[R-package][ci] added CI stage for R package (fixes #2335, fixes #2569) (#2530)

.ci/test.sh

@@ -78,6 +78,11 @@ if [[ $TASK == "if-else" ]]; then
     exit 0
 fi
 
+if [[ $TASK == "r-package" ]]; then
+    bash ${BUILD_DIRECTORY}/.ci/test_r_package.sh || exit -1
+    exit 0
+fi
+
 conda install -q -y -n $CONDA_ENV joblib matplotlib numpy pandas psutil pytest python-graphviz scikit-learn scipy
 
 if [[ $OS_NAME == "macos" ]] && [[ $COMPILER == "clang" ]]; then

.ci/test_r_package.sh

@@ -0,0 +1,90 @@
+#!/bin/bash
+
+# set up R environment
+R_LIB_PATH=~/Rlib
+mkdir -p $R_LIB_PATH
+echo "R_LIBS=$R_LIB_PATH" > ${HOME}/.Renviron
+echo 'options(repos = "https://cran.rstudio.com")' > ${HOME}/.Rprofile
+export PATH="$R_LIB_PATH/R/bin:$PATH"
+
+# installing precompiled R for Ubuntu
+# https://cran.r-project.org/bin/linux/ubuntu/#installation
+# adding steps from https://stackoverflow.com/a/56378217/3986677 to get latest version
+#
+# This only needs to get run on Travis because R environment for Linux
+# used by Azure pipelines is set up in https://github.com/guolinke/lightgbm-ci-docker
+if [[ $TRAVIS == "true" ]] && [[ $OS_NAME == "linux" ]]; then
+    sudo add-apt-repository \
+        "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/"
+    sudo apt-key adv \
+        --keyserver keyserver.ubuntu.com \
+        --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+    sudo apt-get update
+    sudo apt-get install \
+        --no-install-recommends \
+        -y \
+            r-base-dev=${R_TRAVIS_LINUX_VERSION} \
+            texinfo \
+            texlive-latex-recommended \
+            texlive-fonts-recommended \
+            texlive-fonts-extra \
+            qpdf \
+            || exit -1
+fi
+
+# Installing R precompiled for Mac OS 10.11 or higher
+if [[ $OS_NAME == "macos" ]]; then
+
+    brew install qpdf
+    brew cask install basictex
+    export PATH="/Library/TeX/texbin:$PATH"
+    sudo tlmgr update --self
+    sudo tlmgr install inconsolata helvetic
+
+    wget -q https://cran.r-project.org/bin/macosx/R-${R_MAC_VERSION}.pkg -O R.pkg
+    sudo installer \
+        -pkg $(pwd)/R.pkg \
+        -target /
+
+    # Fix "duplicate libomp versions" issue on Mac
+    # by replacing the R libomp.dylib with a symlink to the one installed with brew
+    if [[ $COMPILER == "clang" ]]; then
+        ver_arr=( ${R_MAC_VERSION//./ } )
+        R_MAJOR_MINOR="${ver_arr[0]}.${ver_arr[1]}"
+        sudo ln -sf \
+            "$(brew --cellar libomp)"/*/lib/libomp.dylib \
+            /Library/Frameworks/R.framework/Versions/${R_MAJOR_MINOR}/Resources/lib/libomp.dylib
+    fi
+fi
+
+conda install \
+    -y \
+    -q \
+    --no-deps \
+        pandoc
+
+# Manually install Depends and Imports libraries + 'testthat'
+# to avoid a CI-time dependency on devtools (for devtools::install_deps())
+Rscript -e "install.packages(c('data.table', 'jsonlite', 'Matrix', 'R6', 'testthat'))" || exit -1
+
+cd ${BUILD_DIRECTORY}
+Rscript build_r.R || exit -1
+
+PKG_TARBALL="lightgbm_${LGB_VER}.tar.gz"
+LOG_FILE_NAME="lightgbm.Rcheck/00check.log"
+
+# suppress R CMD check warning from Suggests dependencies not being available
+export _R_CHECK_FORCE_SUGGESTS_=0
+
+# fails tests if either ERRORs or WARNINGs are thrown by
+# R CMD CHECK
+R CMD check ${PKG_TARBALL} \
+    --as-cran \
+|| exit -1
+
+if grep -q -R "WARNING" "$LOG_FILE_NAME"; then
+    echo "WARNINGS have been found by R CMD check!"
+    exit -1
+fi
+
+exit 0

.travis.yml

@@ -24,6 +24,7 @@ env:
     - TASK=mpi METHOD=pip
     - TASK=gpu METHOD=source PYTHON_VERSION=3.5
     - TASK=gpu METHOD=pip PYTHON_VERSION=3.6
+    - TASK=r-package
 
 matrix:
   exclude:
@@ -44,9 +45,11 @@ before_install:
   - if [[ $TRAVIS_OS_NAME == "osx" ]]; then
         export OS_NAME="macos";
         export COMPILER="gcc";
+        export R_MAC_VERSION=3.6.1;
     else
         export OS_NAME="linux";
         export COMPILER="clang";
+        export R_TRAVIS_LINUX_VERSION=3.6.1-3bionic;
     fi
   - export CONDA="$HOME/miniconda"
   - export PATH="$CONDA/bin:$PATH"

