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Jenkinsfile
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pipeline {
agent any
options {
buildDiscarder(logRotator(numToKeepStr: '3'))
}
environment {
IMAGE = 'mergeion2'
NS = 'mergeion2'
REGISTRY = '196229073436.dkr.ecr.eu-west-1.amazonaws.com'
TAG = sh(returnStdout: true, script: "echo $BRANCH_NAME | sed -e 's/[A-Z]/\\L&/g' -e 's/[^a-z0-9._-]/./g'").trim()
REGION = 'eu-west-1'
NOT_CRAN = 'true'
}
stages {
stage('Build Image') {
agent {
kubernetes {
yaml '''
apiVersion: v1
kind: Pod
spec:
containers:
- name: kaniko
image: gcr.io/kaniko-project/executor:v1.5.2-debug
env:
- name: AWS_SDK_LOAD_CONFIG
value: "true"
command:
- /kaniko/docker-credential-ecr-login
- get
tty: true
resources:
requests:
memory: "2048Mi"
ephemeral-storage: "2Gi"
limits:
memory: "4096Mi"
ephemeral-storage: "8Gi"
imagePullPolicy: Always
- name: aws-cli
image: amazon/aws-cli:2.1.33
command:
- cat
tty: true
resources:
requests:
memory: "100Mi"
limits:
memory: "2048Mi"'''
defaultContainer 'kaniko'
}
}
steps {
container('aws-cli') {
sh """aws --region ${env.REGION} ecr describe-repositories \
--repository-names ${env.NS}/${env.IMAGE} \
|| aws --region ${env.REGION} ecr create-repository \
--repository-name ${env.NS}/${env.IMAGE}"""
}
container('kaniko') {
sh """/kaniko/executor \
-v info \
--context ${env.WORKSPACE} \
--cache=true \
--cache-ttl=8760h0m0s \
--cache-repo ${env.REGISTRY}/${env.NS}/${env.IMAGE} \
--cleanup \
--destination ${env.REGISTRY}/${env.NS}/${env.IMAGE}:${env.TAG} \
--registry-mirror ${env.REGISTRY}"""
}
}
}
stage('Packages') {
agent {
kubernetes {
yaml """
apiVersion: v1
kind: Pod
spec:
containers:
- name: r
image: ${env.REGISTRY}/${env.NS}/${env.IMAGE}:${env.TAG}
command:
- cat
tty: true
imagePullPolicy: Always"""
defaultContainer 'r'
}
}
stages {
stage('MergeION') {
stages {
stage('Rcpp Compile Attributes') {
steps {
sh 'R -q -e \'if (requireNamespace("Rcpp", quietly = TRUE)) Rcpp::compileAttributes(".")\''
}
}
stage('Roxygen') {
steps {
sh 'R -q -e \'roxygen2::roxygenize(".")\''
}
}
stage('Build') {
steps {
sh 'R CMD build .'
}
}
stage('Check') {
steps {
script() {
switch(sh(script: 'ls MergeION_*.tar.gz && R CMD check MergeION_*.tar.gz --no-manual', returnStatus: true)) {
case 0: currentBuild.result = 'SUCCESS'
default: currentBuild.result = 'FAILURE'; error('script exited with failure status')
}
}
}
}
stage('Install') {
steps {
sh 'R -q -e \'install.packages(list.files(".", "MergeION_.*.tar.gz"), repos = NULL)\''
}
}
stage('Test and coverage') {
steps {
dir('.') {
sh '''R -q -e \'code <- "testthat::test_package(\\"MergeION\\", reporter = testthat::MultiReporter$new(list(testthat::SummaryReporter$new(file = file.path(getwd(), \\"test-results.txt\\")), testthat::JunitReporter$new(file = file.path(getwd(), \\"results.xml\\")))))"\''''
// packageCoverage <- covr::package_coverage(type = "none", code = code)
// cat(readLines(file.path(getwd(), "test-results.txt")), sep = "\n")
//covr::to_cobertura(packageCoverage)
}
}
/*post {
always {
dir('.') {
junit 'results.xml'
cobertura autoUpdateHealth: false, autoUpdateStability: false, coberturaReportFile: 'cobertura.xml', conditionalCoverageTargets: '70, 0, 0', failUnhealthy: false, failUnstable: false, lineCoverageTargets: '80, 0, 0', maxNumberOfBuilds: 0, methodCoverageTargets: '80, 0, 0', onlyStable: false, sourceEncoding: 'ASCII', zoomCoverageChart: false
}
}
} */
}
}
}
stage('Archive artifacts') {
steps {
archiveArtifacts artifacts: '*.tar.gz, *.pdf, **/00check.log', fingerprint: true
}
}
}
}
}
}