228 lines
8.1 KiB
Shell
Executable file
228 lines
8.1 KiB
Shell
Executable file
#!/bin/bash
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set -e
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export CRAN=${CRAN-"https://cran.rstudio.com"}
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export S3_BUCKET_PREFIX=${S3_BUCKET_PREFIX-""}
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export OS_IDENTIFIER=${OS_IDENTIFIER-"unknown"}
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export TARBALL_NAME="R-${R_VERSION}-${OS_IDENTIFIER}.tar.gz"
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export R_INSTALL_PATH=${R_INSTALL_PATH:-"/opt/R/${R_VERSION}"}
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# Some Dockerfiles may copy a `/env.sh` to set up environment variables
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# that require command substitution. If this file exists, source it.
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if [[ -f /env.sh ]]; then
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echo "Sourcing environment variables"
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source /env.sh
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fi
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# upload_r()
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upload_r() {
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baseName="r/${OS_IDENTIFIER}"
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if [ -n "$S3_BUCKET" ] && [ "$S3_BUCKET" != "" ]; then
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echo "Storing artifact on s3: ${S3_BUCKET}, tarball: ${TARBALL_NAME}"
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aws s3 cp /tmp/${TARBALL_NAME} s3://${S3_BUCKET}/${S3_BUCKET_PREFIX}${baseName}/${TARBALL_NAME}
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# check if PKG_FILE has been set by a packager script and act accordingly
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if [ -n "$PKG_FILE" ] && [ "$PKG_FILE" != "" ]; then
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if [ -f "$PKG_FILE" ]; then
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aws s3 cp ${PKG_FILE} s3://${S3_BUCKET}/${S3_BUCKET_PREFIX}${baseName}/pkgs/$(basename ${PKG_FILE})
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fi
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fi
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fi
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if [ -n "$LOCAL_STORE" ] && [ "$LOCAL_STORE" != '' ]; then
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echo "Storing artifact locally: ${LOCAL_STORE}, tarball: ${TARBALL_NAME}"
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mkdir -p ${LOCAL_STORE}/${baseName}
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cp /tmp/${TARBALL_NAME} ${LOCAL_STORE}/${baseName}/${TARBALL_NAME}
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fi
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}
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# archive_r()
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archive_r() {
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dir=$(dirname "$R_INSTALL_PATH")
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base=$(basename "$R_INSTALL_PATH")
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tar czf "/tmp/${TARBALL_NAME}" --directory="$dir" "$base" --owner=0 --group=0
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}
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fetch_r_source() {
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echo "Downloading R-${1}"
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if [ -n "${R_TARBALL_URL}" ]; then
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# Custom tarball URL for testing (e.g., R alpha and beta releases)
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wget -q "${R_TARBALL_URL}" -O /tmp/R-${1}.tar.gz
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elif [ "${1}" = devel ]; then
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# Download the daily tarball of R devel
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wget -q https://cran.r-project.org/src/base-prerelease/R-devel.tar.gz -O /tmp/R-devel.tar.gz
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elif [ "${1}" = "next" ]; then
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wget -q https://cran.r-project.org/src/base-prerelease/R-latest.tar.gz -O /tmp/R-next.tar.gz
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else
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wget -q "${CRAN}/src/base/R-`echo ${1}| awk 'BEGIN {FS="."} {print $1}'`/R-${1}.tar.gz" -O /tmp/R-${1}.tar.gz
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fi
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echo "Extracting R-${1}"
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tar xf /tmp/R-${1}.tar.gz -C /tmp
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# 'next' may contain R-patched/, R-alpha/, etc. make it R-next/
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if [ "${1}" = "next" ]; then
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dirname=`tar tzvf /tmp/R-next.tar.gz | head -1 | awk '{ print $NF }' | cut -d/ -f1`
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mv /tmp/${dirname} /tmp/R-next
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fi
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rm /tmp/R-${1}.tar.gz
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}
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# Apply a patch for this R version if present. Typically for R-devel.
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patch_r() {
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cd /tmp/R-${1}
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if [ -f "/patches/R-${1}.patch" ]; then
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patch -p1 < "/patches/R-${1}.patch"
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fi
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if [ -f "/patches/R-${1}-${OS_IDENTIFIER}.patch" ]; then
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patch -p1 < "/patches/R-${1}-${OS_IDENTIFIER}.patch"
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fi
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if [ -f "/patches/R-${1}-`arch`.patch" ]; then
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patch -p1 < "/patches/R-${1}-`arch`.patch"
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fi
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}
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# compile_r() - $1 as r version
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compile_r() {
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r_version=${1}
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cd "/tmp/R-${r_version}"
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# tools/config.guess in R versions older than 3.2.2 guess 'unknown' instead of 'pc'
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# test the version and properly set the flag.
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build_flag="--build=$(uname -m)-pc-linux-gnu"
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if _version_is_greater_than "${r_version}" 3.2.2; then
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build_flag=''
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fi
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# R 3.6.1 and below require additional compiler flags for GCC 10 and above
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# (e.g., on Debian 11). Add -fcommon to CFLAGS to work around issues with new
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# default of -fno-common for C (fixed in R 3.6.2). Add -fallow-argument-mismatch
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# to FFLAGS to work around issues with changes to argument mismatch checking
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# in Fortran (fixed in R 3.6.2, but not mentioned in NEWS).
