build.sh

#!/bin/bash
set -e

export CRAN=${CRAN-"https://cran.rstudio.com"}
export OS_IDENTIFIER=${OS_IDENTIFIER-"unknown"}
export TARBALL_NAME="R-${R_VERSION}${R_TYPE}-${OS_IDENTIFIER}.tar.gz"

# Some Dockerfiles may copy a `/env.sh` to set up environment variables
# that require command substitution. If this file exists, source it.
if [[ -f /env.sh ]]; then
    echo "Sourcing environment variables"
    source /env.sh
fi

# archive_r() - $1 as r version
archive_r() {
  tar czf /tmp/${TARBALL_NAME} --directory=/opt/R ${1}${2} --owner=0 --group=0
}

fetch_r_source() {
  echo "Downloading R-${1}"
  if [ -n "${R_TARBALL_URL}" ]; then
    # Custom tarball URL for testing (e.g., R alpha and beta releases)
    wget "${R_TARBALL_URL}" -O /tmp/R-${1}.tar.gz
  elif [ "${1}" = devel ]; then
    # Download the daily tarball of R devel
    wget -q https://cran.r-project.org/src/base-prerelease/R-devel.tar.gz -O /tmp/R-devel.tar.gz
  elif [ "${1}" = "next" ]; then
    wget -q https://cran.r-project.org/src/base-prerelease/R-latest.tar.gz -O /tmp/R-next.tar.gz
  else
    wget -q "${CRAN}/src/base/R-`echo ${1}| awk 'BEGIN {FS="."} {print $1}'`/R-${1}.tar.gz" -O /tmp/R-${1}.tar.gz
  fi
  echo "Extracting R-${1}"
  tar xf /tmp/R-${1}.tar.gz -C /tmp
  # 'next' may contain R-patched/, R-alpha/, etc. make it R-next/
  if [ "${1}" = "next" ]; then
      dirname=`tar tzvf /tmp/R-next.tar.gz | head -1 | awk '{ print $NF }' | cut -d/ -f1`
      mv /tmp/${dirname} /tmp/R-next
  fi
  rm /tmp/R-${1}.tar.gz
}

# compile_r() - $1 as r version
compile_r() {
  cd /tmp/R-${1}

  # tools/config.guess in R versions older than 3.2.2 guess 'unknown' instead of 'pc'
  # test the version and properly set the flag.
  build_flag="--build=$(uname -m)-pc-linux-gnu"
  if _version_is_greater_than ${R_VERSION} 3.2.2; then
    build_flag=''
  fi

  # R 3.6.1 and below require additional compiler flags for GCC 10 and above
  # (e.g., on Debian 11). Add -fcommon to CFLAGS to work around issues with new
  # default of -fno-common for C (fixed in R 3.6.2). Add -fallow-argument-mismatch
  # to FFLAGS to work around issues with changes to argument mismatch checking
  # in Fortran (fixed in R 3.6.2, but not mentioned in NEWS).
  # https://cran.r-project.org/doc/manuals/r-release/NEWS.3.html
  # https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Using-Fortran
  # https://gcc.gnu.org/gcc-10/porting_to.html
  gcc_major_version=$(gcc -dumpversion | cut -d '.' -f 1)
  if _version_is_less_than "${R_VERSION}" 3.6.2 && _version_is_greater_than "${gcc_major_version}" 9; then
    # Default CFLAGS/FFLAGS for all R 3.x versions is '-g -O2' when using GCC
    export CFLAGS='-g -O2 -fcommon'
    export FFLAGS='-g -O2 -fallow-argument-mismatch'
    echo "Setting CFLAGS: ${CFLAGS}"
    echo "Setting FFLAGS: ${FFLAGS}"
  fi

