Merge branch 'install-specific-version' into 'main'

Download and install specific version

See merge request hub/rshiny-k8s!5

.gitlab-ci.yml

@@ -9,21 +9,72 @@ build:
     - docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
   script:
     - docker --version
-    # pull the latest build on master
-    - docker pull "$CI_REGISTRY_IMAGE/master:latest" || true
-    # pull the latest build on this branch
+    # put both versions in a env var, to be used as tag
+    - |
+      if [ "latest" == "${R_VERSION}" ]; then
+        export VERSIONS_TAG="${SHINY_SERVER_VERSION}"
+      else
+        if [ "latest" == "${SHINY_SERVER_VERSION}" ]; then
+          export VERSIONS_TAG="${R_VERSION}"
+        else
+          export VERSIONS_TAG="${R_VERSION}--${SHINY_SERVER_VERSION}"
+        fi
+      fi
+    # pull the latest build
+    - docker pull "$CI_REGISTRY_IMAGE:latest" || true
+    # pull the latest build of the targeted versions
+    - docker pull "$CI_REGISTRY_IMAGE:$VERSIONS_TAG" || true
+    # pull the latest build of the target R version in order to re-use it for the targeted SHINY_SERVER_VERSION
+    - docker pull "$CI_REGISTRY_IMAGE:$R_VERSION" || true
+    # pull the latest build of main
+    - docker pull "$CI_REGISTRY_IMAGE/main:latest" || true
+    # pull the latest build of this branch
     - docker pull "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG:latest" || true
-    # build the image while passing commit SHA and tagging the image with it
+    # build the image while passing commit SHA and versions, and tagging the image with them
     - docker build
-      --build-arg CI_COMMIT_REF_SLUG
-      --build-arg CI_COMMIT_SHA
+      --build-arg R_VERSION
+      --build-arg SHINY_SERVER_VERSION
       --cache-from "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG:latest"
-      --cache-from "$CI_REGISTRY_IMAGE/master:latest"
+      --cache-from "$CI_REGISTRY_IMAGE/main:latest"
+      --cache-from "$CI_REGISTRY_IMAGE:$VERSIONS_TAG"
+      --cache-from "$CI_REGISTRY_IMAGE:$R_VERSION"
+      --cache-from "$CI_REGISTRY_IMAGE:latest"
       --tag "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG:$CI_COMMIT_SHA"
       --tag "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG:latest"
+      --tag "$CI_REGISTRY_IMAGE:$VERSIONS_TAG"
+      --tag "$CI_REGISTRY_IMAGE:$VERSIONS_TAG--$CI_COMMIT_SHORT_SHA"
       -f Dockerfile
       ./
     # push image as latest for the current branch
     - docker push "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG:latest"
     # push image tagged with its sha
     - docker push "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG:$CI_COMMIT_SHA"
+    # push image tagged with its versions
+    - docker push "$CI_REGISTRY_IMAGE:$VERSIONS_TAG"
+    # push image tagged with its versions and the commit sha (debug purpose)
+    - docker push "$CI_REGISTRY_IMAGE:$VERSIONS_TAG--$CI_COMMIT_SHORT_SHA"
+  parallel:
+    matrix:
+      - R_VERSION: ["3.6.3", "4.2.3", "latest"]
+        SHINY_SERVER_VERSION: ["latest"]
+
+
+build-example:
+  stage: build
+  needs: ["build"]
+  before_script:
+    - docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
+  script:
+    # pull the latest example of rshiny-k8s image
+    - docker pull "$CI_REGISTRY_IMAGE/example:example" || true
+    # build the image while passing commit SHA and versions, and tagging the image with them
+    - docker build
+      --cache-from "$CI_REGISTRY_IMAGE/example:latest"
+      --tag "$CI_REGISTRY_IMAGE/example:latest"
+      --tag "$CI_REGISTRY_IMAGE/example:$CI_COMMIT_SHORT_SHA"
+      -f example.Dockerfile
+      ./
+    # push image tagged as example
+    - docker push "$CI_REGISTRY_IMAGE/example:latest"
+    # push image tagged as example with its commit sha (debug purpose)
+    - docker push "$CI_REGISTRY_IMAGE/example:$CI_COMMIT_SHORT_SHA"

Dockerfile

@@ -3,7 +3,8 @@ FROM ubuntu:focal
 # define geographic location during R installation
 ENV TZ=Etc/UTC
 ENV DEBIAN_FRONTEND noninteractive
-ARG SHINY_SERVER_VERSION
+ARG SHINY_SERVER_VERSION=latest
+ARG R_VERSION=latest
 
