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make repo public

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Steve Nolen 2019-03-25 12:59:14 -04:00
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R-*
builder/integration/**
node_modules
serverless-custom.yml

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pipeline {
agent none
environment {
HOME = "."
}
options {
ansiColor('xterm')
}
stages {
stage('build images') {
agent { label 'docker-4x' }
steps {
sh 'make docker-build'
}
}
stage('push images') {
agent { label 'docker-4x' }
when {
branch 'master'
}
steps {
sh 'make docker-push'
}
}
stage('deploy') {
agent {
dockerfile {
dir 'jenkins'
label 'docker-4x'
additionalBuildArgs '--build-arg DOCKER_GID=$(stat -c %g /var/run/docker.sock) --build-arg JENKINS_UID=$(id -u jenkins) --build-arg JENKINS_GID=$(id -g jenkins)'
args '-v /var/run/docker.sock:/var/run/docker.sock --group-add docker'
}
}
when {
branch 'master'
}
steps {
sh 'make serverless-deploy'
}
}
}
}

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GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.

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PLATFORMS := ubuntu-1604 ubuntu-1804 debian-9 centos-6 centos-7 opensuse-42 opensuse-15
npm-install:
npm install
docker-build:
@cd builder && docker-compose build --parallel
AWS_ACCOUNT_ID:=$(shell aws sts get-caller-identity --output text --query 'Account')
AWS_REGION := us-east-1
docker-push: ecr-login docker-build
@for platform in $(PLATFORMS) ; do \
docker tag r-builds:$$platform $(AWS_ACCOUNT_ID).dkr.ecr.$(AWS_REGION).amazonaws.com/r-builds:$$platform; \
docker push $(AWS_ACCOUNT_ID).dkr.ecr.$(AWS_REGION).amazonaws.com/r-builds:$$platform; \
done
docker-down:
@cd builder && docker-compose down
docker-build-r: docker-build
@cd builder && docker-compose up
docker-shell-r-env:
@cd builder && docker-compose run --entrypoint /bin/bash ubuntu-1604
ecr-login:
@eval $(shell aws ecr get-login --no-include-email --region $(AWS_REGION))
fetch-serverless-custom-file:
aws s3 cp s3://rstudio-serverless/serverless/r-builds/serverless-custom.yml .
serverless-deploy: npm-install fetch-serverless-custom-file
serverless deploy --stage dev
.PHONY: docker-build docker-push docker-down docker-build-package docker-shell-package-env ecr-login npm-install fetch-serverless-custom-file serverless-deploy

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# r-builds
The environment which produces R builds obtainable from: https://cdn.rstudio.com/r/versions.json
## Adding a new platform.
### Dockerfile
Create a `builder/Dockerfile.platform-version` (where `platform-version` is `ubuntu-1604` or `centos-74`, etc.) This file must contain four major tasks:
1. an `OS_IDENTIFIER` env with the `platform-version`.
2. a step which ensures the R source build dependencies are installed
3. The `awscli`, most likely installed via `pip` for uploading tarballs to S3
4. `COPY` and `ENTRYPOINT` for the `build.sh` file in `builder/`.
### docker-compose.yml
A new service in the docker-compose file named according to the `platform-version` and containing the proper entries:
```
command: ./build.sh
environment:
- R_VERSION=${R_VERSION} # for testing out R builds locally
- LOCAL_STORE=/tmp/output # ensures that output tarballs are persisted locally
build:
context: .
dockerfile: Dockerfile.debian-9
image: r-builds:debian-9
volumes:
- ./integration/tmp:/tmp/output # path to output tarballs
```
### Job definition
IN `serverless-resources.yml` you'll need to add a job definition that points to the ECR image.
```
rBuildsBatchJobDefinitionDebian9:
Type: AWS::Batch::JobDefinition
Properties:
Type: container
ContainerProperties:
Command:
- ./build.sh
Vcpus: 4
Memory: 4096
JobRoleArn:
"Fn::GetAtt": [ rBuildsEcsTaskIamRole, Arn ]
Image: #{AWS::AccountId}.dkr.ecr.#{AWS::Region}.amazonaws.com/r-builds:debian-9
```
### Environment variables in the serverless.yml functions.
The serverless functions which trigger R builds need to be informed of new platforms.
1. Add a `JOB_DEFINITION_ARN_PlatformVersion` env variable with a ref to the Job definition above.
2. Append the `platform-version` to `SUPPORTED_PLATFORMS`.
```
environment:
# snip
JOB_DEFINITION_ARN_debian_9:
Ref: rBuildsBatchJobDefinitionDebian9
SUPPORTED_PLATFORMS: ubuntu-1604,ubuntu-1804,debian-9
```
### Makefile
In order for the makefile to push these new platforms to ECR, add them to the PLATFORMS variable near the top of the Makefile
### Submit a Pull Request
Once you've followed the steps above, submit a pull request. On successful merge, builds for this platform will begin to be available from the CDN.
## "Break Glass"
Periodically, someone with access to these resources may need to re-trigger every R version/platform combination. This quite easy with the `serverless` tool installed.
```
serverless invoke stepf -n rBuilds -d '{"force": true}'
```

