a20cff273b* Allows building deb packages for R on ubuntu-1804
this update provides a mechanism for building deb packages on Ubunto
1804. Several changes have been necessary to facilitate this:
* Dockerfile has been updated. It now includes:
- fpm - a tool tool to create OS specific packages
- copying the package script into the image
* the OS specific package.ubuntu-1804 packaging script
- this is the script that uses fpm to build the package
* Updates to build.sh. It now includes:
- runs the package script if it exists
- stores the resultant package to s3
* removed duplicate dependencies
* fixed minor bug with output directory creation
* moved package creation to after the clean step
* Changed deb priority to "optional"
The fpm default priority is "extra" which is now deprecated.
https://github.com/jordansissel/fpm/issues/1398
* Added additional package fields
Added 'Bugs', URL (Homepage), 'Description', 'Maintainer' and 'License'
* Fixed the repo URL
* Added passthrough for Jenkins BUILD_NUMBER
Jenkins sets the BUILD_NUMBER environment variable for all jobs.
This change sets that env var inside the container as BUILD_NO.
BUILD_NO is used bythe packaging scripts in place of a version number
for all of the created packages.
* removed liblapack
* Improved consistency of environment variable use
Removed the needless renaming of environment variables to improve
overall consistency and readability
* No longer tries to version the packages
Previous commits relied on the idea that the Jenkins BUILD_NUMBER
environment variable could be used as a version number for the package
itself (in addition to R's existing version numbers). This is not the
case and having a version number for the package is not deemed desirable
at this time. This change pins *all* packages produced to version 1.
* Moved additional apt package installations
Packages were being installed in two places, have rationalised to a
single location to reduce the number of layers in the final container.
* Tidy up of package script
Alphabetised the dependencies to make things easier to find.
* Added additional dependencies
These dependencies were added as they were identified to be missing when
running against the R 3.6.1 build during testing
* Removed an unrequired dependency
Further trimming down the dependency list based on reviewer feedback.
* Swapped liblapack-dev for libopenblas-dev
123 lines
3.3 KiB
Shell
Executable file
123 lines
3.3 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}-${OS_IDENTIFIER}.tar.gz"
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# Some Dockerfiles may copy a `/env.sh` to set up environment variables
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# that require command substitution. If this file exists, source it.
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if [[ -f /env.sh ]]; then
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echo "Sourcing environment variables"
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source /env.sh
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fi
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# upload_r()
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upload_r() {
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baseName="r/${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}.tar.gz
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fi
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}
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# archive_r() - $1 as r version
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archive_r() {
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tar czf /tmp/${TARBALL_NAME} --directory=/opt/R ${1} --owner=0 --group=0
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}
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fetch_r_source() {
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echo "Downloading R-${1}"
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wget -q ${CRAN}/src/base/R-3/R-${1}.tar.gz -O /tmp/R-${1}.tar.gz
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echo "Extracting R-${1}"
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tar xf /tmp/R-${1}.tar.gz -C /tmp
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rm /tmp/R-${1}.tar.gz
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}
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# On CentOS 6, we need to clean up references to the static library and header paths.
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clean_r() {
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if [[ -f /clean.sh ]]; then
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echo "Cleaning R build on CentOS 6"
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source /clean.sh
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fi
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}
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# compile_r() - $1 as r version
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compile_r() {
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cd /tmp/R-${1}
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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=x86_64-pc-linux-gnu'
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if _version_is_greater_than ${R_VERSION} 3.2.2; then
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build_flag=''
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fi
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# Default configure options. Some Dockerfiles override this with an ENV directive.
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default_configure_options="\
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--enable-R-shlib \
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--with-tcltk \
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--enable-memory-profiling \
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--with-x \
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--with-blas \
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--with-lapack"
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CONFIGURE_OPTIONS=${CONFIGURE_OPTIONS:-$default_configure_options}
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# set some common environment variables for the configure step
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AWK=/usr/bin/awk \
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LIBnn=lib \
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PERL=/usr/bin/perl \
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R_PDFVIEWER=xdg-open \
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R_BROWSER=xdg-open \
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R_PAPERSIZE=letter \
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R_PRINTCMD=/usr/bin/lpr \
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R_UNZIPCMD=/usr/bin/unzip \
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R_ZIPCMD=/usr/bin/zip \
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./configure \
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--prefix=/opt/R/${1} \
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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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}
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# check for packager script
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## If it exists this build is ready for packaging with fpm, 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=${1}
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source /package.sh
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fi
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}
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set_up_environment() {
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mkdir -p /opt/R
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}
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_version_is_greater_than() {
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test "$(printf '%s\n' "$@" | sort -V | head -n 1)" != "$1"
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}
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###### RUN R COMPILE PROCEDURE ######
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set_up_environment
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fetch_r_source $R_VERSION
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compile_r $R_VERSION
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clean_r
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package_r $R_VERSION
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archive_r $R_VERSION
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upload_r $R_VERSION
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