ARROW-1325: [R] Initial R package that builds against the arrow C++ l…

…ibrary

This is very minimal in functionality, it just gives a simple R package that calls a function from the arrow C++ library.

Author: Romain Francois <[email protected]>
Author: Wes McKinney <[email protected]>

Closes apache#2489 from romainfrancois/r-bootstrap and squashes the following commits:

89f14b4 <Wes McKinney> Add license addendums
9e3ffb4 <Romain Francois> skip using rpath linker option
79c5001 <Romain Francois> follow up from @wesm comments on apache#2489
a1a5e7c <Romain Francois> + installation instructions
fb412ca <Romain Francois> not checking for headers on these files
2848fd1 <Romain Francois> initial R 📦 with travis setup and testthat suite, that links to arrow c++ library and calls arrow::int32()

.gitignore

@@ -38,3 +38,4 @@ python/.eggs/
 .idea/
 .pytest_cache/
 pkgs
+.Rproj.user

.travis.yml

@@ -246,6 +246,16 @@ matrix:
     after_success:
     - pushd ${TRAVIS_BUILD_DIR}/go/arrow
     - bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports"
+  # R
+  - language: r
+    cache: packages
+    latex: false
+    before_install:
+    - $TRAVIS_BUILD_DIR/ci/travis_install_linux.sh
+    - $TRAVIS_BUILD_DIR/ci/travis_before_script_cpp.sh --only-library
+    - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$TRAVIS_BUILD_DIR/cpp-install/lib
+    - export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$TRAVIS_BUILD_DIR/cpp-install/lib/pkgconfig
+    - pushd ${TRAVIS_BUILD_DIR}/r
 
 
 after_failure:

LICENSE.txt

@@ -672,3 +672,27 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
+
+--------------------------------------------------------------------------------
+
+The script r/configure has the following license (MIT)
+
+Copyright (c) 2017, Jeroen Ooms and Jim Hester
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

ci/travis_env_common.sh

@@ -30,6 +30,7 @@ export ARROW_JS_DIR=${TRAVIS_BUILD_DIR}/js
 export ARROW_INTEGRATION_DIR=$TRAVIS_BUILD_DIR/integration
 export ARROW_RUBY_DIR=$TRAVIS_BUILD_DIR/ruby
 export ARROW_RUST_DIR=${TRAVIS_BUILD_DIR}/rust
+export ARROW_R_DIR=${TRAVIS_BUILD_DIR}/r
 
 if [ "$ARROW_TRAVIS_COVERAGE" == "1" ]; then
     export ARROW_CPP_COVERAGE_FILE=${TRAVIS_BUILD_DIR}/coverage.info

dev/release/rat_exclude_files.txt

@@ -116,3 +116,12 @@ c_glib/doc/reference/gtk-doc.make
 *.svg
 *.devhelp2
 *.scss
+r/R/RcppExports.R
+r/src/RcppExports.cpp
+r/DESCRIPTION
+r/LICENSE.md
+r/NAMESPACE
+r/.Rbuildignore
+r/arrow.Rproj
+r/README.md
+r/README.Rmd

r/.Rbuildignore

@@ -0,0 +1,3 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$

r/.gitignore

@@ -0,0 +1,10 @@
+*.o
+*.o-*
+*.d
+*.so
+*.dll
+.RData
+.Rproj.user
+.Rhistory
+src/Makevars
+

r/DESCRIPTION

@@ -0,0 +1,21 @@
+Package: arrow
+Title: R Integration to 'Apache' 'Arrow'
+Version: 0.0.0.9000
+Authors@R: c(
+    person("Romain", "François", email = "[email protected]", role = c("aut", "cre")), 
+    person("Apache Arrow", email = "[email protected]", role = c("aut", "cph"))
+  )
+Description: R Integration to 'Apache' 'Arrow'.
+Depends: R (>= 3.5)
+License: Apache License (>= 2.0)
+Encoding: UTF-8
+LazyData: true
+SystemRequirements: C++11
+LinkingTo: 
+    Rcpp
+Imports: 
+    Rcpp
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 6.0.1.9000
+Suggests: 
+    testthat

r/NAMESPACE

@@ -0,0 +1,4 @@
+# Generated by roxygen2: do not edit by hand
+
+importFrom(Rcpp,sourceCpp)
+useDynLib(arrow, .registration = TRUE)

r/R/RcppExports.R

@@ -0,0 +1,7 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+ping_arrow <- function() {
+    .Call(`_arrow_ping_arrow`)
+}
+

r/R/zzz.R

@@ -0,0 +1,20 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+#' @useDynLib arrow, .registration = TRUE
+#' @importFrom Rcpp sourceCpp
+NULL

r/README.Rmd

@@ -0,0 +1,40 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+# arrow
+
+R integration with Apache Arrow.
+
+## Installation
+
+First install a release build of the C++ bindings to arrow.
+
+```shell
+git clone https://github.com/apache/arrow.git
+cd arrow/cpp && mkdir release && cd release
+
+# It is important to statically link to boost libraries
+cmake .. -DCMAKE_BUILD_TYPE=Release -DARROW_BOOST_USE_SHARED:BOOL=Off
+make install
+```
+
+Then the R package: 
+
+```r
+devtools::install_github("apache/arrow/r")
+```
+
+## Example
+
+(not yet)

