diff --git a/r/vignettes/developing.Rmd b/r/vignettes/developing.Rmd index 3d7f82e3619..59c231724aa 100644 --- a/r/vignettes/developing.Rmd +++ b/r/vignettes/developing.Rmd @@ -9,13 +9,11 @@ vignette: > ```{r setup-options, include=FALSE} knitr::opts_chunk$set(error = TRUE, eval = FALSE) - # Get environment variables describing what to evaluate run <- tolower(Sys.getenv("RUN_DEVDOCS", "false")) == "true" macos <- tolower(Sys.getenv("DEVDOCS_MACOS", "false")) == "true" ubuntu <- tolower(Sys.getenv("DEVDOCS_UBUNTU", "false")) == "true" sys_install <- tolower(Sys.getenv("DEVDOCS_SYSTEM_INSTALL", "false")) == "true" - # Update the source knit_hook to save the chunk (if it is marked to be saved) knit_hooks_source <- knitr::knit_hooks$get("source") knitr::knit_hooks$set(source = function(x, options) { @@ -40,90 +38,111 @@ set -e set -x ``` -If you're looking to contribute to `arrow`, this document can help you set up a development environment that will enable you to write code and run tests locally. It outlines how to build the various components that make up the Arrow project and R package, as well as some common troubleshooting and workflows developers use. Many contributions can be accomplished with the instructions in [R-only development](#r-only-development). But if you're working on both the C++ library and the R package, the [Developer environment setup](#-developer-environment-setup) section will guide you through setting up a developer environment. +If you're looking to contribute to arrow, this vignette can help you set up a development environment that will enable you to write code and run tests locally. It outlines: + +* how to build the components that make up the Arrow project and R package +* workflows that developers use +* some common troubleshooting steps and solutions + +This document is intended only for **developers** of Apache Arrow or the Arrow R package. R package users do not need to do any of this setup. If you're looking for how to install Arrow, see [the instructions in the readme](https://arrow.apache.org/docs/r/#installation). + +This document is a work in progress and will grow and change as the Apache Arrow project grows and changes. We have tried to make these steps as robust as possible (in fact, we even test exactly these instructions on our nightly CI to ensure they don't become stale!), but custom configurations might conflict with these instructions and there are differences of opinion across developers about how to set up development environments like this. -This document is intended only for developers of Apache Arrow or the Arrow R package. Users of the package in R do not need to do any of this setup. If you're looking for how to install Arrow, see [the instructions in the readme](https://arrow.apache.org/docs/r/#installation); Linux users can find more details on building from source at `vignette("install", package = "arrow")`. +We welcome any feedback you have about things that are confusing or additions you would like to see here - please [report an issue](https://issues.apache.org/jira/projects/ARROW/issues) if you have any suggestions or requests. -This document is a work in progress and will grow + change as the Apache Arrow project grows and changes. We have tried to make these steps as robust as possible (in fact, we even test exactly these instructions on our nightly CI to ensure they don't become stale!), but certain custom configurations might conflict with these instructions and there are differences of opinion across developers about if and what the one true way to set up development environments like this is. We also solicit any feedback you have about things that are confusing or additions you would like to see here. Please [report an issue](https://issues.apache.org/jira/projects/ARROW/issues) if there you see anything that is confusing, odd, or just plain wrong. +# Developer environment setup -## R-only development +## R-only {.tabset} Windows and macOS users who wish to contribute to the R package and -don’t need to alter the Arrow C++ library may be able to obtain a -recent version of the library without building from source. On macOS, -you may install the C++ library using [Homebrew](https://brew.sh/): +don't need to alter libarrow (Arrow's C++ library) may be able to obtain a +recent version of the library without building from source. + +### Linux + +On Linux, you can download a .zip file containing libarrow from the +nightly repository. + +To see what nightlies are available, you can use arrow's (or any other S3 client's) S3 listing functionality to see what is in the bucket `s3://arrow-r-nightly/libarrow/bin`: -``` shell +``` +nightly <- s3_bucket("arrow-r-nightly") +nightly$ls("libarrow/bin") +``` +Version numbers in that repository correspond to dates. + +You'll need to create a `libarrow` directory inside the R package directory and unzip the zip file containing the compiled libarrow binary files into it. + +### macOS +On macOS, you can install libarrow using [Homebrew](https://brew.sh/): + +```bash # For the released version: brew install apache-arrow # Or for a development version, you can try: brew install apache-arrow --HEAD ``` -On Windows and Linux, you can download a .zip file with the arrow dependencies from the -nightly repository. -Windows users then can set the `RWINLIB_LOCAL` environment variable to point to that -zip file before installing the `arrow` R package. On Linux, you'll need to create a `libarrow` directory inside the R package directory and unzip that file into it. Version numbers in that -repository correspond to dates, and you will likely want the most recent. +### Windows + +On Windows, you can download a .zip file containing libarrow from the nightly repository. -To see what nightlies are available, you can use Arrow's (or any other S3 client's) S3 listing functionality to see what is in the bucket `s3://arrow-r-nightly/libarrow/bin`: +To see what nightlies are available, you can use arrow's (or any other S3 client's) S3 listing functionality to see what is in the bucket `s3://arrow-r-nightly/libarrow/bin`: ``` nightly <- s3_bucket("arrow-r-nightly") nightly$ls("libarrow/bin") ``` +Version numbers in that repository correspond to dates. -## Developer environment setup +You can set the `RWINLIB_LOCAL` environment variable to point to the zip file containing libarrow before installing the arrow R package. -If you need to alter both the Arrow C++ library and the R package code, or if you can’t get a binary version of the latest C++ library elsewhere, you’ll need to build it from source too. This section discusses how to set up a C++ build configured to work with the R package. For more general resources, see the [Arrow C++ developer -guide](https://arrow.apache.org/docs/developers/cpp/building.html). -There are four major steps to the process — the first three are relevant to all Arrow developers, and the last one is specific to the R bindings: +## R and C++ -1. Configuring the Arrow library build (using `cmake`) — this specifies how you want the build to go, what features to include, etc. -2. Building the Arrow library — this actually compiles the Arrow library -3. Install the Arrow library — this organizes and moves the compiled Arrow library files into the location specified in the configuration -4. Building the R package — this builds the C++ code in the R package, and installs the R package for you +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](https://arrow.apache.org/docs/developers/cpp/building.html). -### Install dependencies {.tabset} +There are five major steps to the process. -The Arrow C++ library will by default use system dependencies if suitable versions are found; if they are not present, it will build them during its own build process. The only dependencies that one needs to install outside of the build process are `cmake` (for configuring the build) and `openssl` if you are building with S3 support. +### Step 1 - Install dependencies {.tabset} -For a faster build, you may choose to install on the system more C++ library dependencies (such as `lz4`, `zstd`, etc.) so that they don't need to be built from source in the Arrow build. This is optional. +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](https://cmake.org/) (for configuring the build) and [openssl](https://www.openssl.org/) if you are building with S3 support. -#### macOS -```{bash, save=run & macos} -brew install cmake openssl -``` +For a faster build, you may choose to pre-install more C++ library dependencies (such as [lz4](http://lz4.github.io/lz4/), [zstd](https://facebook.github.io/zstd/), etc.) on the system so that they don't need to be built from source in the libarrow build. #### Ubuntu ```{bash, save=run & ubuntu} sudo apt install -y cmake libcurl4-openssl-dev libssl-dev ``` -### Configure the Arrow build {.tabset} +#### macOS +```{bash, save=run & macos} +brew install cmake openssl +``` -You can choose to build and then install the Arrow library into a user-defined directory or into a system-level directory. You only need to do one of these two options. +#### Windows -It is recommended that you install the arrow library to a user-level directory to be used in development. This is so that the development version you are using doesn't overwrite a released version of Arrow you may have installed. You are also able to have more than one version of the Arrow library to link to with this approach (by using different `ARROW_HOME` directories for the different versions). This approach also matches the recommendations for other Arrow bindings like [Python](http://arrow.apache.org/docs/developers/python.html). +Currently, the R package cannot be made to work with a local libarrow build. This will be resolved in a future release. -#### Configure for installing to a user directory +### Step 2 - Configure the libarrow build -In this example we will install it to a directory called `dist` that has the same parent as our `arrow` checkout, but it could be named or located anywhere you would like. However, note that your installation of the Arrow R package will point to this directory and need it to remain intact for the package to continue to work. This is one reason we recommend *not* placing it inside of the arrow git checkout. +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. ```{bash, save=run & !sys_install} export ARROW_HOME=$(pwd)/dist mkdir $ARROW_HOME ``` -_Special instructions on Linux:_ You will need to set `LD_LIBRARY_PATH` to the `lib` directory that is under where we set `$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 we do not need to do this because the macOS shared library paths are hardcoded to their locations during build time. +_Special instructions on Linux:_ You will need to set `LD_LIBRARY_PATH` to the `lib` directory that is under where you set `$ARROW_HOME`, before launching R and using arrow. One way to do this is to add it to your profile (we use `~/.bash_profile` here, but you might need to put this in a different file depending on your setup, e.g. if you use a shell other than `bash`). On macOS you do not need to do this because the macOS shared library paths are hardcoded to their locations during build time. ```{bash, save=run & ubuntu & !sys_install} export LD_LIBRARY_PATH=$ARROW_HOME/lib:$LD_LIBRARY_PATH echo "export LD_LIBRARY_PATH=$ARROW_HOME/lib:$LD_LIBRARY_PATH" >> ~/.bash_profile ``` -Now we can move into the arrow repository to start the build process. You will need to create a directory into which the C++ build will put its contents. It is recommended to 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). And then, change directories to be inside `cpp/build`: +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`: ```{bash, save=run & !sys_install} pushd arrow @@ -131,7 +150,7 @@ 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 the C++ library using `-D` flags: +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: ```{bash, save=run & !sys_install} cmake \ @@ -151,45 +170,13 @@ cmake \ .. ``` -`..` refers to the C++ source directory: we're in `cpp/build`, and the source is in `cpp`. - -#### Configure to install to a system directory - -If you would like to install Arrow as a system library you can do that as well. This is in some respects simpler, but if you already have Arrow libraries installed there, it would disrupt them and possibly require `sudo` permissions. - -Now we can move into the arrow repository to start the build process. You will need to create a directory into which the C++ build will put its contents. It is recommended to 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). And then, change directories to be inside `cpp/build`: +`..` refers to the C++ source directory: you're in `cpp/build` and the source is in `cpp`. -```{bash, save=run & sys_install} -pushd arrow -mkdir -p cpp/build -pushd cpp/build -``` +#### Enabling more Arrow features -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 the C++ library using `-D` flags: +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): -```{bash, save=run & sys_install} -cmake \ - -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: we're in `cpp/build`, and the source is in `cpp`. - -### 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 (the trailing `\` makes them easier to paste into a bash shell on a new line): - -``` shell +```bash -DARROW_MIMALLOC=ON \ -DARROW_S3=ON \ -DARROW_WITH_BROTLI=ON \ @@ -201,12 +188,13 @@ To enable optional features including: S3 support, an alternative memory allocat 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. +* `-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. -_Note_ `cmake` is particularly sensitive to whitespacing, if you see errors, check that you don't have any errant whitespace around +_Note_ `cmake` is particularly sensitive to whitespacing, if you see errors, check that you don't have any errant whitespace. -### Build Arrow +### Step 3 - Building libarrow You can add `-j#` between `make` and `install` here too to speed up compilation by running in parallel (where `#` is the number of cores you have available). @@ -214,49 +202,39 @@ You can add `-j#` between `make` and `install` here too to speed up compilation make -j8 install ``` -If you are installing on linux, and you are installing to the system, you may -need to use `sudo`: - -```{bash, save=run & sys_install & ubuntu} -sudo make install -``` - +### Step 4 - Build the Arrow R package -### Build the Arrow R package - -Once you’ve built the C++ library, you can install the R package and its +Once you've built libarrow, you can install the R package and its dependencies, along with additional dev dependencies, from the git checkout: ```{bash, save=run} 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 . ``` -### Compilation flags +#### 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 -``` shell +```bash export ARROW_R_CXXFLAGS=-fno-omit-frame-pointer ``` -### Developer Experience +#### Recompiling the C++ code -With the setups described here, you should not need to rebuild the Arrow library or even the C++ source in the R package as you iterated 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 Arrow library C++ has changed and there is a mismatch between the Arrow Library 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. +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).

-``` shell +```bash cmake \ -DCMAKE_INSTALL_PREFIX=$ARROW_HOME \ -DCMAKE_INSTALL_LIBDIR=lib \ @@ -280,193 +258,141 @@ cmake \ .. ```

-