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FROM centos:centos6
ENV OS_IDENTIFIER centos-6
RUN yum -y update \
&& yum -y install epel-release \
&& yum clean all
RUN yum -y update \
&& yum -y install \
atlas-devel \
blas-devel \
bzip2-devel \
cairo-devel \
gcc-c++ \
gcc-gfortran \
gcc-objc \
glibc-devel \
groff \
java-1.8.0-openjdk-devel \
krb5-devel \
krb5-libs \
lapack-devel \
less \
libICE-devel \
libSM-devel \
libX11-devel \
libXmu-devel \
libXt-devel \
libgssapi-devel \
libicu-devel \
libidn-devel \
libjpeg-devel \
libmetalink-devel \
libpng-devel \
libssh2-devel \
libtiff-devel \
ncurses-devel \
openldap \
openldap-devel \
openssh-clients \
openssh-server \
openssl-devel \
pango-devel \
pcre-devel \
pcre2-devel \
pkgconfig \
python \
python-pip \
readline-devel \
stunnel \
tcl-devel \
tex \
texinfo-tex \
texlive-latex \
tk-devel \
valgrind-devel \
wget \
xz-devel \
zlib-devel \
&& yum clean all
RUN pip install awscli
RUN chmod 0777 /opt
# Compile newer versions of zlib, bzip2, xz, pcre, and curl.
#
# Several compression libraries that were at one time included in R-devel have been removed.
# Instead of providing these libraries, R-devel assumes they are pre-installed. On RedHat 6,
# this results in build errors when zlib, bzip, pcre, curl, and xz are required. These
# libraries must be downloaded and compiled before building R-devel. Reference:
# http://pj.freefaculty.org/blog/?p=315
#
# It's also import to build the static versions of these libraries and link them
# statically when building R. This allows us to use the R binaries we build on
# another CentOS/RHEL 6 OS without updating the same five libraries.
# For more info, see the "R.spec" RPM spec file in the EPEL source archive at:
# http://download-ib01.fedoraproject.org/pub/epel/7/SRPMS/Packages/r/R-3.5.2-2.el7.src.rpm
# (search for "zlibhack" in R.spec).
#
# First, reate a directory for the additional libraries.
RUN mkdir -p /tmp/extra
# zlib 1.2.8
#
# Note: zlib 1.2.11 works fine for all R versions except 3.3.0, 3.3.1, and 3.3.2,
# so I went with an older version (1.2.8) to accommodate the flaky R versions. See the
# following note on https://www.r-statistics.com/2017/03/r-3-3-3-is-released/:
#
# The configure check for the zlib version is now robust to versions longer than 5 characters,
# including 1.2.11.
#
ARG ZLIB_VERSION=1.2.8
ARG ZLIB_DOWNLOAD_SHA256=36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d
RUN curl -fsSL "https://zlib.net/fossils/zlib-${ZLIB_VERSION}.tar.gz" -o zlib.tar.gz \
&& echo "$ZLIB_DOWNLOAD_SHA256 zlib.tar.gz" | sha256sum -c - \
&& CWD=`pwd` && TMP=`mktemp -d` \
&& tar -C $TMP -zxvf zlib.tar.gz \
&& cd $TMP/zlib* \
&& ./configure --prefix=/tmp/extra --static \
&& make CFLAGS="-fpic -fPIC" \
&& make install \
&& cd $CWD && rm -rf $TMP && rm -rf zlib.tar.gz
# bzip2 1.0.6
ARG BZIP2_VERSION=1.0.6
ARG BZIP2_DOWNLOAD_SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002
RUN curl -fsSL "https://sourceforge.net/projects/bzip2/files/bzip2-{$BZIP2_VERSION}.tar.gz/download" -o bzip2.tar.gz \
&& echo "$BZIP2_DOWNLOAD_SHA1 bzip2.tar.gz" | sha1sum -c - \
&& CWD=`pwd` && TMP=`mktemp -d` \
&& tar -C $TMP -zxvf bzip2.tar.gz \
&& cd $TMP/bzip2* \
&& make libbz2.a CFLAGS="-D_FILE_OFFSET_BITS=64 -fpic -fPIC" PREFIX=/tmp/extra \
&& make install PREFIX=/tmp/extra \
&& cd $CWD && rm -rf $TMP && rm -rf bzip2.tar.gz
# xz 5.2.4 (for lzma libraries)
ARG XZ_VERSION=5.2.4
ARG XZ_DOWNLOAD_SHA1=63ca380029597b951ce9afc6dec28f44f70bb5bd
RUN curl -fsSL "https://sourceforge.net/projects/lzmautils/files/xz-{$XZ_VERSION}.tar.gz/download" -o xz.tar.gz \
&& echo "$XZ_DOWNLOAD_SHA1 xz.tar.gz" | sha1sum -c - \
&& CWD=`pwd` && TMP=`mktemp -d` \
&& tar -C $TMP -zxvf xz.tar.gz \
&& cd $TMP/xz* \
&& CFLAGS="-fpic -fPIC" ./configure --enable-static=yes --enable-shared=no --prefix=/tmp/extra \
&& make -j8 \
&& make install \
&& cd $CWD && rm -rf $TMP && rm -rf xz.tar.gz
# PCRE 8.42
#
# The PCRE library provides PGP signatures for verifying downloads. Originally, I tried to do some
# PGP validation in the Dockerfile, but I ran into trouble with flaky key servers. To streamline
# things, I verified the download manually and then generated a sha256 checksum with the following
# commands:
# gpg --recv-key FB0F43D8
# gpg pcre-8.42.tar.gz.sig
# sha256sum pcre-8.42.tar.gz
#
ARG PCRE_VERSION=8.42
ARG PCRE_DOWNLOAD_SHA256=69acbc2fbdefb955d42a4c606dfde800c2885711d2979e356c0636efde9ec3b5
RUN curl -fsSL "https://ftp.pcre.org/pub/pcre/pcre-{$PCRE_VERSION}.tar.gz" -o pcre.tar.gz \
&& echo "$PCRE_DOWNLOAD_SHA256 pcre.tar.gz" | sha256sum -c - \
&& CWD=`pwd` && TMP=`mktemp -d` \
&& tar -C $TMP -zxvf pcre.tar.gz \
&& cd $TMP/pcre* \
&& mkdir -p /tmp/extra \
&& CFLAGS="-fpic -fPIC" ./configure --enable-static=yes --enable-shared=no --enable-utf --enable-unicode-properties --enable-pcre8 --enable-pcre16 --enable-pcre32 --prefix=/tmp/extra \
&& make -j8 \
&& make install \
&& cd $CWD && rm -rf $TMP && rm -rf pcre.tar.gz
# Curl 7.63.0
#
# The curl library provides PGP signatures for verifying downloads. Originally, I tried to do some
# PGP validation in the Dockerfile, but I ran into trouble with flaky key servers. To streamline
# things, I verified the download manually and then generated a sha256 checksum with the following
# commands:
# gpg --recv-key B71E12C2
# gpg curl-7.63.0.tar.gz.asc
# sha256sum curl-7.63.0.tar.gz
#
ARG CURL_VERSION=7.63.0
ARG CURL_DOWNLOAD_SHA256=d483b89062832e211c887d7cf1b65c902d591b48c11fe7d174af781681580b41
RUN curl -fsSL "https://curl.haxx.se/download/curl-{$CURL_VERSION}.tar.gz" -o curl.tar.gz \
&& echo "$CURL_DOWNLOAD_SHA256 curl.tar.gz" | sha256sum -c - \
&& CWD=`pwd` && TMP=`mktemp -d` \
&& tar -C $TMP -zxvf curl.tar.gz \
&& cd $TMP/curl* \
&& CFLAGS="-fpic -fPIC" ./configure --enable-static=yes --enable-shared=no --with-ssl --enable-ipv6 --with-gssapi --with-libidn --enable-ldaps --with-libssh2 --enable-threaded-resolver --with-libmetalink --prefix=/tmp/extra \
&& make V=1 \
&& make install \
&& cd $CWD && rm -rf $TMP && rm -rf curl.tar.gz
# Compiler and linker flags for statically linking updated libraries
ENV CFLAGS="-fpic -fPIC -I/tmp/extra/include"
ENV CURL_CFLAGS='-DCURL_STATICLIB -I/tmp/extra/include'
ENV CURL_CPPFLAGS='-DCURL_STATICLIB -I/tmp/extra/include'
# Configure flags for CentOS 6 that don't use the defaults in build.sh
ENV CONFIGURE_OPTIONS="\
--enable-R-shlib \
--with-tcltk \
--enable-memory-profiling \
--with-x \
--with-system-valgrind-headers \
--with-tcl-config=/usr/lib64/tclConfig.sh \
--with-tk-config=/usr/lib64/tkConfig.sh \
--enable-BLAS-shlib \
--enable-prebuilt-html"
# RHEL 6 doesn't have texi2any, so use makeinfo.
ENV MAKEINFO=makeinfo
# RHEL 6 doesn't have the inconsolata font, so override the defaults.
ENV R_RD4PDF="times,hyper"
# Copy a script to help set up the environment
COPY env_centos6.sh ./env.sh
COPY build.sh .
# Copy a script to clean up after the build
COPY clean_centos6.sh ./clean.sh
ENTRYPOINT ./build.sh

