Merge pull request #130 from rstudio/glin-test

Add tests for R binaries and packages

Makefile

@@ -39,6 +39,26 @@ rebuild-all: deps fetch-serverless-custom-file
 serverless-deploy.%: deps fetch-serverless-custom-file
 	$(SLS_BINARY) deploy --stage $*
 
+define GEN_TARGETS
+docker-build-$(platform):
+	@cd builder && docker-compose build $(platform)
+
+build-r-$(platform):
+	@cd builder && R_VERSION=$(R_VERSION) docker-compose up $(platform)
+
+test-r-$(platform):
+	@cd test && R_VERSION=$(R_VERSION) docker-compose up $(platform)
+
+bash-$(platform):
+	docker run -it --rm --entrypoint /bin/bash -v $(CURDIR):/r-builds r-builds:$(platform)
+
+.PHONY: docker-build-$(platform) build-r-$(platform) test-r-$(platform) bash-$(platform)
+endef
+
+$(foreach platform,$(PLATFORMS), \
+    $(eval $(GEN_TARGETS)) \
+)
+
 # Helper for launching a bash session on a docker image of your choice. Defaults
 # to "ubuntu:xenial".
 TARGET_IMAGE?=ubuntu:xenial

README.md

@@ -244,33 +244,34 @@ serverless invoke stepf -n rBuilds -d '{"force": true, "versions": ["3.6.3", "4.
 
 ## Testing
 
-To test the R builds locally, you can build the images:
+To test the R builds locally, you can use the `build-r-$PLATFORM` and `test-r-$PLATFORM`
+targets to build R and run the tests. The tests use the quick install script to install R,
+using a locally built R if present, or otherwise a build from the CDN.
 
 ```bash
-# Build images for all platforms
-make docker-build
+# Build R 4.1.3 for Ubuntu 22
+R_VERSION=4.1.3 make build-r-ubuntu-2204
 
-# Or build the image for a single platform
-(cd builder && docker-compose build ubuntu-2004)
+# Test R 4.1.3 for Ubuntu 22
+R_VERSION=4.1.3 make test-r-ubuntu-2204
 ```
 
