LightGBM/R-package

LightGBM R-package

Contents

• Installation
  • Installing the CRAN Package
  • Installing from Source with CMake
  • Installing a GPU-enabled Build
  • Installing Precompiled Binaries
  • Installing from a Pre-compiled lib_lightgbm
• Examples
• Testing
  • Running the Tests
  • Code Coverage
• Updating Documentation
• Preparing a CRAN Package
• External Repositories
• Known Issues

Installation

For the easiest installation, go to "Installing the CRAN package".

If you experience any issues with that, try "Installing from Source with CMake". This can produce a more efficient version of the library on Windows systems with Visual Studio.

To build a GPU-enabled version of the package, follow the steps in "Installing a GPU-enabled Build".

If any of the above options do not work for you or do not meet your needs, please let the maintainers know by opening an issue.

When your package installation is done, you can check quickly if your LightGBM R-package is working by running the following:

library(lightgbm)
data(agaricus.train, package='lightgbm')
train <- agaricus.train
dtrain <- lgb.Dataset(train$data, label = train$label)
model <- lgb.cv(
    params = list(
        objective = "regression"
        , metric = "l2"
    )
    , data = dtrain
)

Installing the CRAN package

{lightgbm} is available on CRAN, and can be installed with the following R code.

install.packages("lightgbm", repos = "https://cran.r-project.org")

This is the easiest way to install {lightgbm}. It does not require CMake or Visual Studio, and should work well on many different operating systems and compilers.

Each CRAN package is also available on LightGBM releases, with a name like lightgbm-{VERSION}-r-cran.tar.gz.

Custom Installation (Linux, Mac)

The steps above should work on most systems, but users with highly-customized environments might want to change how R builds packages from source.

To change the compiler used when installing the CRAN package, you can create a file ~/.R/Makevars which overrides CC (C compiler) and CXX (C++ compiler).

For example, to use gcc instead of clang on Mac, you could use something like the following:

# ~/.R/Makevars
CC=gcc-8
CXX=g++-8
CXX11=g++-8

Installing from Source with CMake

You need to install git and CMake first.

Note: this method is only supported on 64-bit systems. If you need to run LightGBM on 32-bit Windows (i386), follow the instructions in "Installing the CRAN Package".

Windows Preparation

NOTE: Windows users may need to run with administrator rights (either R or the command prompt, depending on the way you are installing this package).

Installing a 64-bit version of Rtools is mandatory.

After installing Rtools and CMake, be sure the following paths are added to the environment variable PATH. These may have been automatically added when installing other software.

• Rtools
  • If you have Rtools 3.x, example:
    • C:\Rtools\mingw_64\bin
  • If you have Rtools 4.0, example:
    • C:\rtools40\mingw64\bin
    • C:\rtools40\usr\bin
  • If you have Rtools 4.2+, example:
    • C:\rtools42\x86_64-w64-mingw32.static.posix\bin
    • C:\rtools42\usr\bin
    • NOTE: this is e.g. rtools43\ for R 4.3
• CMake
  • example: C:\Program Files\CMake\bin
• R
  • example: C:\Program Files\R\R-3.6.1\bin

NOTE: Two Rtools paths are required from Rtools 4.0 onwards because paths and the list of included software was changed in Rtools 4.0.

NOTE: Rtools42 and later take a very different approach to the compiler toolchain than previous releases, and how you install it changes what is required to build packages. See "Howto: Building R 4.2 and packages on Windows".

Windows Toolchain Options

A "toolchain" refers to the collection of software used to build the library. The R package can be built with three different toolchains.

Warning for Windows users: it is recommended to use Visual Studio for its better multi-threading efficiency in Windows for many core systems. For very simple systems (dual core computers or worse), MinGW64 is recommended for maximum performance. If you do not know what to choose, it is recommended to use Visual Studio, the default compiler. Do not try using MinGW in Windows on many core systems. It may result in 10x slower results than Visual Studio.

Visual Studio (default)

By default, the package will be built with Visual Studio Build Tools.

MinGW (R 3.x)

If you are using R 3.x and installation fails with Visual Studio, LightGBM will fall back to using MinGW bundled with Rtools.

If you want to force LightGBM to use MinGW (for any R version), pass --use-mingw to the installation script.

Rscript build_r.R --use-mingw

MSYS2 (R 4.x)

If you are using R 4.x and installation fails with Visual Studio, LightGBM will fall back to using MSYS2. This should work with the tools already bundled in Rtools 4.0.

If you want to force LightGBM to use MSYS2 (for any R version), pass --use-msys2 to the installation script.

Rscript build_r.R --use-msys2

Mac OS Preparation

You can perform installation either with Apple Clang or gcc. In case you prefer Apple Clang, you should install OpenMP (details for installation can be found in Installation Guide) first. In case you prefer gcc, you need to install it (details for installation can be found in Installation Guide) and set some environment variables to tell R to use gcc and g++. If you install these from Homebrew, your versions of g++ and gcc are most likely in /usr/local/bin, as shown below.