  # Avoid a PCRE2 dependency for R 3.5 and 3.6. R 3.x uses PCRE1, but R 3.5+
  # will link against PCRE2 if present, although it is not actually used.
  # Since there's no way to disable this in the configure script, and we need
  # PCRE2 for R 4.x, we hide PCRE2 from the configure script by temporarily
  # removing the pkg-config file and pcre2-config script.
  #
  # The INCLUDE_PCRE2_IN_R_3 environment variable can be set to include PCRE2
  # in R 3.x builds, for distributions where PCRE2 is always required.
  # In Debian 11/Ubuntu 22/RHEL 9, Pango now depends on PCRE2, so R 3.x will not be compiled with
  # Pango support if the PCRE2 pkg-config file is missing.
  if [[ "${1}" =~ ^3 ]] && pkg-config --exists libpcre2-8 && [ -z "$INCLUDE_PCRE2_IN_R_3" ]; then
    mkdir -p /tmp/pcre2
    pc_dir=$(pkg-config --variable pcfiledir libpcre2-8)
    mv ${pc_dir}/libpcre2-8.pc /tmp/pcre2
    config_bin=$(which pcre2-config)
    mv ${config_bin} /tmp/pcre2
    trap "{ mv /tmp/pcre2/libpcre2-8.pc ${pc_dir}; mv /tmp/pcre2/pcre2-config ${config_bin}; }" EXIT
  fi

  # Default configure options. Some Dockerfiles override this with an ENV directive.
  default_configure_options="\
    --enable-R-shlib \
    --with-tcltk \
    --enable-memory-profiling \
    --with-x \
    --with-blas \
    --with-lapack"

  CONFIGURE_OPTIONS="${CONFIGURE_OPTIONS:-$default_configure_options} ${XCONFIGURE_OPTIONS}"

  if [[ -e "/config.site.$(uname -m)" ]]; then
      cp "/config.site.$(uname -m)" ./config.site
  elif [[ -e /config.site ]]; then
      cp /config.site .
  fi

  # set some common environment variables for the configure step
  eval "ARGS=( $CONFIGURE_OPTIONS )"
  AWK=/usr/bin/awk \
  LIBnn=lib \
  PERL=/usr/bin/perl \
  R_PDFVIEWER=xdg-open \
  R_BROWSER=xdg-open \
  R_PAPERSIZE=letter \
  R_PRINTCMD=/usr/bin/lpr \
  R_UNZIPCMD=/usr/bin/unzip \
  R_ZIPCMD=/usr/bin/zip \
  ./configure \
    --prefix=/opt/R/${1}${2} \
    "${ARGS[@]}" \
    ${build_flag}
  make clean
  make
  make install

  # Add OS identifier to the default HTTP user agent.
  # Set this in the system Rprofile so it works when R is run with --vanilla.
  cat <<EOF >> /opt/R/${1}${2}/lib/R/library/base/R/Rprofile
## Set the default HTTP user agent
local({
  os_identifier <- if (file.exists("/etc/os-release")) {
    os <- readLines("/etc/os-release")
    id <- gsub('^ID=|"', "", grep("^ID=", os, value = TRUE))
    version <- gsub('^VERSION_ID=|"', "", grep("^VERSION_ID=", os, value = TRUE))
    sprintf("%s-%s", id, version)
  } else {
    "${OS_IDENTIFIER}"
  }
  options(HTTPUserAgent = sprintf("R/%s (%s) R (%s)", getRversion(), os_identifier,
    paste(getRversion(), R.version\$platform, R.version\$arch, R.version\$os)))
})
EOF
}

# check for packager script
## If it exists this build is ready for packaging with nFPM, so run the script
## else do nothing
package_r() {
  if [[ -f /package.sh ]]; then
    export R_VERSION=${1}
    export R_TYPE=${2}
    source /package.sh
  fi
}

set_up_environment() {
  mkdir -p /opt/R
}

_version_is_greater_than() {
  test "$(printf '%s\n' "$@" | sort -V | head -n 1)" != "$1"
}

_version_is_less_than() {
  test "$(printf '%s\n' "$@" | sort -V | head -n 1)" != "$2"
}

###### RUN R COMPILE PROCEDURE ######
set_up_environment
fetch_r_source $R_VERSION
compile_r $R_VERSION $R_TYPE
package_r $R_VERSION $R_TYPE
archive_r $R_VERSION $R_TYPE