-Then run the build script:
+Alternatively, you can build an image using the `docker-build-$PLATFORM`
+target, launch a bash session within a container using the `bash-$PLATFORM` target,
+and interactively run the build script:
 
 ```bash
-# Build R for all platforms
-R_VERSION=4.0.5 make docker-build-r
+# Build the image for Ubuntu 22
+make docker-build-ubuntu-2204
 
-# Build R for a single platform
-(cd builder && R_VERSION=4.0.5 docker-compose up ubuntu-2004)
+# Launch a bash session for Ubuntu 22
+make bash-ubuntu-2204
 
-# Alternatively, run the build script from within a container
-docker run -it --rm --entrypoint "/bin/bash" r-builds:ubuntu-2004
+# Build R 4.1.3
+R_VERSION=4.1.3 ./build.sh
 
-# Build R 4.0.5
-R_VERSION=4.0.5 ./build.sh
-
-# Build R devel
-R_VERSION=devel ./build.sh
+# Build R devel with parallel execution to speed up the build
+MAKEFLAGS=-j4 R_VERSION=devel ./build.sh
 
 # Build a prerelease version of R (e.g., alpha or beta)
 R_VERSION=rc R_TARBALL_URL=https://cran.r-project.org/src/base-prerelease/R-latest.tar.gz ./build.sh

install.sh

@@ -110,7 +110,7 @@ detect_os_version () {
         cat /etc/os-release | grep -e "^VERSION_ID\=*" | cut -f 2 -d '=' | sed -e 's/"//g'
     fi
   fi
-  if [[ "${os}" == "Ubuntu" ]]; then
+  if [[ "${os}" == "Ubuntu" ]] || [[ "${os}" == "Debian" ]]; then
     cat /etc/os-release | grep -e "^VERSION_ID\=*" | cut -f 2 -d '=' | sed -e 's/[".]//g'
   fi
   if [[ "${os}" == "SLES15" ]] || [[ "${os}" == "LEAP15" ]]; then
@@ -277,6 +277,7 @@ install_deb () {
   if [[ "${RUN_UNATTENDED}" -ne "0" ]]; then
       yes="--n"
       yesapt="-y"
+      export DEBIAN_FRONTEND=noninteractive
   fi
   echo "Updating package indexes..."
   ${SUDO} apt-get update

test/docker-compose.yml

@@ -0,0 +1,67 @@
+version: '2.0'
+
+services:
+  ubuntu-1804:
+    image: ubuntu:bionic
+    command: /r-builds/test/test-apt.sh
+    environment:
+      - OS_IDENTIFIER=ubuntu-1804
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ../:/r-builds
+  ubuntu-2004:
+    image: ubuntu:focal
+    command: /r-builds/test/test-apt.sh
+    environment:
+      - OS_IDENTIFIER=ubuntu-2004
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ../:/r-builds
+  ubuntu-2204:
+    image: ubuntu:jammy
+    command: /r-builds/test/test-apt.sh
+    environment:
+      - OS_IDENTIFIER=ubuntu-2204
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ../:/r-builds
+  debian-11:
+    image: debian:bullseye
+    command: /r-builds/test/test-apt.sh
+    environment:
+      - OS_IDENTIFIER=debian-11
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ../:/r-builds
+  debian-10:
+    image: debian:buster
+    command: /r-builds/test/test-apt.sh
+    environment:
+      - OS_IDENTIFIER=debian-10
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ../:/r-builds
+  centos-7:
+    image: centos:centos7
+    command: /r-builds/test/test-yum.sh
+    environment:
+      - OS_IDENTIFIER=centos-7
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ../:/r-builds
+  centos-8:
+    image: rockylinux:8
+    command: /r-builds/test/test-yum.sh
+    environment:
+      - OS_IDENTIFIER=centos-8
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ../:/r-builds
+  opensuse-153:
+    image: opensuse/leap:15.3
+    command: /r-builds/test/test-zypper.sh
+    environment:
+      - OS_IDENTIFIER=opensuse-153
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ../:/r-builds

test/test-apt.sh

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+set -ex
+
+SCRIPT_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
+
+# Install quick install script prerequisites
+if ! command -v curl > /dev/null 2>&1; then
+    apt update -qq
+    apt install -y curl
+fi
+
+# Run the quick install script. Use a locally built file if present, otherwise from the CDN.
+tmpdir=$(mktemp -d)
+cp -r "${SCRIPT_DIR}/../builder/integration/tmp/${OS_IDENTIFIER}/." "$tmpdir" > /dev/null 2>&1 || true
+(cd "$tmpdir" && SCRIPT_ACTION=install R_VERSION="${R_VERSION}" RUN_UNATTENDED=1 "${SCRIPT_DIR}/../install.sh")
+
+# Show DEB info
+apt show "r-${R_VERSION}"
+
+"${SCRIPT_DIR}/test-r.sh"
+
+apt remove -y "r-${R_VERSION}"
+
+if [ -d "/opt/R/${R_VERSION}" ]; then
+    echo "Failed to uninstall completely"
+    exit 1
+fi

test/test-r.sh

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+set -ex
+
+SCRIPT_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
+
+R_HOME=/opt/R/${R_VERSION}/lib/R
+"${R_HOME}/bin/R" --version
+"${R_HOME}/bin/Rscript" -e 'sessionInfo()'
+
+# List R devel dependencies