# replace 8 with version of gcc installed on your machine
export CXX=/usr/local/bin/g++-8 CC=/usr/local/bin/gcc-8

Install with CMake

After following the "preparation" steps above for your operating system, build and install the R-package with the following commands:

git clone --recursive https://github.com/microsoft/LightGBM
cd LightGBM
Rscript build_r.R

The build_r.R script builds the package in a temporary directory called lightgbm_r. It will destroy and recreate that directory each time you run the script. That script supports the following command-line options:

• --no-build-vignettes: Skip building vignettes.
• -j[jobs]: Number of threads to use when compiling LightGBM. E.g., -j4 will try to compile 4 objects at a time.
  • by default, this script uses single-thread compilation
  • for best results, set -j to the number of physical CPUs
• --skip-install: Build the package tarball, but do not install it.
• --use-gpu: Build a GPU-enabled version of the library.
• --use-mingw: Force the use of MinGW toolchain, regardless of R version.
• --use-msys2: Force the use of MSYS2 toolchain, regardless of R version.

Note: for the build with Visual Studio/VS Build Tools in Windows, you should use the Windows CMD or PowerShell.

Installing a GPU-enabled Build

You will need to install Boost and OpenCL first: details for installation can be found in Installation-Guide.

After installing these other libraries, follow the steps in "Installing from Source with CMake". When you reach the step that mentions build_r.R, pass the flag --use-gpu.

Rscript build_r.R --use-gpu

You may also need or want to provide additional configuration, depending on your setup. For example, you may need to provide locations for Boost and OpenCL.

Rscript build_r.R \
    --use-gpu \
    --opencl-library=/usr/lib/x86_64-linux-gnu/libOpenCL.so \
    --boost-librarydir=/usr/lib/x86_64-linux-gnu

The following options correspond to the CMake FindBoost options by the same names.

• --boost-root
• --boost-dir
• --boost-include-dir
• --boost-librarydir

The following options correspond to the CMake FindOpenCL options by the same names.

• --opencl-include-dir
• --opencl-library

Installing Precompiled Binaries

Precompiled binaries for Mac and Windows are prepared by CRAN a few days after each release to CRAN. They can be installed with the following R code.

install.packages(
    "lightgbm"
    , type = "both"
    , repos = "https://cran.r-project.org"
)

These packages do not require compilation, so they will be faster and easier to install than packages that are built from source.

CRAN does not prepare precompiled binaries for Linux, and as of this writing neither does this project.

Installing from a Pre-compiled lib_lightgbm

Previous versions of LightGBM offered the ability to first compile the C++ library (lib_lightgbm.{dll,dylib,so}) and then build an R package that wraps it.

As of version 3.0.0, this is no longer supported. If building from source is difficult for you, please open an issue.

Examples

Please visit demo:

• Basic walkthrough of wrappers
• Boosting from existing prediction
• Early Stopping
• Cross Validation
• Multiclass Training/Prediction
• Leaf (in)Stability
• Weight-Parameter Adjustment Relationship

Testing

The R package's unit tests are run automatically on every commit, via integrations like GitHub Actions. Adding new tests in R-package/tests/testthat is a valuable way to improve the reliability of the R package.

Running the Tests

While developing the R package, run the code below to run the unit tests.

sh build-cran-package.sh \
    --no-build-vignettes

R CMD INSTALL --with-keep.source lightgbm*.tar.gz
cd R-package/tests
Rscript testthat.R

To run the tests with more verbose logs, set environment variable LIGHTGBM_TEST_VERBOSITY to a valid value for parameter verbosity.

export LIGHTGBM_TEST_VERBOSITY=1
cd R-package/tests
Rscript testthat.R

Code Coverage

When adding tests, you may want to use test coverage to identify untested areas and to check if the tests you've added are covering all branches of the intended code.

The example below shows how to generate code coverage for the R package on a macOS or Linux setup. To adjust for your environment, refer to the customization step described above.

# Install
sh build-cran-package.sh \
    --no-build-vignettes

# Get coverage
Rscript -e " \
    library(covr);
    coverage <- covr::package_coverage('./lightgbm_r', type = 'tests', quiet = FALSE);
    print(coverage);
    covr::report(coverage, file = file.path(getwd(), 'coverage.html'), browse = TRUE);
    "

Updating Documentation

The R package uses {roxygen2} to generate its documentation. The generated DESCRIPTION, NAMESPACE, and man/ files are checked into source control. To regenerate those files, run the following.

Rscript \
    --vanilla \
    -e "install.packages('roxygen2', repos = 'https://cran.rstudio.com')"

sh build-cran-package.sh --no-build-vignettes
R CMD INSTALL \
  --with-keep.source \
  ./lightgbm_*.tar.gz

cd R-package
Rscript \
    --vanilla \
    -e "roxygen2::roxygenize(load = 'installed')"

Preparing a CRAN Package

This section is primarily for maintainers, but may help users and contributors to understand the structure of the R package.

Most of LightGBM uses CMake to handle tasks like setting compiler and linker flags, including header file locations, and linking to other libraries. Because CRAN packages typically do not assume the presence of CMake, the R package uses an alternative method that is in the CRAN-supported toolchain for building R packages with C++ code: Autoconf.