+ -### Documentation +## Installing a version of the R package with a specific git reference -The documentation for the R package uses features of `roxygen2` that haven't yet been released on CRAN, such as conditional inclusion of examples via the `@examplesIf` tag. If you are making changes which require updating the documentation, please install the development version of `roxygen2` from GitHub. +If you need an arrow installation from a specific repository or git reference, on most platforms except Windows, you can run: ```{r} -remotes::install_github("r-lib/roxygen2") -``` - -## Troubleshooting - -Note that after any change to the C++ library, 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 the C++ library 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 the Arrow library 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 +remotes::install_github("apache/arrow/r", build = FALSE) ``` -To resolve this, try rebuilding the Arrow library from [Building Arrow above](#building-arrow). +The `build = FALSE` argument is important so that the installation can access the +C++ source in the `cpp/` directory in `apache/arrow`. -### Multiple versions of Arrow library +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. -If rebuilding the Arrow library doesn't work and you are [installing from a user-level directory](#installing-to-another-directory) and you already have a previous installation of libarrow in a system directory or you get you may get errors like the following when you install the R package: +For example, to install from the (fictional) branch `bugfix` from `apache/arrow` you could run: -``` -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 +```r +Sys.setenv(LIBARROW_MINIMAL="false") +remotes::install_github("apache/arrow/r@bugfix", build = FALSE) ``` -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: +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](https://github.com/ursacomputing/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 `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) +* 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. -```{bash, save=run & !sys_install & macos, hide=TRUE} -# Setup troubleshooting section -# install a system-level arrow on macOS -brew install apache-arrow +* 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: +```{r} +withr::with_makevars(list(CPPFLAGS = "", LDFLAGS = ""), remotes::install_github(...)) ``` +# Common developer workflow tasks -```{bash, save=run & !sys_install & ubuntu, hide=TRUE} -# Setup troubleshooting section -# install a system-level arrow on Ubuntu -sudo apt update -sudo apt install -y -V ca-certificates lsb-release wget -wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb -sudo apt install -y -V ./apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb -sudo apt update -sudo apt install -y -V libarrow-dev -``` +The `arrow/r` directory contains a `Makefile` to help with some common tasks from the command line (e.g. `make test`, `make doc`, `make clean`, etc.). -```{bash, save=run & !sys_install & macos} -MAKEFLAGS="LDFLAGS=" R CMD INSTALL . -``` +## Loading arrow +You can load the R package via `devtools::load_all()`. -### `rpath` issues +## Rebuilding the documentation -If the package fails to install/load with an error like this: +The R documentation uses the [`@examplesIf`](https://roxygen2.r-lib.org/articles/rd.html#functions) tag introduced in `roxygen2` version 7.1.1.9001, which hasn't yet been released on CRAN at the time of writing. If you are making changes which require updating the documentation, please install the development version of `roxygen2` from GitHub. -``` - ** 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 +```{r} +remotes::install_github("r-lib/roxygen2") ``` -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. +You can use `devtools::document()` and `pkgdown::build_site()` to rebuild the documentation and preview the results. -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](https://arrow.apache.org/docs/developers/cpp/building.html). +```r +# Update roxygen documentation +devtools::document() +# To preview the documentation website +pkgdown::build_site(preview=TRUE) +``` -## Using `remotes::install_github(...)` +## Styling and linting -If you need an Arrow installation from a specific repository or at a specific ref, -`remotes::install_github("apache/arrow/r", build = FALSE)` -should work on most platforms (with the notable exception of Windows). -The `build = FALSE` argument is important so that the installation can access the -C++ source in the `cpp/` directory in `apache/arrow`. +### R code -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. +The R code in the package follows [the tidyverse style](https://style.tidyverse.org/). On PR submission (and on pushes) our CI will run linting and will flag possible errors on the pull request with annotations. -For example, to install from the (fictional) branch `bugfix` from `apache/arrow` one could: +To run the [lintr](https://github.com/jimhester/lintr) locally, install the lintr package (note, we currently use a fork that includes fixes not yet accepted upstream, see how lintr is being installed in the file `ci/docker/linux-apt-lint.dockerfile` for the current status) and then run -```r -Sys.setenv(LIBARROW_MINIMAL="false") -remotes::install_github("apache/arrow/r@bugfix", build = FALSE) +```{r} +lintr::lint_package("arrow/r") ``` -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](https://github.com/ursacomputing/arrowbench) to install development versions of arrow isolated from the system install). If you already have Arrow C++ libraries 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 Arrow libraries 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 Arrow. One way to do this temporarily is wrapping your `remotes::install_github()` call like so: `withr::with_makevars(list(CPPFLAGS = "", LDFLAGS = ""), remotes::install_github(...))