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FROM centos:centos7
ENV OS_IDENTIFIER centos-7
RUN yum -y update \
&& yum -y install epel-release \
&& yum clean all
RUN yum -y update \
&& yum -y install \
atlas-devel \
autoconf \
automake \
blas-devel \
bzip2-devel \
cairo-devel \
gcc-c++ \
gcc-gfortran \
gcc-objc \
java-1.8.0-openjdk-devel \
java-1.8.0-openjdk-headless \
lapack-devel \
less \
libICE-devel \
libSM-devel \
libX11-devel \
libXmu-devel \
libXt-devel \
libcurl-devel \
libicu-devel \
libjpeg-devel \
libpng-devel \
libtiff-devel \
libtool \
make \
ncurses-devel \
openblas-devel \
pango-devel \
pcre-devel \
pcre2-devel \
python-pip \
readline-devel \
tcl-devel \
tex \
texinfo-tex \
texlive-collection-latexrecommended \
tk-devel \
tre-devel \
valgrind-devel \
wget \
xpdf \
xz-devel \
zlib-devel \
&& yum clean all
RUN pip install awscli
RUN chmod 0777 /opt
# Configure flags for CentOS 7 that don't use the defaults in build.sh
ENV CONFIGURE_OPTIONS="\
--enable-R-shlib \
--with-tcltk \
--enable-memory-profiling \
--with-x \
--with-system-valgrind-headers \
--with-tcl-config=/usr/lib64/tclConfig.sh \
--with-tk-config=/usr/lib64/tkConfig.sh \
--enable-BLAS-shlib \
--enable-prebuilt-html \
--with-system-tre"
# RHEL 7 doesn't have the inconsolata font, so override the defaults.
ENV R_RD4PDF="times,hyper"
COPY build.sh .
ENTRYPOINT ./build.sh