+gcc --version
+g++ --version
+gfortran --version
+
+# List shared library dependencies (e.g. BLAS/LAPACK)
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${R_HOME}/lib ldd "${R_HOME}/lib/libR.so"
+
+DIR=$SCRIPT_DIR "${R_HOME}/bin/Rscript" "${SCRIPT_DIR}/test.R"

test/test-yum.sh

@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+set -ex
+
+SCRIPT_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
+
+if command -v dnf > /dev/null 2>&1; then
+    YUM=dnf
+else
+    YUM=yum
+fi
+
+# Install quick install script prerequisites
+if ! command -v curl > /dev/null 2>&1; then
+    $YUM install -y curl
+fi
+
+# Run the quick install script. Use a locally built file if present, otherwise from the CDN.
+tmpdir=$(mktemp -d)
+cp -r "${SCRIPT_DIR}/../builder/integration/tmp/${OS_IDENTIFIER}/." "$tmpdir" > /dev/null 2>&1 || true
+(cd "$tmpdir" && SCRIPT_ACTION=install R_VERSION="${R_VERSION}" RUN_UNATTENDED=1 "${SCRIPT_DIR}/../install.sh")
+
+# Show rpm info
+rpm -qi "R-${R_VERSION}"
+
+"${SCRIPT_DIR}/test-r.sh"
+
+$YUM -y remove "R-${R_VERSION}"
+
+if [ -d "/opt/R/${R_VERSION}" ]; then
+    echo "Failed to uninstall completely"
+    exit 1
+fi

test/test-zypper.sh

@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+set -ex
+
+SCRIPT_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
+
+# Install quick install script prerequisites
+if ! command -v curl > /dev/null 2>&1; then
+    zypper --non-interactive install curl
+fi
+
+# Run the quick install script. Use a locally built file if present, otherwise from the CDN.
+tmpdir=$(mktemp -d)
+cp -r "${SCRIPT_DIR}/../builder/integration/tmp/${OS_IDENTIFIER}/." "$tmpdir" > /dev/null 2>&1 || true
+(cd "$tmpdir" && SCRIPT_ACTION=install R_VERSION="${R_VERSION}" RUN_UNATTENDED=1 "${SCRIPT_DIR}/../install.sh")
+
+# Show RPM info
+rpm -qi "R-${R_VERSION}"
+
+"${SCRIPT_DIR}/test-r.sh"
+
+zypper --non-interactive remove "R-${R_VERSION}"
+
+if [ -d "/opt/R/${R_VERSION}" ]; then
+    echo "Failed to uninstall completely"
+    exit 1
+fi

test/test.R

@@ -0,0 +1,103 @@
+# HTTP mirror to support R 3.1
+options(repos = c("https://cloud.r-project.org", "http://cloud.r-project.org"))
+
+# Create a temp lib to avoid installing into the system library
+temp_lib <- tempdir()
+.libPaths(temp_lib)
+
+# Install a package from CRAN
+install.packages("R6")
+library(R6)
+
+# Install a package with C/C++ and Fortran code, which links against libR, BLAS, LAPACK
+curr_dir <- Sys.getenv("DIR", ".")
+install.packages(file.path(curr_dir, "testpkg"), repos = NULL, clean = TRUE)
+source(file.path(curr_dir, "testpkg/tests/test.R"))
+
+# Check iconv support
+if (!capabilities("iconv") || !all(c("ASCII", "LATIN1", "UTF-8") %in% iconvlist())) {
+  stop("missing iconv support")
+}
+
+# Check that built-in packages can be loaded
+for (pkg in rownames(installed.packages(priority = c("base", "recommended")))) {
+  if (!require(pkg, character.only = TRUE)) {
+    stop(sprintf("failed to load built-in package %s", pkg))
+  }
+}
+
+# Show capabilities. Warnings are returned on missing libraries.
+tryCatch(capabilities(), warning = function(w) {
+  print(capabilities())
+  stop(sprintf("missing libraries: %s", w$message))
+})
+
+# Check graphics devices
+# https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/Devices.html
+for (dev_name in c("png", "jpeg", "tiff", "svg", "bmp", "pdf", "postscript",
+                   "xfig", "pictex", "cairo_pdf", "cairo_ps")) {
+  # Skip unsupported graphics devices (e.g. tiff in R >= 3.3 on CentOS 6)
+  if (dev_name %in% names(capabilities()) && capabilities(dev_name) == FALSE) {
+    next
+  }
+  dev <- getFromNamespace(dev_name, "grDevices")
+  tryCatch({
+    file <- tempfile()
+    on.exit(unlink(file))
+    if (dev_name == "xfig") {
+      # Suppress warning from xfig when onefile = FALSE (the default)
+      dev(file, onefile = TRUE)
+    } else {
+      dev(file)
+    }
+    plot(1)
+    dev.off()
+  }, warning = function(w) {
+    # Catch errors which manifest as warnings (e.g. "failed to load cairo DLL")
+    stop(sprintf("graphics device %s failed: %s", dev_name, w$message))
+  })
+}
+
+# Check for unexpected output from graphics/text rendering.
+# Run externally to capture output from external processes.
+# For example, "Pango-WARNING **: failed to choose a font, expect ugly output"
+# messages when rendering text without any system fonts installed.
+output <- system2(R.home("bin/Rscript"), "-e 'png(tempfile()); plot(1)'", stdout = TRUE, stderr = TRUE)
+if (length(output) > 0) {