For more information on this approach, see "Writing R Extensions".

Build a CRAN Package

From the root of the repository, run the following.

git submodule update --init --recursive
sh build-cran-package.sh

This will create a file lightgbm_${VERSION}.tar.gz, where VERSION is the version of LightGBM.

That script supports the following command-line options:

• --no-build-vignettes: Skip building vignettes.
• --r-executable=[path-to-executable]: Use an alternative build of R.

Also, CRAN package is generated with every commit to any repo's branch and can be found in "Artifacts" section of the associated Azure Pipelines run.

Standard Installation from CRAN Package

After building the package, install it with a command like the following:

R CMD install lightgbm_*.tar.gz

Changing the CRAN Package

A lot of details are handled automatically by R CMD build and R CMD install, so it can be difficult to understand how the files in the R package are related to each other. An extensive treatment of those details is available in "Writing R Extensions".

This section briefly explains the key files for building a CRAN package. To update the package, edit the files relevant to your change and re-run the steps in Build a CRAN Package.

Linux or Mac

At build time, configure will be run and used to create a file Makevars, using Makevars.in as a template.

1. Edit configure.ac.

2. Create configure with autoconf. Do not edit it by hand. This file must be generated on Ubuntu 22.04.

   If you have an Ubuntu 22.04 environment available, run the provided script from the root of the LightGBM repository.

   ./R-package/recreate-configure.sh
   

   If you do not have easy access to an Ubuntu 22.04 environment, the configure script can be generated using Docker by running the code below from the root of this repo.

   docker run \
       --rm \
       -v $(pwd):/opt/LightGBM \
       -w /opt/LightGBM \
       ubuntu:22.04 \
       ./R-package/recreate-configure.sh
   

   The version of autoconf used by this project is stored in R-package/AUTOCONF_UBUNTU_VERSION. To update that version, update that file and run the commands above. To see available versions, see https://packages.ubuntu.com/search?keywords=autoconf.

3. Edit src/Makevars.in.

Alternatively, GitHub Actions can re-generate this file for you. On a pull request (only on internal one, does not work for ones from forks), create a comment with this phrase:

/gha run r-configure

Configuring for Windows

At build time, configure.win will be run and used to create a file Makevars.win, using Makevars.win.in as a template.

1. Edit configure.win directly.
2. Edit src/Makevars.win.in.

Testing the CRAN Package

{lightgbm} is tested automatically on every commit, across many combinations of operating system, R version, and compiler. This section describes how to test the package locally while you are developing.

Windows, Mac, and Linux

sh build-cran-package.sh
R CMD check --as-cran lightgbm_*.tar.gz

ASAN and UBSAN

All packages uploaded to CRAN must pass builds using gcc and clang, instrumented with two sanitizers: the Address Sanitizer (ASAN) and the Undefined Behavior Sanitizer (UBSAN).

For more background, see

• this blog post
• top-level CRAN documentation on these checks
• CRAN's configuration of these checks

You can replicate these checks locally using Docker. For more information on the image used for testing, see https://github.com/wch/r-debug.

In the code below, environment variable R_CUSTOMIZATION should be set to one of two values.

• "san" = replicates CRAN's gcc-ASAN and gcc-UBSAN checks
• "csan" = replicates CRAN's clang-ASAN and clang-UBSAN checks

docker run \
  --rm \
  -it \
  -v $(pwd):/opt/LightGBM \
  -w /opt/LightGBM \
  --env R_CUSTOMIZATION=san \
  wch1/r-debug:latest \
  /bin/bash

# install dependencies
RDscript${R_CUSTOMIZATION} \
  -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${R_CUSTOMIZATION}
RD${R_CUSTOMIZATION} \
  CMD INSTALL lightgbm_*.tar.gz

# run tests
cd R-package/tests
rm -f ./tests.log
RDscript${R_CUSTOMIZATION} testthat.R >> tests.log 2>&1

# check that tests passed
echo "test exit code: $?"
tail -300 ./tests.log

Valgrind

All packages uploaded to CRAN must be built and tested without raising any issues from valgrind. valgrind is a profiler that can catch serious issues like memory leaks and illegal writes. For more information, see this blog post.

You can replicate these checks locally using Docker. Note that instrumented versions of R built to use valgrind run much slower, and these tests may take as long as 20 minutes to run.

docker run \
    --rm \
    -v $(pwd):/opt/LightGBM \
    -w /opt/LightGBM \
    -it \
        wch1/r-debug

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

RDvalgrind CMD INSTALL \
    --preclean \
    --install-tests \
        lightgbm_*.tar.gz

cd R-package/tests

RDvalgrind \
    --no-readline \
    --vanilla \
    -d "valgrind --tool=memcheck --leak-check=full --track-origins=yes" \
        -f testthat.R \
2>&1 \
| tee out.log \
| cat

These tests can also be triggered on any pull request by leaving a comment in a pull request:

/gha run r-valgrind

Known Issues

For information about known issues with the R package, see the R-package section of LightGBM's main FAQ page.