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FROM debian:stretch
ENV OS_IDENTIFIER debian-9
RUN set -x \
&& export DEBIAN_FRONTEND=noninteractive \
&& echo 'deb-src http://deb.debian.org/debian stretch main' >> /etc/apt/sources.list \
&& apt-get update \
&& apt-get install -y libatlas3-base libcurl4-openssl-dev libicu-dev wget python-pip \
&& apt-get build-dep -y r-base
RUN pip install awscli
RUN chmod 0777 /opt
COPY build.sh .
ENTRYPOINT ./build.sh

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FROM opensuse/leap:15.0
ENV OS_IDENTIFIER opensuse-15
# Most of these packages, and also the configure options that follow were determined
# by reviewing "R-base.spec" from the following OpenSUSE RPM:
# https://download.opensuse.org/repositories/devel:/languages:/R:/released/openSUSE_Leap_42.3/src/R-base-3.5.3-103.1.src.rpm
RUN zypper --non-interactive update
RUN zypper --non-interactive --gpg-auto-import-keys -n install \
atlascpp-devel \
blas-devel \
bzip2 \
cairo-devel \
fdupes \
gcc \
gcc-c++ \
gcc-fortran \
glib2-devel \
glibc-locale \
help2man \
java-1_8_0-openjdk-devel \
lapack-devel \
libX11-devel \
libXScrnSaver-devel \
libXmu-devel \
libXt-devel \
libbz2-devel \
libcurl-devel \
libicu-devel \
libjpeg-devel \
libpng-devel \
libtiff-devel \
pango-devel \
pcre-devel \
perl \
perl-macros \
python \
python-pip \
readline-devel \
rpm-build \
shadow \
tcl-devel \
texinfo \
texlive-bibtex \
texlive-cm-super \
texlive-dvips \
texlive-helvetic \
texlive-inconsolata \
texlive-latex \
texlive-makeindex \
texlive-metafont \
texlive-psnfss \
texlive-tex \
texlive-times \
tk-devel \
unzip \
wget \
xdg-utils \
xorg-x11-devel \
xz-devel \
zip \
zlib-devel \
&& zypper clean
RUN pip install awscli
RUN chmod 0777 /opt
# Configure flags for SUSE that don't use the defaults in build.sh
ENV CONFIGURE_OPTIONS="\
--enable-R-shlib \
--with-blas \
--with-lapack \
--with-tcltk \
--with-x \
--enable-memory-profiling \
--with-tcl-config=/usr/lib64/tclConfig.sh \
--with-tk-config=/usr/lib64/tkConfig.sh"
COPY build.sh .
ENTRYPOINT ./build.sh

