpcBLASctl,
-    rmarkdown,
     testthat
 Depends:
     R (>= 3.5)

R-package/README.md

@@ -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}
@@ -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

R-package/vignettes/basic_walkthrough.Rmd

@@ -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}
 ---
 
@@ -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)
 ```
 

docs/env.yml

@@ -9,9 +9,9 @@ dependencies:
   - r-data.table=1.14.2
   - r-jsonlite=1.7.2
   - r-knitr=1.37
+  - r-markdown
   - r-matrix=1.4_0
   - r-pkgdown=1.6.1
-  - r-rmarkdown=2.11
   - r-roxygen2=7.2.1
   - scikit-learn
   - sphinx