Add tests for R builds

test/docker-compose.yml

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+version: '2.0'
+
+services:
+  ubuntu-1804:
+    image: ubuntu:bionic
+    command: /test/test-deb.sh
+    environment:
+      - OS_IDENTIFIER=ubuntu-1804
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ./:/test
+      - ../builder/integration/tmp:/packages
+  ubuntu-2004:
+    image: ubuntu:focal
+    command: /test/test-deb.sh
+    environment:
+      - OS_IDENTIFIER=ubuntu-2004
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ./:/test
+      - ../builder/integration/tmp:/packages
+  ubuntu-2204:
+    image: ubuntu:jammy
+    command: /test/test-deb.sh
+    environment:
+      - OS_IDENTIFIER=ubuntu-2204
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ./:/test
+      - ../builder/integration/tmp:/packages
+  debian-11:
+    image: debian:bullseye
+    command: /test/test-deb.sh
+    environment:
+      - OS_IDENTIFIER=debian-11
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ./:/test
+      - ../builder/integration/tmp:/packages
+  debian-10:
+    image: debian:buster
+    command: /test/test-deb.sh
+    environment:
+      - OS_IDENTIFIER=debian-10
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ./:/test
+      - ../builder/integration/tmp:/packages
+  centos-7:
+    image: centos:centos7
+    command: /test/test-centos.sh
+    environment:
+      - OS_IDENTIFIER=centos-7
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ./:/test
+      - ../builder/integration/tmp:/packages
+  centos-8:
+    image: rockylinux:8
+    command: /test/test-centos.sh
+    environment:
+      - OS_IDENTIFIER=centos-8
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ./:/test
+      - ../builder/integration/tmp:/packages
+  opensuse-153:
+    image: opensuse/leap:15.3
+    command: /test/test-opensuse.sh
+    environment:
+      - OS_IDENTIFIER=opensuse-153
+      - R_VERSION=${R_VERSION}
+    volumes:
+      - ./:/test
+      - ../builder/integration/tmp:/packages

test/test-centos.sh

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+#!/usr/bin/env bash
+set -ex
+
+PKG_FILE=/packages/${OS_IDENTIFIER}/R-${R_VERSION}-1-1.x86_64.rpm
+
+if [ ! -f ${PKG_FILE} ]; then
+    echo "No package found, skipping tests"
+    exit 0
+fi
+
+yum -y -q update
+yum -y install epel-release
+yum -y install ${PKG_FILE}
+
+# Show rpm info
+rpm -qi R-${R_VERSION}
+
+/test/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-deb.sh

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+#!/usr/bin/env bash
+set -ex
+
+PKG_FILE=/packages/${OS_IDENTIFIER}/r-${R_VERSION}_1_amd64.deb
+
+if [ ! -f ${PKG_FILE} ]; then
+    echo "No package found, skipping tests"
+    exit 0
+fi
+
+export DEBIAN_FRONTEND=noninteractive 
+apt-get update -qq
+apt-get install -f -y ${PKG_FILE}
+
+# Show deb info
+apt-cache show r-${R_VERSION}
+
+/test/test-r.sh
+
+apt-get remove -y r-${R_VERSION}
+
+if [ -d /opt/R/${R_VERSION} ]; then
+    echo "Failed to uninstall completely"
+    exit 1
+fi

test/test-opensuse.sh

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+#!/usr/bin/env bash
+set -ex
+
+PKG_FILE=/packages/${OS_IDENTIFIER}/R-${R_VERSION}-1-1.x86_64.rpm
+
+if [ ! -f ${PKG_FILE} ]; then
+    echo "No package found, skipping tests"
+    exit 0
+fi
+
+zypper --non-interactive --no-gpg-checks install ${PKG_FILE}
+
+# Show rpm info
+rpm -qi R-${R_VERSION}
+
+/test/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.sh

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+#!/usr/bin/env bash
+set -ex
+
+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 "${R_HOME}/lib/libR.so"
+
+DIR=${DIR} "${R_HOME}/bin/Rscript" /test/test.R

test/test-rhel.sh

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+#!/usr/bin/env bash
+set -ex
+
+PKG_FILE=/packages/${OS_IDENTIFIER}/R-${R_VERSION}-1-1.x86_64.rpm
+
+if [ ! -f ${PKG_FILE} ]; then
+    echo "No package found, skipping tests"
+    exit 0
+fi
+
+dnf -y install dnf-plugins-core
+dnf config-manager --set-enabled crb
+dnf -y install epel-release
+dnf -y install ${PKG_FILE}
+
+# Show rpm info
+rpm -qi R-${R_VERSION}
+
+/test/test-r.sh
+
+dnf -y remove R-${R_VERSION}
+
+if [ -d /opt/R/${R_VERSION} ]; then
+    echo "Failed to uninstall completely"
+    exit 1
+fi

test/test.R

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+# 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

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+^.*\.Rproj$
+^\.Rproj\.user$

test/testpkg/.gitignore

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

test/testpkg/DESCRIPTION

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+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

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+#' @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

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+# 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

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+% 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

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+CXX_STD=CXX11
+PKG_LIBS=$(MAIN_LDFLAGS) $(LDFLAGS) $(LIBR) $(LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(SHLIB_OPENMP_CFLAGS)

test/testpkg/src/add.c

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+#include <R.h>
+#include <Rinternals.h>
+
+SEXP add(SEXP a, SEXP b)
+{
+  SEXP result = PROTECT(allocVector(REALSXP, 1));
+  REAL(result)[0] = asReal(a) + asReal(b);
+  UNPROTECT(1);
+  return result;
+}

test/testpkg/src/init.c

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+#include <R.h>
+#include <Rinternals.h>
+#include <R_ext/Rdynload.h>
+
+#define CALLDEF(name, n)  {#name, (DL_FUNC) &name, n}
+#define FDEF(name)  {#name, (DL_FUNC) &F77_SUB(name), sizeof(name ## _t)/sizeof(name ## _t[0]), name ##_t}
+
+extern SEXP add(SEXP, SEXP);
+extern SEXP subtract(SEXP, SEXP);
+
+void F77_SUB(square)(int *n, int *answer);
+
+static R_NativePrimitiveArgType square_t[] = {
+    INTSXP,
+    INTSXP
+};
+
+static const R_CallMethodDef CallEntries[] = {
+    CALLDEF(add, 2),
+    CALLDEF(subtract, 2),
+    {NULL, NULL, 0}
+};
+
+static const R_FortranMethodDef fMethods[] = {
+    FDEF(square),
+    {NULL, NULL, 0}
+};
+
+void R_init_testpkg(DllInfo *dll)
+{
+    R_registerRoutines(dll, NULL, CallEntries, fMethods, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}