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FROM opensuse:42.3
ENV OS_IDENTIFIER opensuse-42
# Most of these packages, and also the configure options that follow were determined
# by reviewing "R-base.spec" from the following OpenSUSE RPM:
# https://download.opensuse.org/repositories/devel:/languages:/R:/released/openSUSE_Leap_42.3/src/R-base-3.5.3-103.1.src.rpm
RUN zypper --non-interactive update
RUN zypper --non-interactive --gpg-auto-import-keys -n install \
atlascpp-devel \
blas-devel \
bzip2 \
cairo-devel \
fdupes \
gcc \
gcc-c++ \
gcc-fortran \
glib2-devel \
glibc-locale \
help2man \
java-1_8_0-openjdk-devel \
lapack-devel \
libX11-devel \
libXScrnSaver-devel \
libXmu-devel \
libXt-devel \
libbz2-devel \
libcurl-devel \
libicu-devel \
libjpeg-devel \
libpng-devel \
libtiff-devel \
pango-devel \
pcre-devel \
perl \
perl-macros \
python \
python-pip \
readline-devel \
rpm-build \
shadow \
tcl-devel \
texinfo \
texlive-bibtex \
texlive-cm-super \
texlive-dvips \
texlive-helvetic \
texlive-inconsolata \
texlive-latex \
texlive-makeindex \
texlive-metafont \
texlive-psnfss \
texlive-tex \
texlive-times \
tk-devel \
unzip \
wget \
xdg-utils \
xorg-x11-devel \
xz-devel \
zip \
zlib-devel \
&& zypper clean
RUN pip install awscli
RUN chmod 0777 /opt
# SUSE 12 doesn't have texi2any, so use makeinfo.
ENV MAKEINFO=makeinfo
# Configure flags for SUSE that don't use the defaults in build.sh
ENV CONFIGURE_OPTIONS="\
--enable-R-shlib \
--with-blas \
--with-lapack \
--with-tcltk \
--with-x \
--enable-memory-profiling \
--with-tcl-config=/usr/lib64/tclConfig.sh \
--with-tk-config=/usr/lib64/tkConfig.sh \
--enable-prebuilt-html"
COPY build.sh .
ENTRYPOINT ./build.sh

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FROM ubuntu:xenial
ENV OS_IDENTIFIER ubuntu-1604
RUN set -x \
&& sed -i "s|# deb-src|deb-src|g" /etc/apt/sources.list \
&& export DEBIAN_FRONTEND=noninteractive \
&& apt-get update \
&& apt-get install -y libatlas3-base libcurl4-openssl-dev libicu-dev wget python-pip \
&& apt-get build-dep -y r-base
RUN pip install awscli
RUN chmod 0777 /opt
COPY build.sh .
ENTRYPOINT ./build.sh

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FROM ubuntu:bionic
ENV OS_IDENTIFIER ubuntu-1804
RUN set -x \
&& sed -i "s|# deb-src|deb-src|g" /etc/apt/sources.list \
&& export DEBIAN_FRONTEND=noninteractive \
&& apt-get update \
&& apt-get install -y libatlas3-base libcurl4-openssl-dev libicu-dev wget python-pip \
&& apt-get build-dep -y r-base
RUN pip install awscli
RUN chmod 0777 /opt
COPY build.sh .
ENTRYPOINT ./build.sh