 EXPOSE 3838
 CMD ["shiny-server"]
@@ -14,15 +15,30 @@ RUN apt-get update \
         nano \
         wget \
         curl \
-        r-base \
-        r-base-dev \
-        r-recommended \
         lsb-release \
- && rm -rf /var/lib/apt/lists/* \
- && R --version
+        libcurl4-openssl-dev \
+        gcc \
+        gfortran \
+        g++ \
+        libreadline-dev \
+        zlib1g-dev \
+        libbz2-dev \
+        liblzma-dev \
+        libpcre2-dev \
+        libcairo-dev \
+        libpng-dev \
+        libicu-dev \
+        make \
+        libtiff-dev \
+ && rm -rf /var/lib/apt/lists/*
 
 COPY ./scripts /opt/scripts
 
+#install R, along with its dependencies
+RUN /opt/scripts/install_r_cran.sh
+# test R in another layer
+RUN R -q -e "sessionInfo()"
+
 # Install R packages included Shiny, then install shiny server
 RUN Rscript /opt/scripts/install_r_packages.R
 RUN /opt/scripts/install_shiny_server.sh
@@ -30,9 +46,6 @@ RUN /opt/scripts/install_shiny_server.sh
 # allows trafic from all ips
 RUN sed -i "s/3838/3838 0.0.0.0/g" /etc/shiny-server/shiny-server.conf
 
-# copy my shiny app.
-COPY ./example_proj /srv/shiny-server
-
 #RUN chown shiny:shiny /var/lib/shiny-server
 RUN mkdir -p /var/log/shiny-server \
  && chown shiny:shiny /var/log/shiny-server

example-in-pod.yaml

+apiVersion: v1
+kind: Pod
+metadata:
+  name: example
+spec:
+  containers:
+    - name: example
+      image: registry-gitlab.pasteur.fr/hub/rshiny-k8s/example:latest
+      securityContext:
+        runAsGroup: 999
+        runAsUser: 999
+      ports:
+        - name: http
+          containerPort: 3838
+          protocol: TCP

example.Dockerfile

+# FROM registry-gitlab.pasteur.fr/hub/rshiny-k8s:4.2.3--1.5.21.1006
+# FROM registry-gitlab.pasteur.fr/hub/rshiny-k8s:1.5.21.1006
+# FROM registry-gitlab.pasteur.fr/hub/rshiny-k8s:4.2.3
+FROM registry-gitlab.pasteur.fr/hub/rshiny-k8s:latest
+
+# Copy your dependencies, destination filename must be "packages_to_install.csv"
+COPY ./example_proj/my_packages_to_install.csv /opt/scripts/packages_to_install.csv
+
+# Install R packages
+RUN Rscript /opt/scripts/install_r_packages.R
+
+# Copy you shiny app
+COPY ./example_proj /srv/shiny-server
+

example_proj/my_packages_to_install.csv

+Package_name;Deposit_name
+shiny;cran
+shinythemes;cran

scripts/install_r_cran.sh

+#!/bin/bash
+set -e
+
+R_VERSION=${1:-${R_VERSION:-latest}}
+R_HOME=${R_HOME:-"/usr/local/lib/R"}
+CRAN="https://cran.r-project.org"
+
+cd /tmp
+
+if [ ! -f "R-${R_VERSION}.tar.gz" ]; then
+    echo "/tmp/R-${R_VERSION}.tar.gz is missing, downloading it"
+    if [ "$R_VERSION" = "latest" ]; then
+        curl -O https://cran.r-project.org/src/base/R-latest.tar.gz
+    else
+        curl -O https://cran.rstudio.com/src/base/R-${R_VERSION::1}/R-${R_VERSION}.tar.gz
+    fi
+fi
+tar -xzvf R-${R_VERSION}.tar.gz
+
+# go in uncompressed dir, when using R_VERSION="R-latest", 
+# the dir is not R-latest, but the one with the version
+cd R-*/
+# Configure the sources, check dependencies
+./configure \
+    --enable-R-shlib \
+    --enable-memory-profiling \
+    --with-blas \
+    --with-lapack \
+    --with-x=no \
+    --with-cairo=yes \
+    --enable-java=no
+
+make
+make install
+
+echo "Install completed, testing R"
+
+R -q -e "sessionInfo()" || exit 1
+
+echo "R found in path, good to go!"
+
+make clean
+rm /tmp/R-${R_VERSION}.tar.gz
+
+cat <<EOF >"${R_HOME}/etc/Rprofile.site"
+options(
+    repos = c( CRAN = '${CRAN}'),
+    download.file.method = 'libcurl'
+)
+EOF