`. +You can automatically change the formatting of the code in the package using the [styler](https://styler.r-lib.org/) package. There are two ways to do this: -## What happens when you `R CMD INSTALL`? +1. Use the comment bot to do this automatically with the command `@github-actions autotune` on a PR, and commit it back to the branch. -There are a number of scripts that are triggered when `R CMD INSTALL .`. For Arrow users, these should all just work without configuration and pull in the most complete pieces (e.g. official binaries that we host) so the installation process is easy. However knowing about these scripts can help troubleshoot if things go wrong in them or things go wrong in an install: +2. Run the styler locally either via Makefile commands: -* `configure` and `configure.win` These scripts are triggered during `R CMD INSTALL .` on non-Windows and Windows platforms, respectively. They handle finding the Arrow library, setting up the build variables necessary, and writing the package Makevars file that is used to compile the C++ code in the R package. -* `tools/nixlibs.R` This script is sometimes called by `configure` on Linux (or on any non-windows OS with the environment variable `FORCE_BUNDLED_BUILD=true`). This sets up the build process for our bundled builds (which is the default on linux). The operative logic is at the end of the script, but it will do the following (and it will stop with the first one that succeeds and some of the steps are only checked if they are enabled via an environment variable): - * Check if there is an already built libarrow in `arrow/r/libarrow-{version}`, use that to link against if it exists. - * Check if a binary is available from our hosted unofficial builds. - * Download the Arrow source and build the Arrow Library from source. - * `*** Proceed without C++` dependencies (this is an error and the package will not work, but if you see this message you know the previous steps have not succeeded/were not enabled) -* `inst/build_arrow_static.sh` this script builds Arrow for a bundled, static build. It is called by `tools/nixlibs.R` when the Arrow library is being built. (If you're looking at this script, and you've gotten this far, it should look _incredibly_ familiar: it's basically the contents of this guide in script form — with a few important changes) - -## Styling and linting of the R code in the R package - -The R code in the package follows [the tidyverse style](https://style.tidyverse.org/). On PR submission (and on pushes) our CI will run linting and will flag possible errors on the pull request with annotations. +```bash +make style # (for only the files changed) +make style-all # (for all files) +``` -To run the [lintr](https://github.com/jimhester/lintr) locally, install the lintr package (note, we currently use a fork that includes fixes not yet accepted upstream, see how lintr is being installed in the file `ci/docker/linux-apt-lint.dockerfile` for the current status) and then run `lintr::lint_package("arrow/r")`. +or in R: -One can automatically change the formatting of the code in the package using the [styler](https://styler.r-lib.org/) package. There are two ways to do this: +```{r} +# note the two excluded files which should not be styled +styler::style_pkg(exclude_files = c("tests/testthat/latin1.R", "data-raw/codegen.R")) -1. Use the comment bot to do this automatically with the command `@github-actions autotune` on a PR and commit it back to the branch. -2. Locally, with the command `make style` (for only the files changed), `make style-all` (for all files), or use `styler::style_pkg(exclude_files = c("tests/testthat/latin1.R", "data-raw/codegen.R"))` note the two excluded files which should not be styled. +``` -The styler package will fix many styling errors, thought not all lintr errors are automatically fixable with styler. The list of files we habitually do not style is in `r/.styler_excludes.R`. +The styler package will fix many styling errors, thought not all lintr errors are automatically fixable with styler. The list of files we intentionally do not style is in `r/.styler_excludes.R`. -## Editing C++ code in the R package +### C++ code -The `arrow` package uses some customized tools on top of `cpp11` to prepare its -C++ code in `src/`. This is because we have some features that are only enabled +The arrow package uses some customized tools on top of [cpp11](https://cpp11.r-lib.org/) to