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#!/bin/bash
set -e
export CRAN=${CRAN-"https://cran.rstudio.com"}
export S3_BUCKET_PREFIX=${S3_BUCKET_PREFIX-""}
export OS_IDENTIFIER=${OS_IDENTIFIER-"unknown"}
export TARBALL_NAME="R-${R_VERSION}-${OS_IDENTIFIER}.tar.gz"
# Some Dockerfiles may copy a `/env.sh` to set up environment variables
# that require command substitution. If this file exists, source it.
if [[ -f /env.sh ]]; then
echo "Sourcing environment variables"
source /env.sh
fi
# upload_r()
upload_r() {
baseName="r/${OS_IDENTIFIER}"
if [ -n "$S3_BUCKET" ] && [ "$S3_BUCKET" != "" ]; then
echo "Storing artifact on s3: ${S3_BUCKET}, tarball: ${TARBALL_NAME}"
aws s3 cp /tmp/${TARBALL_NAME} s3://${S3_BUCKET}/${S3_BUCKET_PREFIX}${baseName}/${TARBALL_NAME}
fi
if [ -n "$LOCAL_STORE" ] && [ "$LOCAL_STORE" != '' ]; then
echo "Storing artifact locally: ${LOCAL_STORE}, tarball: ${TARBALL_NAME}"
mkdir -p ${LOCAL_STORE}/${baseName}
cp /tmp/${TARBALL_NAME} ${LOCAL_STORE}/${baseName}/${TARBALL_NAME}.tar.gz
fi
}
# archive_r() - $1 as r version
archive_r() {
tar czf /tmp/${TARBALL_NAME} --directory=/opt/R ${1} --owner=0 --group=0
}
fetch_r_source() {
echo "Downloading R-${1}"
wget -q ${CRAN}/src/base/R-3/R-${1}.tar.gz -O /tmp/R-${1}.tar.gz
echo "Extracting R-${1}"
tar xf /tmp/R-${1}.tar.gz -C /tmp
rm /tmp/R-${1}.tar.gz
}
# On CentOS 6, we need to clean up references to the static library and header paths.
clean_r() {
if [[ -f /clean.sh ]]; then
echo "Cleaning R build on CentOS 6"
source /clean.sh
fi
}
# 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=x86_64-pc-linux-gnu'
if _version_is_greater_than ${R_VERSION} 3.2.2; then
build_flag=''
fi
# Default configure options. Some Dockerfiles override this with an ENV directive.
default_configure_options="\
--enable-R-shlib \
--with-tcltk \
--enable-memory-profiling \
--with-x \
--with-blas \
--with-lapack"
CONFIGURE_OPTIONS=${CONFIGURE_OPTIONS:-$default_configure_options}
# set some common environment variables for the configure step
AWK=/usr/bin/awk \
LIBnn=lib \
PAGER=/usr/bin/pager \
PERL=/usr/bin/perl \
R_PDFVIEWER=xdg-open \
R_BROWSER=xdg-open \
R_PAPERSIZE=letter \
R_PRINTCMD=/usr/bin/lpr \
R_UNZIPCMD=/usr/bin/unzip \
R_ZIPCMD=/usr/bin/zip \
./configure \
--prefix=/opt/R/${1} \
${CONFIGURE_OPTIONS} \
${build_flag}
make clean
make
make install
}
set_up_environment() {
mkdir -p /opt/R
}
_version_is_greater_than() {
test "$(printf '%s\n' "$@" | sort -V | head -n 1)" != "$1"
}
###### RUN R COMPILE PROCEDURE ######
set_up_environment
fetch_r_source $R_VERSION
compile_r $R_VERSION
clean_r
archive_r $R_VERSION
upload_r $R_VERSION

14
builder/clean_centos6.sh Executable file
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#!/bin/bash
# For CentOS 6, we need to clean references to the static library and header paths
# out of the R configuration files
sed -i 's|-Wl,--whole-archive /tmp/extra/lib/libz.a /tmp/extra/lib/libbz2.a /tmp/extra/lib/liblzma.a /tmp/extra/lib/libpcre.a /tmp/extra/lib/libcurl.a -Wl,--no-whole-archive -L/tmp/extra/lib/||g' /opt/R/${R_VERSION}/lib/R/etc/Makeconf
sed -i 's|-Wl,--whole-archive /tmp/extra/lib/libz.a /tmp/extra/lib/libbz2.a /tmp/extra/lib/liblzma.a /tmp/extra/lib/libpcre.a /tmp/extra/lib/libcurl.a -Wl,--no-whole-archive -L/tmp/extra/lib/||g' /opt/R/${R_VERSION}/lib/pkgconfig/libR.pc
sed -i 's|-ldl -lpthread .* -lldap -lz -lrt||g' /opt/R/${R_VERSION}/lib/R/etc/Makeconf
sed -i 's|-ldl -lpthread .* -lldap -lz -lrt||g' /opt/R/${R_VERSION}/lib/pkgconfig/libR.pc
sed -i 's|-I/tmp/extra/include||g' /opt/R/${R_VERSION}/lib/R/etc/Makeconf
sed -i 's|-I/tmp/extra/include||g' /opt/R/${R_VERSION}/lib/R/bin/libtool
sed -i 's|-ldl -lpthread .* -lldap -lz||g' /opt/R/${R_VERSION}/lib/R/etc/Makeconf
sed -i 's|-ldl -lpthread .* -lldap||g' /opt/R/${R_VERSION}/lib/R/etc/Makeconf
sed -i 's|:/tmp/extra/lib||g' /opt/R/${R_VERSION}/lib/R/etc/ldpaths
sed -i 's|/tmp/extra/lib||g' /opt/R/${R_VERSION}/lib/R/etc/ldpaths