r/README.md

@@ -0,0 +1,29 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# arrow
+
+R integration with Apache Arrow.
+
+## Installation
+
+First install a release build of the C++ bindings to arrow.
+
+``` shell
+git clone https://github.com/apache/arrow.git
+cd arrow/cpp && mkdir release && cd release
+
+# It is important to statically link to boost libraries
+cmake .. -DCMAKE_BUILD_TYPE=Release -DARROW_BOOST_USE_SHARED:BOOL=Off
+make install
+```
+
+Then the R package:
+
+``` r
+devtools::install_github("apache/arrow/r")
+```
+
+## Example
+
+(not yet)

r/arrow.Rproj

@@ -0,0 +1,21 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

r/cleanup

@@ -0,0 +1,21 @@
+#!/bin/sh
+
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+rm -f src/Makevars
+

r/configure

@@ -0,0 +1,97 @@
+#!/bin/bash
+
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+# Anticonf (tm) script by Jeroen Ooms, Jim Hester (2017)
+# License: MIT
+#
+# This script will query 'pkg-config' for the required cflags and ldflags.
+# If pkg-config is unavailable or does not find the library, try setting
+# INCLUDE_DIR and LIB_DIR manually via e.g:
+# R CMD INSTALL --configure-vars='INCLUDE_DIR=/.../include LIB_DIR=/.../lib'
+
+# Library settings
+PKG_CONFIG_NAME="arrow"
+PKG_DEB_NAME="arrow"
+PKG_RPM_NAME="arrow"
+PKG_CSW_NAME="arrow"
+PKG_BREW_NAME="apache-arrow"
+PKG_TEST_HEADER="<arrow/api.h>"
+PKG_LIBS="-larrow"
+
+# Use pkg-config if available
+pkg-config --version >/dev/null 2>&1
+if [ $? -eq 0 ]; then
+  PKGCONFIG_CFLAGS=`pkg-config --cflags --silence-errors ${PKG_CONFIG_NAME}`
+  PKGCONFIG_LIBS=`pkg-config --libs ${PKG_CONFIG_NAME}`
+fi
+
+# Note that cflags may be empty in case of success
+if [ "$INCLUDE_DIR" ] || [ "$LIB_DIR" ]; then
+  echo "Found INCLUDE_DIR and/or LIB_DIR!"
+  PKG_CFLAGS="-I$INCLUDE_DIR $PKG_CFLAGS"
+  PKG_LIBS="-L$LIB_DIR $PKG_LIBS"
+elif [ "$PKGCONFIG_CFLAGS" ] || [ "$PKGCONFIG_LIBS" ]; then
+  echo "Found pkg-config cflags and libs!"
+  PKG_CFLAGS=${PKGCONFIG_CFLAGS}
+  PKG_LIBS=${PKGCONFIG_LIBS}
+elif [[ "$OSTYPE" == "darwin"* ]]; then
+  if [ "$(command -v brew)" ]; then
+    BREWDIR=$(brew --prefix)
+  else
+    curl -sfL "https://jeroen.github.io/autobrew/default" > autobrew
+    source autobrew
+  fi
+  PKG_CFLAGS="-I$BREWDIR/opt/$PKG_BREW_NAME/include"
+  PKG_LIBS="-L$BREWDIR/opt/$PKG_BREW_NAME/lib $PKG_LIBS"
+fi
+
+# For debugging
+echo "PKG_CFLAGS=$PKG_CFLAGS"
+echo "PKG_LIBS=$PKG_LIBS"
+
+# Find compiler
+CXXCPP=$("${R_HOME}"/bin/R CMD config CXXCPP)
+CXX11FLAGS=$("${R_HOME}"/bin/R CMD config CXX11FLAGS)
+CXX11STD=$("${R_HOME}"/bin/R CMD config CXX11STD)
+CPPFLAGS=$("${R_HOME}"/bin/R CMD config CPPFLAGS)
+
+# Test configuration
+echo "#include $PKG_TEST_HEADER" | ${CXXCPP} ${CPPFLAGS} ${PKG_CFLAGS} ${CXX11FLAGS} ${CXX11STD} -xc++ - >/dev/null 2>&1
+
+# Customize the error
+if [ $? -ne 0 ]; then
+  echo "------------------------- ANTICONF ERROR ---------------------------"
+  echo "Configuration failed because $PKG_CONFIG_NAME was not found. Try installing:"
+  echo " * deb: $PKG_DEB_NAME (Debian, Ubuntu, etc)"
+  echo " * rpm: $PKG_RPM_NAME (Fedora, CentOS, RHEL)"
+  echo " * csw: $PKG_CSW_NAME (Solaris)"
+  echo " * brew: $PKG_BREW_NAME (Mac OSX)"
+  echo "If $PKG_CONFIG_NAME is already installed, check that 'pkg-config' is in your"
+  echo "PATH and PKG_CONFIG_PATH contains a $PKG_CONFIG_NAME.pc file. If pkg-config"
+  echo "is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:"
+  echo "R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'"
+  echo "--------------------------------------------------------------------"
+  exit 1;
+fi
+
+# Write to Makevars
+sed -e "s|@cflags@|$PKG_CFLAGS|" -e "s|@libs@|$PKG_LIBS|" src/Makevars.in > src/Makevars
+
+# Success
+exit 0

r/src/.gitignore

@@ -0,0 +1,3 @@
+*.o
+*.so
+*.dll

r/src/Makevars.in

@@ -0,0 +1,21 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+PKG_CPPFLAGS=@cflags@
+PKG_CXXFLAGS=$(C_VISIBILITY)
+CXX_STD=CXX11
+PKG_LIBS=@libs@