prepare its +C++ code in `src/`. This is because there are some features that are only enabled and built conditionally during build time. If you change C++ code in the R package, you will need to set the `ARROW_R_DEV` environment variable to `true` (optionally, add it to your `~/.Renviron` file to persist across sessions) so -that the `data-raw/codegen.R` file is used for code generation. The `Makefile` +that the `data-raw/codegen.R` file is used for code generation. The `Makefile` commands also handles this automatically. We use Google C++ style in our C++ code. The easiest way to accomplish this is -use an editors/IDE that formats your code for you. Many popular editors/IDEs -have support for running `clang-format` on C++ files when you save them. +use an editors/IDE that formats your code for you. Many popular editors/IDEs +have support for running `clang-format` on C++ files when you save them. Installing/enabling the appropriate plugin may save you much frustration. Check for style errors with -``` shell +```bash ./lint.sh ``` Fix any style issues before committing with -``` shell +```bash ./lint.sh --fix ``` The lint script requires Python 3 and `clang-format-8`. If the command -isn’t found, you can explicitly provide the path to it like -`CLANG_FORMAT=$(which clang-format-8) ./lint.sh`. On macOS, you can get -this by installing LLVM via Homebrew and running the script as -`CLANG_FORMAT=$(brew --prefix llvm@8)/bin/clang-format ./lint.sh` +isn't found, you can explicitly provide the path to it like: + +```bash +CLANG_FORMAT=$(which clang-format-8) ./lint.sh +``` -_Note_ that the lint script requires Python 3 and the Python dependencies +On macOS, you can get this by installing LLVM via Homebrew and running the script as: +```bash +CLANG_FORMAT=$(brew --prefix llvm@8)/bin/clang-format ./lint.sh +``` + +_Note_ that the lint script requires Python 3 and the Python dependencies (note that `cmake_format is pinned to a specific version): * autopep8 @@ -475,65 +401,191 @@ _Note_ that the lint script requires Python 3 and the Python dependencies ## Running tests +Tests can be run either using `devtools::test()` or the Makefile alternative. + +```r +# Run the test suite, optionally filtering file names +devtools::test(filter="^regexp$") + +# or the Makefile alternative from the arrow/r directory in a shell: +make test file=regexp +``` + Some tests are conditionally enabled based on the availability of certain features in the package build (S3 support, compression libraries, etc.). Others are generally skipped by default but can be enabled with environment variables or other settings: +* All tests are skipped on Linux if the package builds without the C++ libarrow. + To make the build fail if libarrow is not available (as in, to test that + the C++ build was successful), set `TEST_R_WITH_ARROW=true` + * Some tests are disabled unless `ARROW_R_DEV=true` + * Tests that require allocating >2GB of memory to test Large types are disabled unless `ARROW_LARGE_MEMORY_TESTS=true` + * Integration tests against a real S3 bucket are disabled unless credentials are set in `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY`; these are available on request + * S3 tests using [MinIO](https://min.io/) locally are enabled if the `minio server` process is found running. If you're running MinIO with custom settings, you can set `MINIO_ACCESS_KEY`, `MINIO_SECRET_KEY`, and `MINIO_PORT` to override the defaults. -## Github workflows +## Running checks -On a pull request, there are some actions you can trigger by commenting on the PR. We have additional CI checks that run nightly and can be requested on demand using an internal tool called [crosssbow](https://arrow.apache.org/docs/developers/crossbow.html). A few important GitHub comment commands include: +You can run package checks by using `devtools::check()` and check test coverage +with `covr::package_coverage()`. -* `@github-actions crossbow submit -g r` for all extended R CI tests -* `@github-actions crossbow submit {task-name}` for running a specific task. See the `r:` group definition near the beginning of the [crossbow configuration](https://github.com/apache/arrow/blob/master/dev/tasks/tasks.yml) for a list of glob expression patterns that match names of items in the `tasks:` list below it. -* `@github-actions autotune` will run and fix lint c++ linting errors + run R documentation (among other cleanup tasks) and commit them to the branch +```r +# All package checks +devtools::check() +# See test coverage statistics +covr::report() +covr::package_coverage() +``` -## Useful functions for Arrow developers +For full package validation, you can run the following commands from a terminal. -Within an R session, these can help with package development: +``` +R CMD build . +R CMD check arrow_*.tar.gz --as-cran +``` -``` r -# Load the dev package -devtools::load_all() -# Run the test suite, optionally filtering file names -devtools::test(filter="^regexp$") -# or the Makefile alternative from the arrow/r directory in a shell: -make test file=regexp +## Running additional CI checks -# Update roxygen documentation -devtools::document() +On a pull