80
builder/docker-compose.yml Normal file
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version: '2.0'
services:
ubuntu-1604:
command: ./build.sh
environment:
- R_VERSION=${R_VERSION}
- LOCAL_STORE=/tmp/output
build:
context: .
dockerfile: Dockerfile.ubuntu-1604
image: r-builds:ubuntu-1604
volumes:
- ./integration/tmp:/tmp/output
ubuntu-1804:
command: ./build.sh
environment:
- R_VERSION=${R_VERSION}
- LOCAL_STORE=/tmp/output
build:
context: .
dockerfile: Dockerfile.ubuntu-1804
image: r-builds:ubuntu-1804
volumes:
- ./integration/tmp:/tmp/output
debian-9:
command: ./build.sh
environment:
- R_VERSION=${R_VERSION}
- LOCAL_STORE=/tmp/output
build:
context: .
dockerfile: Dockerfile.debian-9
image: r-builds:debian-9
volumes:
- ./integration/tmp:/tmp/output
centos-6:
command: ./build.sh
environment:
- R_VERSION=${R_VERSION}
- LOCAL_STORE=/tmp/output
build:
context: .
dockerfile: Dockerfile.centos-6
image: r-builds:centos-6
volumes:
- ./integration/tmp:/tmp/output
centos-7:
command: ./build.sh
environment:
- R_VERSION=${R_VERSION}
- LOCAL_STORE=/tmp/output
build:
context: .
dockerfile: Dockerfile.centos-7
image: r-builds:centos-7
volumes:
- ./integration/tmp:/tmp/output
opensuse-42:
command: ./build.sh
environment:
- R_VERSION=${R_VERSION}
- LOCAL_STORE=/tmp/output
build:
context: .
dockerfile: Dockerfile.opensuse-42
image: r-builds:opensuse-42
volumes:
- ./integration/tmp:/tmp/output
opensuse-15:
command: ./build.sh
environment:
- R_VERSION=${R_VERSION}
- LOCAL_STORE=/tmp/output
build:
context: .
dockerfile: Dockerfile.opensuse-15
image: r-builds:opensuse-15
volumes:
- ./integration/tmp:/tmp/output

14
builder/env_centos6.sh Executable file
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# Test to see if $R_VERSION is <= 3.1.3. If so, append some additional configure options
# to the $CONFIGURE_OPTIONS env var.
NEWLINE=$'\n'
if [[ "$(printf '%s\n' "${R_VERSION}${NEWLINE}3.1.3" | sort -V | head -n 1)" == "$R_VERSION" ]]; then \
export CONFIGURE_OPTIONS="${CONFIGURE_OPTIONS} \
--with-system-zlib \
--with-system-bzlib \
--with-system-pcre \
--with-system-xz"
fi
# Get library linking information from CURL. This is then used to populate LDFLAGS
export CURL_LIBS="`/tmp/extra/bin/curl-config --libs`"
export LDFLAGS="-ldl -lpthread -lc -lrt -Wl,--as-needed -Wl,--whole-archive /tmp/extra/lib/libz.a /tmp/extra/lib/libbz2.a /tmp/extra/lib/liblzma.a /tmp/extra/lib/libpcre.a /tmp/extra/lib/libcurl.a -Wl,--no-whole-archive -L/tmp/extra/lib/ ${CURL_LIBS}"

