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Configuring a developer environment

Source: vignettes/developers/setup.Rmd
setup.Rmd

The Arrow R package is unique compared to other R packages that you may have contributed to because it builds on top of the large and feature-rich Arrow C++ implementation. Because the R package integrates tightly with Arrow C++, it typically requires a dedicated copy of the library (i.e., it is usually not possible to link to a system version of libarrow during development).

Option 1: Using nightly libarrow binaries

On Linux, MacOS, and Windows you can use the same workflow you might use for another package that contains compiled code (e.g., R CMD INSTALL . from a terminal, devtools::load_all() from an R prompt, or Install & Restart from RStudio). If the arrow/r/libarrow directory is not populated, the configure script will attempt to download the latest nightly libarrow binary, extract it to the arrow/r/libarrow directory (MacOS, Linux) or arrow/r/windows directory (Windows), and continue building the R package as usual.

Most of the time, you won’t need to update your version of libarrow because the R package rarely changes with updates to the C++ library; however, if you start to get errors when rebuilding the R package, you may have to remove the libarrow directory (MacOS, Linux) or windows directory (Windows) and do a “clean” rebuild. You can do this from a terminal with R CMD INSTALL . --preclean, from RStudio using the “Clean and Install” option from “Build” tab, or using make clean if you are using the Makefile located in the root of the R package.

Option 2: Use a local Arrow C++ development build

If you need to alter both libarrow and the R package code, or if you can’t get a binary version of the latest libarrow elsewhere, you’ll need to build it from source. This section discusses how to set up a C++ libarrow build configured to work with the R package. For more general resources, see the Arrow C++ developer guide.

There are five major steps to the process.

Step 1 - Install dependencies

When building libarrow, by default, system dependencies will be used if suitable versions are found. If system dependencies are not present, libarrow will build them during its own build process. The only dependencies that you need to install outside of the build process are cmake (for configuring the build) and openssl if you are building with S3 support.

For a faster build, you may choose to pre-install more C++ library dependencies (such as lz4, zstd, etc.) on the system so that they don’t need to be built from source in the libarrow build.

Ubuntu 
sudo apt install -y cmake libcurl4-openssl-dev libssl-dev
macOS 
brew install cmake openssl

Step 2 - Configure the libarrow build

We recommend that you configure libarrow to be built to a user-level directory rather than a system directory for your development work. This is so that the development version you are using doesn’t overwrite a released version of libarrow you may already have installed, and so that you are also able work with more than one version of libarrow (by using different ARROW_HOME directories for the different versions).

In the example below, libarrow is installed to a directory called dist that has the same parent directory as the arrow checkout. Your installation of the Arrow R package can point to any directory with any name, though we recommend not placing it inside of the arrow git checkout directory as unwanted changes could stop it working properly.

export ARROW_HOME=$(pwd)/dist
mkdir $ARROW_HOME

Special instructions on Linux: You will need to set LD_LIBRARY_PATH to the lib directory that is under where you set $ARROW_HOME, before launching R and using arrow. One way to do this is to add it to your profile (we use ~/.bash_profile here, but you might need to put this in a different file depending on your setup, e.g. if you use a shell other than bash). On macOS you do not need to do this because the macOS shared library paths are hardcoded to their locations during build time.

export LD_LIBRARY_PATH=$ARROW_HOME/lib:$LD_LIBRARY_PATH
echo "export LD_LIBRARY_PATH=$ARROW_HOME/lib:$LD_LIBRARY_PATH" >> ~/.bash_profile

Start by navigating in a terminal to the arrow repository. You will need to create a directory into which the C++ build will put its contents. We recommend that you make a build directory inside of the cpp directory of the Arrow git repository (it is git-ignored, so you won’t accidentally check it in). Next, change directories to be inside cpp/build:

pushd arrow
mkdir -p cpp/build
pushd cpp/build

You’ll first call cmake to configure the build and then make install. For the R package, you’ll need to enable several features in libarrow using -D flags:

Linux / Mac OS 
cmake \
  -DCMAKE_INSTALL_PREFIX=$ARROW_HOME \
  -DCMAKE_INSTALL_LIBDIR=lib \
  -DARROW_COMPUTE=ON \
  -DARROW_CSV=ON \
  -DARROW_DATASET=ON \
  -DARROW_EXTRA_ERROR_CONTEXT=ON \
  -DARROW_FILESYSTEM=ON \
  -DARROW_INSTALL_NAME_RPATH=OFF \
  -DARROW_JEMALLOC=ON \
  -DARROW_JSON=ON \
  -DARROW_PARQUET=ON \
  -DARROW_WITH_SNAPPY=ON \
  -DARROW_WITH_ZLIB=ON \
  ..

.. refers to the C++ source directory: you’re in cpp/build and the source is in cpp.