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# https://cran.r-project.org/doc/manuals/r-release/NEWS.3.html
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# https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Using-Fortran
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# https://gcc.gnu.org/gcc-10/porting_to.html
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gcc_major_version=$(gcc -dumpversion | cut -d '.' -f 1)
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if _version_is_less_than "${r_version}" 3.6.2 && _version_is_greater_than "${gcc_major_version}" 9; then
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# Default CFLAGS/FFLAGS for all R 3.x versions is '-g -O2' when using GCC
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export CFLAGS='-g -O2 -fcommon'
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export FFLAGS='-g -O2 -fallow-argument-mismatch'
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echo "Setting CFLAGS: ${CFLAGS}"
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echo "Setting FFLAGS: ${FFLAGS}"
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fi
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# Avoid a PCRE2 dependency for R 3.5 and 3.6. R 3.x uses PCRE1, but R 3.5+
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# will link against PCRE2 if present, although it is not actually used.
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# Since there's no way to disable this in the configure script, and we need
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# PCRE2 for R 4.x, we hide PCRE2 from the configure script by temporarily
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# removing the pkg-config file and pcre2-config script.
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#
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# The INCLUDE_PCRE2_IN_R_3 environment variable can be set to include PCRE2
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# in R 3.x builds, for distributions where PCRE2 is always required.
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# In Debian 11/Ubuntu 22/RHEL 9, Pango now depends on PCRE2, so R 3.x will not be compiled with
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# Pango support if the PCRE2 pkg-config file is missing.
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if [[ "${r_version}" =~ ^3 ]] && pkg-config --exists libpcre2-8 && [ -z "$INCLUDE_PCRE2_IN_R_3" ]; then
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mkdir -p /tmp/pcre2
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pc_dir=$(pkg-config --variable pcfiledir libpcre2-8)
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mv ${pc_dir}/libpcre2-8.pc /tmp/pcre2
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config_bin=$(which pcre2-config)
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mv ${config_bin} /tmp/pcre2
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trap "{ mv /tmp/pcre2/libpcre2-8.pc ${pc_dir}; mv /tmp/pcre2/pcre2-config ${config_bin}; }" EXIT
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fi
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# Allow libcurl 8.x to be used in R 4.2 and below. Despite a change in major
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# version number, libcurl 8 changes neither API nor ABI. This applies the same
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# change to configure made in R 4.3.0, replacing exit(1) with exit(0) when
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# LIBCURL_VERSION_MAJOR > 7.
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# https://github.com/wch/r-source/commit/da6638896413bcbb5970b2335b92582853f94e3c
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if _version_is_less_than "${r_version}" 4.3.0; then
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sed -i -z 's/#if LIBCURL_VERSION_MAJOR > 7\n exit(1)/#if LIBCURL_VERSION_MAJOR > 7\n exit(0)/' configure
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fi
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# Default configure options. Some Dockerfiles override this with an ENV directive.
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default_configure_options="\
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--enable-R-shlib \
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--with-tcltk \
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--enable-memory-profiling \
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--with-x \
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--with-blas \
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--with-lapack"
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CONFIGURE_OPTIONS=${CONFIGURE_OPTIONS:-$default_configure_options}
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# For RHEL 9, link to external FlexiBLAS starting from R 4.3.0 to align with EPEL 9
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if _version_is_greater_than "${R_VERSION}" 4.2.10; then
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if [[ "${OS_IDENTIFIER}" = "rhel-9" ]]; then
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CONFIGURE_OPTIONS="$CONFIGURE_OPTIONS \
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--with-blas=flexiblas --with-lapack=flexiblas"
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fi
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fi
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echo "Using CONFIGURE_OPTIONS: ${CONFIGURE_OPTIONS}"
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# set some common environment variables for the configure step
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AWK=/usr/bin/awk \
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LIBnn=lib \
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PERL=/usr/bin/perl \
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R_PDFVIEWER=xdg-open \
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R_BROWSER=xdg-open \
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R_PAPERSIZE=letter \
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R_PRINTCMD=/usr/bin/lpr \
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R_UNZIPCMD=/usr/bin/unzip \
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R_ZIPCMD=/usr/bin/zip \
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./configure \
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--prefix="${R_INSTALL_PATH}" \
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${CONFIGURE_OPTIONS} \
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${build_flag}
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make clean
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make
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make install
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# Add OS identifier to the default HTTP user agent.
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# Set this in the system Rprofile so it works when R is run with --vanilla.
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cat <<EOF >> "${R_INSTALL_PATH}"/lib/R/library/base/R/Rprofile
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## Set the default HTTP user agent
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local({
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os_identifier <- if (file.exists("/etc/os-release")) {
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os <- readLines("/etc/os-release")
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id <- gsub('^ID=|"', "", grep("^ID=", os, value = TRUE))
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version <- gsub('^VERSION_ID=|"', "", grep("^VERSION_ID=", os, value = TRUE))
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sprintf("%s-%s", id, version)
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} else {
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"${OS_IDENTIFIER}"
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}
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options(HTTPUserAgent = sprintf("R/%s (%s) R (%s)", getRversion(), os_identifier,
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paste(getRversion(), R.version\$platform, R.version\$arch, R.version\$os)))
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})
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EOF
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}
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# check for packager script
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## If it exists this build is ready for packaging with nFPM, so run the script
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## else do nothing
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package_r() {
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if [[ -f /package.sh ]]; then
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export R_VERSION=${1}
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source /package.sh
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fi
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}
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set_up_environment() {
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mkdir -p "$R_INSTALL_PATH"
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}
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_version_is_greater_than() {
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test "$(printf '%s\n' "$@" | sort -V | head -n 1)" != "$1"
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}
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_version_is_less_than() {
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test "$(printf '%s\n' "$@" | sort -V | head -n 1)" != "$2"
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}
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###### RUN R COMPILE PROCEDURE ######
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set_up_environment
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fetch_r_source $R_VERSION
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patch_r $R_VERSION
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compile_r $R_VERSION
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package_r $R_VERSION
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archive_r
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upload_r $R_VERSION
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