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import os
from bs4 import BeautifulSoup
import requests
import json
import boto3
import botocore
CRAN_SRC_R_URL = 'https://cran.rstudio.com/src/base/R-3/'
batch_client = boto3.client('batch', region_name='us-east-1')
def _to_list(input):
"""Normalize a list (list or string) to list."""
if isinstance(input, list):
return input
return input.split(',')
def _persist_r_versions(data):
"""Ship current list to s3."""
s3 = boto3.resource('s3')
obj = s3.Object(os.environ['S3_BUCKET'], 'r/versions.json')
obj.put(Body=json.dumps(data), ContentType='application/json')
def _cran_r_versions():
"""Perform a lookup of CRAN-known R version."""
r = requests.get(CRAN_SRC_R_URL)
soup = BeautifulSoup(r.text, 'html.parser')
r_versions = []
for link in soup.find_all('a'):
href = link.get('href')
if 'R-' in href:
v = href.replace('.tar.gz', '').replace('R-', '')
if '-revised' not in v: # reject 3.2.4-revised
r_versions.append(v)
return {'r_versions': r_versions}
def _known_r_versions():
"""Ship current list to s3."""
try:
s3 = boto3.resource('s3')
obj = s3.Object(os.environ['S3_BUCKET'], 'r/versions.json')
str = obj.get()['Body'].read().decode('utf-8')
except botocore.exceptions.ClientError:
print('Key not found, using empty list')
str = '{"r_versions":[]}'
return json.loads(str)
def _compare_versions(fresh, known):
"""Compare fresh cran list to new list and return unknown versions."""
new = set(fresh) - set(known)
return list(new)
def _container_overrides(version):
"""Generate container override parameter for jobs."""
overrides = {}
overrides['environment'] = [
{'name': 'R_VERSION', 'value': version},
{'name': 'S3_BUCKET', 'value': os.environ['S3_BUCKET']}
]
return overrides
def _submit_job(version, platform):
"""Submit an R build job to AWS Batch."""
job_name = '-'.join(['R', version, platform])
job_name = job_name.replace('.', '_')
job_definition_arn = 'JOB_DEFINITION_ARN_{}'.format(platform.replace('-','_'))
args = {
'jobName': job_name,
'jobQueue': os.environ['JOB_QUEUE_ARN'],
'jobDefinition': os.environ[job_definition_arn],
'containerOverrides': _container_overrides(version)
}
if os.environ.get('DRYRUN'):
print('DRYRUN: would have queued {}'.format(job_name))
return 'dryrun-no-job-{}'.format(job_name)
else:
response = batch_client.submit_job(**args)
print("Started job for R:{},Platform:{},id:{}".format(version, platform, response['jobId']))
return response['jobId']
def _versions_to_build(force):
cran_versions = _cran_r_versions()['r_versions']
known_versions = _known_r_versions()['r_versions']
new_versions = _compare_versions(cran_versions, known_versions)
if len(new_versions) > 0:
print('New R Versions found: %s' % new_versions)
_persist_r_versions(_cran_r_versions())
if force in [True, 'True', 'true']:
return cran_versions
else:
return new_versions
def _check_for_job_status(jobs, status):
"""Return a subset of job ids which match a given status."""
r = batch_client.list_jobs(jobQueue=os.environ['JOB_QUEUE_ARN'], jobStatus=status)
return [i['jobId'] for i in r['jobSummaryList'] if i['jobId'] in jobs]
def queue_builds(event, context):
"""Queue some builds."""
event['versions_to_build'] = _versions_to_build(event.get('force', False))
event['supported_platforms'] = _to_list(os.environ.get('SUPPORTED_PLATFORMS', 'ubuntu-1604'))
job_ids = []
for version in event['versions_to_build']:
for platform in event['supported_platforms']:
# skip bionic builds with a configure script bug
if (platform == 'ubuntu-1804' or platform == 'opensuse-15') and version in ['3.3.0', '3.3.1', '3.3.2']:
continue
job_ids.append(_submit_job(version, platform))
event['jobIds'] = job_ids
return event
def poll_running_jobs(event, context):
"""Query job queue for current queue depth."""
event['failedJobIds'] = _check_for_job_status(event['jobIds'], 'FAILED')
event['succeededJobIds'] = _check_for_job_status(event['jobIds'], 'SUCCEEDED')
event['failedJobCount'] = len(event['failedJobIds'])
event['finishedJobCount'] = len(event['failedJobIds']) + len(event['succeededJobIds'])
event['unfinishedJobCount'] = len(event['jobIds']) - event['finishedJobCount']
return event

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jenkins/Dockerfile Normal file
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FROM node:8
ARG JENKINS_UID=386
ARG JENKINS_GID=386
ARG DOCKER_GID=999
RUN apt-get update -qq && apt-get install -y python-pip
RUN pip install awscli
# install docker cli
RUN wget -q -O /tmp/docker-cli.deb https://download.docker.com/linux/debian/dists/stretch/pool/stable/amd64/docker-ce-cli_18.09.2~3-0~debian-stretch_amd64.deb \
&& dpkg -i /tmp/docker-cli.deb
RUN npm install -g serverless
# Create the jenkins user with the same id:gid as the jenkins node
RUN groupadd -g $JENKINS_GID jenkins \
&& useradd -m -d /var/lib/jenkins -u $JENKINS_UID -g jenkins jenkins
# create docker group, add jenkins user to it
RUN groupadd -g $DOCKER_GID docker \
&& usermod -aG docker jenkins
USER jenkins

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package.json Normal file
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{
"name": "r-builds",
"description": "",
"version": "0.1.0",
"dependencies": {},
"devDependencies": {
"serverless-pseudo-parameters": "^2.2.0",
"serverless-python-requirements": "^4.2.5",
"serverless-step-functions": "^1.8.0"
}
}

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