.vsts-ci.yml

@@ -42,6 +42,8 @@ jobs:
         TASK: gpu
         METHOD: source
         PYTHON_VERSION: 3.6
+      r_package:
+        TASK: r-package
   steps:
   - script: |
       echo "##vso[task.setvariable variable=HOME_DIRECTORY]$AGENT_HOMEDIRECTORY"
@@ -84,6 +86,8 @@ jobs:
         PYTHON_VERSION: 3.5
       bdist:
         TASK: bdist
+      r_package:
+        TASK: r-package
   steps:
   - script: |
       echo "##vso[task.setvariable variable=HOME_DIRECTORY]$AGENT_HOMEDIRECTORY"
@@ -95,6 +99,7 @@ jobs:
       echo "##vso[task.setvariable variable=CONDA]$CONDA"
       echo "##vso[task.prependpath]$CONDA/bin"
       echo "##vso[task.setvariable variable=JAVA_HOME]$JAVA_HOME_8_X64"
+      echo "##vso[task.setvariable variable=R_MAC_VERSION]3.6.1"
     displayName: 'Set variables'
   - bash: $(Build.SourcesDirectory)/.ci/setup.sh
     displayName: Setup

R-package/.Rbuildignore

@@ -12,3 +12,14 @@
 
 # Code copied in at build time
 ^src/CMakeLists.txt$
+
+# unnecessary files from submodules
+^src/compute/.appveyor.yml$
+^src/compute/.coveralls.yml$
+^src/compute/.travis.yml$
+^src/compute/test/$
+^src/compute/index.html$
+^src/compute/.git$
+^src/compute/.gitignore$
+^src/compute/CONTRIBUTING.md$
+^src/compute/README.md$

R-package/DESCRIPTION

@@ -36,4 +36,4 @@ Imports:
     jsonlite (>= 1.0),
     Matrix (>= 1.1-0),
     methods
-RoxygenNote: 6.0.1
+RoxygenNote: 7.0.2

R-package/man/lgb.cv.Rd

@@ -53,6 +53,8 @@ lgb.cv(
 
 \item{eval_freq}{evaluation output frequency, only effect when verbose > 0}
 
+\item{showsd}{\code{boolean}, whether to show standard deviation of cross validation}
+
 \item{stratified}{a \code{boolean} indicating whether sampling of folds should be stratified
 by the values of outcome labels.}
 
@@ -88,8 +90,6 @@ into a predictor model which frees up memory and the original datasets}
                        the number of real CPU cores, not the number of threads (most
                        CPU using hyper-threading to generate 2 threads per CPU core).}
 }}
-
-\item{showsd}{\code{boolean}, whether to show standard deviation of cross validation}
 }
 \value{
 a trained model \code{lgb.CVBooster}.

R-package/man/lgb.prepare_rules2.Rd

@@ -24,3 +24,42 @@ This is useful if you have a specific need for integer dataset instead of numeri
 Note that there are programs which do not support integer-only input.
 Consider this as a half memory technique which is dangerous, especially for LightGBM.
 }
+\examples{
+library(lightgbm)
+data(iris)
+
+str(iris)
+
+new_iris <- lgb.prepare_rules2(data = iris) # Autoconverter
+str(new_iris$data)
+
+data(iris) # Erase iris dataset
+iris$Species[1L] <- "NEW FACTOR" # Introduce junk factor (NA)
+
+# Use conversion using known rules
+# Unknown factors become 0, excellent for sparse datasets
+newer_iris <- lgb.prepare_rules2(data = iris, rules = new_iris$rules)
+
+# Unknown factor is now zero, perfect for sparse datasets
+newer_iris$data[1L, ] # Species became 0 as it is an unknown factor
+
+newer_iris$data[1L, 5L] <- 1.0 # Put back real initial value
+
+# Is the newly created dataset equal? YES!
+all.equal(new_iris$data, newer_iris$data)
+
+# Can we test our own rules?
+data(iris) # Erase iris dataset
+
+# We remapped values differently
+personal_rules <- list(
+  Species = c(
+    "setosa" = 3L
+    , "versicolor" = 2L
+    , "virginica" = 1L
+  )
+)
+newest_iris <- lgb.prepare_rules2(data = iris, rules = personal_rules)
+str(newest_iris$data) # SUCCESS!
+
+}

R-package/src/install.libs.R

@@ -99,6 +99,32 @@ if (!use_precompile) {
 
   # Install
   system(paste0(cmake_cmd, " .."))
+
+  # R CMD check complains about the .NOTPARALLEL directive created in the cmake
+  # Makefile. We don't need it here anyway since targets are built serially, so trying
+  # to remove it with this hack
+  generated_makefile <- file.path(
+    R_PACKAGE_SOURCE
+    , "src"
+    , "build"
+    , "Makefile"
+  )
+  if (file.exists(generated_makefile)) {
+    makefile_txt <- readLines(
+      con = generated_makefile
+    )
+    makefile_txt <- gsub(
+      pattern = ".*NOTPARALLEL.*"
+      , replacement = ""
+      , x = makefile_txt
+    )
+    writeLines(
+      text = makefile_txt
+      , con = generated_makefile
+      , sep = "\n"
+    )
+  }
+
   system(build_cmd)
   src <- file.path(lib_folder, paste0("lib_lightgbm", SHLIB_EXT), fsep = "/")
 

R-package/tests/testthat.R

@@ -1,4 +1,8 @@
 library(testthat)
 library(lightgbm)
 
-test_check("lightgbm")
+test_check(
+    package = "lightgbm"
+    , stop_on_failure = TRUE
+    , stop_on_warning = FALSE
+)

build_r.R

@@ -85,5 +85,5 @@ version <- gsub(
 )
 tarball <- file.path(getwd(), sprintf("lightgbm_%s.tar.gz", version))
 
-cmd <- sprintf("R CMD INSTALL %s --no-multiarch", tarball)
+cmd <- sprintf("R CMD INSTALL %s --no-multiarch --with-keep.source", tarball)
 .run_shell_command(cmd)