request, there are some actions you can trigger by commenting on the +PR. We have additional CI checks that run nightly and can be requested on demand +using an internal tool called +[crossbow](https://arrow.apache.org/docs/developers/crossbow.html). +A few important GitHub comment commands are shown below. -# To preview the documentation website -pkgdown::build_site() +#### Run all extended R CI tasks +``` +@github-actions crossbow submit -g r +``` -# All package checks; see also below -devtools::check() +This runs each of the R-related CI tasks. -# See test coverage statistics -covr::report() -covr::package_coverage() +#### Run a specific task +``` +@github-actions crossbow submit {task-name} ``` -Any of those can be run from the command line by wrapping them in `R -e -'$COMMAND'`. There’s also a `Makefile` to help with some common tasks -from the command line (`make test`, `make doc`, `make clean`, etc.) +See the `r:` group definition near the beginning of the [crossbow configuration](https://github.com/apache/arrow/blob/master/dev/tasks/tasks.yml) +for a list of glob expression patterns that match names of items in the `tasks:` +list below it. -### Full package validation +#### Run linting and documentation building tasks -``` shell -R CMD build . -R CMD check arrow_*.tar.gz --as-cran ``` +@github-actions autotune +``` + +This will run and fix lint C++ linting errors, run R documentation (among other +cleanup tasks), run styler on any changed R code, and commit the resulting +updates to the branch. + +# 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](#step-3-building-arrow). + +## 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) + +```{bash, save=run & !sys_install & macos, hide=TRUE} +# Setup troubleshooting section +# install a system-level arrow on macOS +brew install apache-arrow +``` + + +```{bash, save=run & !sys_install & ubuntu, hide=TRUE} +# Setup troubleshooting section +# install a system-level arrow on Ubuntu +sudo apt update +sudo apt install -y -V ca-certificates lsb-release wget +wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb +sudo apt install -y -V ./apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb +sudo apt update +sudo apt install -y -V libarrow-dev +``` + +```{bash, save=run & !sys_install & macos} +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](https://arrow.apache.org/docs/developers/cpp/building.html). + +## 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 installation vignette](./install.html#how-dependencies-are-resolved) for more information. \ No newline at end of file diff --git a/r/vignettes/install.Rmd b/r/vignettes/install.Rmd index aca860473d8..d7588302e70 100644 --- a/r/vignettes/install.Rmd +++ b/r/vignettes/install.Rmd @@ -164,9 +164,46 @@ Depending on your system, building Arrow C++ from source may be slow. For the specific mechanics of how all this works, see the R package `configure` script, which calls `tools/nixlibs.R`. + If the C++ library is built from source, `inst/build_arrow_static.sh` is executed. This build script is also what is used to generate the prebuilt binaries. +## How the package is installed - advanced + +This subsection contains information which is likely to be most relevant mostly +to Arrow developers and is not necessary for Arrow users to install Arrow. + +There are a number of scripts that are triggered when `R CMD INSTALL .` is run. +For Arrow users, these should all just work without configuration and pull in +the most complete pieces (e.g. official binaries that we host). + +An overview of these scripts is shown below: + +* `configure` and `configure.win` - these scripts are triggered during +`R CMD INSTALL .` on non-Windows and Windows platforms, respectively. They +handle finding the Arrow library, setting up the build variables necessary, and +writing the package Makevars file that is used to compile the C++ code in the R +package. + +* `tools/nixlibs.R` - this script is sometimes called by `configure` on Linux +(or on any non-windows OS with the environment variable +`FORCE_BUNDLED_BUILD=true`). This sets up the build process for our bundled +builds (which is the default on linux). The operative logic is at the end of +the script, but it will do the following (and it will stop with the first one +that succeeds and some of the steps are only checked if they are enabled via an +environment variable): + * Check if there is an already built libarrow in `arrow/r/libarrow-{version}`, + use that to link against if it exists. + * Check if a binary is available from our hosted unofficial builds. + * Download the Arrow source and build the Arrow Library from source. + * `*** Proceed without C++` dependencies (this is an error and the package + will not work, but if you see this message you know the previous steps have + not succeeded/were not enabled) + +* `inst/build_arrow_static.sh` - called by `tools/nixlibs.R` when the Arrow +library is being built. It builds Arrow for a bundled, static build, and +mirrors the steps described in the ["Arrow R Developer Guide" vignette]("./developing.html") + # Troubleshooting The intent is that `install.packages("arrow")` will just work and handle all C++