Enabling more Arrow features

To enable optional features including: S3 support, an alternative memory allocator, and additional compression libraries, add some or all of these flags to your call to cmake (the trailing \ makes them easier to paste into a bash shell on a new line):

  -DARROW_GCS=ON \
  -DARROW_MIMALLOC=ON \
  -DARROW_S3=ON \
  -DARROW_WITH_BROTLI=ON \
  -DARROW_WITH_BZ2=ON \
  -DARROW_WITH_LZ4=ON \
  -DARROW_WITH_SNAPPY=ON \
  -DARROW_WITH_ZSTD=ON \

Other flags that may be useful:

  • -DBoost_SOURCE=BUNDLED and -DThrift_SOURCE=BUNDLED, for example, or any other dependency *_SOURCE, if you have a system version of a C++ dependency that doesn’t work correctly with Arrow. This tells the build to compile its own version of the dependency from source.

  • -DCMAKE_BUILD_TYPE=debug or -DCMAKE_BUILD_TYPE=relwithdebinfo can be useful for debugging. You probably don’t want to do this generally because a debug build is much slower at runtime than the default release build.

  • -DARROW_BUILD_STATIC=ON and -DARROW_BUILD_SHARED=OFF if you want to use static libraries instead of dynamic libraries. With static libraries there isn’t a risk of the R package linking to the wrong library, but it does mean if you change the C++ code you have to recompile both the C++ libraries and the R package. Compilers typically will link to static libraries only if the dynamic ones are not present, which is why we need to set -DARROW_BUILD_SHARED=OFF. If you are switching after compiling and installing previously, you may need to remove the .dll or .so files from $ARROW_HOME/dist/bin.

Note cmake is particularly sensitive to whitespacing, if you see errors, check that you don’t have any errant whitespace.

Step 3 - Building libarrow

You can add -j# at the end of the command here too to speed up compilation by running in parallel (where # is the number of cores you have available).

cmake --build . --target install -j8

Step 4 - Build the Arrow R package

Once you’ve built libarrow, you can install the R package and its dependencies, along with additional dev dependencies, from the git checkout:

popd # To go back to the root directory of the project, from cpp/build
pushd r
R -e "install.packages('remotes'); remotes::install_deps(dependencies = TRUE)"
R CMD INSTALL --no-multiarch .

The --no-multiarch flag makes it only compile on the “main” architecture. This will compile for the architecture that the R in your path corresponds to. If you compile on one architecture and then switch to another, make sure to pass the --preclean flag so that the R package code is recompiled for the new architecture. Otherwise, you may see errors like LoadLibrary failure: %1 is not a valid Win32 application.

Compilation flags

If you need to set any compilation flags while building the C++ extensions, you can use the ARROW_R_CXXFLAGS environment variable. For example, if you are using perf to profile the R extensions, you may need to set

export ARROW_R_CXXFLAGS=-fno-omit-frame-pointer
Recompiling the C++ code

With the setup described here, you should not need to rebuild the Arrow library or even the C++ source in the R package as you iterate and work on the R package. The only time those should need to be rebuilt is if you have changed the C++ in the R package (and even then, R CMD INSTALL . should only need to recompile the files that have changed) or if the libarrow C++ has changed and there is a mismatch between libarrow and the R package. If you find yourself rebuilding either or both each time you install the package or run tests, something is probably wrong with your set up.

For a full build: a cmake command with all of the R-relevant optional dependencies turned on. Development with other languages might require different flags as well. For example, to develop Python, you would need to also add -DARROW_PYTHON=ON (though all of the other flags used for Python are already included here).

cmake \
  -DCMAKE_INSTALL_PREFIX=$ARROW_HOME \
  -DCMAKE_INSTALL_LIBDIR=lib \
  -DARROW_COMPUTE=ON \
  -DARROW_CSV=ON \
  -DARROW_DATASET=ON \
  -DARROW_EXTRA_ERROR_CONTEXT=ON \
  -DARROW_FILESYSTEM=ON \
  -DARROW_GCS=ON \
  -DARROW_INSTALL_NAME_RPATH=OFF \
  -DARROW_JEMALLOC=ON \
  -DARROW_JSON=ON \
  -DARROW_MIMALLOC=ON \
  -DARROW_PARQUET=ON \
  -DARROW_S3=ON \
  -DARROW_WITH_BROTLI=ON \
  -DARROW_WITH_BZ2=ON \
  -DARROW_WITH_LZ4=ON \
  -DARROW_WITH_SNAPPY=ON \
  -DARROW_WITH_ZLIB=ON \
  -DARROW_WITH_ZSTD=ON \
  ..

Installing a version of the R package with a specific git reference

If you need an arrow installation from a specific repository or git reference, on most platforms except Windows, you can run:

remotes::install_github("apache/arrow/r", build = FALSE)

The build = FALSE argument is important so that the installation can access the C++ source in the cpp/ directory in apache/arrow.