+  stop(sprintf("unexpected output returned from plotting:\n%s", paste(output, collapse = "\n")))
+}
+
+# Check download methods: libcurl (supported in R >= 3.2) and internal (based on libxml)
+if ("libcurl" %in% names(capabilities())) {
+  download.file("https://cloud.r-project.org", tempfile(), "libcurl")
+}
+tmpfile <- tempfile()
+write.csv("test", tmpfile)
+download.file(sprintf("file://%s", tmpfile), tempfile(), "internal")
+
+# Check that a pager is configured and help pages work
+# https://stat.ethz.ch/R-manual/R-devel/library/base/html/file.show.html
+output <- system2(R.home("bin/Rscript"), "-e 'help(stats)'", stdout = TRUE)
+if (length(output) == 0) {
+  stop("failed to display help pages; check that a pager is configured properly")
+}
+
+# Smoke test BLAS/LAPACK functionality. R may start just fine with an incompatible
+# BLAS/LAPACK library, and only fail when calling a BLAS or LAPACK routine.
+stopifnot(identical(crossprod(matrix(1)), matrix(1)))
+stopifnot(identical(chol(matrix(1)), matrix(1)))
+
+# Check that R 3.x depends on PCRE1, and R 4.x depends on PCRE2.
+# R 3.5 and 3.6 will link against PCRE2 if present, and take on an unnecessary dependency.
+# Some distros do always require PCRE2, however, such as Debian 11.
+ld_flags <- system2(R.home("bin/R"), c("CMD", "config", "--ldflags"), stdout = TRUE)
+has_pcre1 <- grepl("-lpcre\\b", ld_flags)
+has_pcre2 <- grepl("-lpcre2-8\\b", ld_flags)
+if (getRversion() >= "3.5.0" && getRversion() < "4.0.0") {
+  stopifnot(has_pcre1)
+  if (has_pcre2) {
+    message(sprintf("Info: %s is linked against PCRE2, which may be unnecessary", R.version.string))
+  }
+} else if (getRversion() >= "4.0.0") {
+  stopifnot(has_pcre2 && !has_pcre1)
+}

test/testpkg/.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

test/testpkg/.gitignore

@@ -0,0 +1,2 @@
+.Rproj.user
+.Rhistory

test/testpkg/DESCRIPTION

@@ -0,0 +1,12 @@
+Package: testpkg
+Type: Package
+Title: A Test Package
+Version: 0.1.0
+Authors@R: person("Test", "Pkg", email = "test@test", role = c("aut", "cre"))
+Description: A test package.
+License: MIT
+Depends:
+    R (>= 3.1)
+SystemRequirements: C++11
+RoxygenNote: 6.1.1
+Encoding: UTF-8

test/testpkg/NAMESPACE

@@ -0,0 +1,6 @@
+# Generated by roxygen2: do not edit by hand
+
+export(add_it)
+export(square_it)
+export(subtract_it)
+useDynLib(testpkg, .registration = TRUE)

test/testpkg/R/testpkg.R

@@ -0,0 +1,32 @@
+#' @useDynLib testpkg, .registration = TRUE
+"_PACKAGE"
+
+#' Add it together
+#'
+#' @param a Number
+#' @param b Number
+#' @return Sum of numbers
+#' @export
+add_it <- function(a, b) {
+  .Call("add", a, b)
+}
+
+#' Subtract it
+#'
+#' @param a Number
+#' @param b Number
+#' @return Difference of numbers
+#' @export
+subtract_it <- function(a, b) {
+  .Call("subtract", a, b)
+}
+
+#' Square it up
+#'
+#' @param n Integer
+#' @return Square
+#' @export
+square_it <- function(n) {
+  result <- .Fortran("square", n = as.integer(n), answer = as.integer(1))
+  result$answer
+}

test/testpkg/README.md

@@ -0,0 +1,3 @@
+# testpkg
+
+Test package with C/C++ and Fortran code, which links against libR, BLAS, LAPACK (see [Makevars](src/Makevars)).

test/testpkg/man/add_it.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/testpkg.R
+\name{add_it}
+\alias{add_it}
+\title{Add it together}
+\usage{
+add_it(a, b)
+}
+\arguments{
+\item{a}{Number}
+
+\item{b}{Number}
+}
+\value{
+Sum of numbers
+}
+\description{
+Add it together
+}

test/testpkg/man/square_it.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/testpkg.R
+\name{square_it}
+\alias{square_it}
+\title{Square it up}
+\usage{
+square_it(n)
+}
+\arguments{
+\item{n}{Integer}
+}
+\value{
+Square
+}
+\description{
+Square it up
+}

test/testpkg/man/subtract_it.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/testpkg.R
+\name{subtract_it}
+\alias{subtract_it}
+\title{Subtract it}
+\usage{
+subtract_it(a, b)
+}
+\arguments{
+\item{a}{Number}
+
+\item{b}{Number}
+}
+\value{
+Difference of numbers
+}
+\description{
+Subtract it
+}

test/testpkg/man/testpkg-package.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/testpkg.R
+\docType{package}
+\name{testpkg-package}
+\alias{testpkg}
+\alias{testpkg-package}
+\title{testpkg: A Test Package}
+\description{
+A test package.
+}
+\author{
+\strong{Maintainer}: Test Pkg \email{test@test}
+
+}

test/testpkg/src/Makevars

@@ -0,0 +1,2 @@
+CXX_STD=CXX11
+PKG_LIBS=$(MAIN_LDFLAGS) $(LDFLAGS) $(LIBR) $(LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(SHLIB_OPENMP_CFLAGS)