As with other installation methods, setting the environment variables LIBARROW_MINIMAL=false and ARROW_R_DEV=true will provide a more full-featured version of Arrow and provide more verbose output, respectively.

For example, to install from the (fictional) branch bugfix from apache/arrow you could run:

Sys.setenv(LIBARROW_MINIMAL="false")
remotes::install_github("apache/arrow/r@bugfix", build = FALSE)

Developers may wish to use this method of installing a specific commit separate from another Arrow development environment or system installation (e.g. we use this in arrowbench to install development versions of libarrow isolated from the system install). If you already have libarrow installed system-wide, you may need to set some additional variables in order to isolate this build from your system libraries:

  • Setting the environment variable FORCE_BUNDLED_BUILD to true will skip the pkg-config search for libarrow and attempt to build from the same source at the repository+ref given.

  • You may also need to set the Makevars CPPFLAGS and LDFLAGS to "" in order to prevent the installation process from attempting to link to already installed system versions of libarrow. One way to do this temporarily is wrapping your remotes::install_github() call like so:

withr::with_makevars(list(CPPFLAGS = "", LDFLAGS = ""), remotes::install_github(...))

Summary of environment variables

  • See the user-facing article on installation for a large number of environment variables that determine how the build works and what features get built.
  • TEST_OFFLINE_BUILD: When set to true, the build script will not download prebuilt the C++ library binary. It will turn off any features that require a download, unless they’re available in ARROW_THIRDPARTY_DEPENDENCY_DIR or the tools/thirdparty_download/ subfolder. create_package_with_all_dependencies() creates that subfolder. Regardless of this flag’s value, cmake will be downloaded if it’s unavailable.

Troubleshooting

Note that after any change to libarrow, you must reinstall it and run make clean or git clean -fdx . to remove any cached object code in the r/src/ directory before reinstalling the R package. This is only necessary if you make changes to libarrow source; you do not need to manually purge object files if you are only editing R or C++ code inside r/.

Arrow library - R package mismatches

If libarrow and the R package have diverged, you will see errors like:

Error: package or namespace load failed for ‘arrow' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-r/00new/arrow/libs/arrow.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-r/00new/arrow/libs/arrow.so, 6): Symbol not found: __ZN5arrow2io16RandomAccessFile9ReadAsyncERKNS0_9IOContextExx
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-r/00new/arrow/libs/arrow.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-r/00new/arrow/libs/arrow.so
Error: loading failed
Execution halted
ERROR: loading failed

To resolve this, try rebuilding the Arrow library.

Multiple versions of libarrow

If you are installing from a user-level directory, and you already have a previous installation of libarrow in a system directory, you get you may get errors like the following when you install the R package:

Error: package or namespace load failed for ‘arrow' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-r/00new/arrow/libs/arrow.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-r/00new/arrow/libs/arrow.so, 6): Library not loaded: /usr/local/lib/libarrow.400.dylib
  Referenced from: /usr/local/lib/libparquet.400.dylib
  Reason: image not found

If this happens, you need to make sure that you don’t let R link to your system library when building arrow. You can do this a number of different ways:

  • Setting the MAKEFLAGS environment variable to "LDFLAGS=" (see below for an example) this is the recommended way to accomplish this
  • Using {withr}’s with_makevars(list(LDFLAGS = ""), ...)
  • adding LDFLAGS= to your ~/.R/Makevars file (the least recommended way, though it is a common debugging approach suggested online)
MAKEFLAGS="LDFLAGS=" R CMD INSTALL .

rpath issues

If the package fails to install/load with an error like this:

  ** testing if installed package can be loaded from temporary location
  Error: package or namespace load failed for 'arrow' in dyn.load(file, DLLpath = DLLpath, ...):
  unable to load shared object '/Users/you/R/00LOCK-r/00new/arrow/libs/arrow.so':
  dlopen(/Users/you/R/00LOCK-r/00new/arrow/libs/arrow.so, 6): Library not loaded: @rpath/libarrow.14.dylib

ensure that -DARROW_INSTALL_NAME_RPATH=OFF was passed (this is important on macOS to prevent problems at link time and is a no-op on other platforms). Alternatively, try setting the environment variable R_LD_LIBRARY_PATH to wherever Arrow C++ was put in make install, e.g. export R_LD_LIBRARY_PATH=/usr/local/lib, and retry installing the R package.

When installing from source, if the R and C++ library versions do not match, installation may fail. If you’ve previously installed the libraries and want to upgrade the R package, you’ll need to update the Arrow C++ library first.

For any other build/configuration challenges, see the C++ developer guide.

Other installation issues

There are a number of scripts that are triggered when the arrow R package is installed. For package users who are not interacting with the underlying code, these should all just work without configuration and pull in the most complete pieces (e.g. official binaries that we host). However, knowing about these scripts can help package developers troubleshoot if things go wrong in them or things go wrong in an install. See the article on R package installation for more information.