RShiny base image

shiny for R

  • Dockerfile

  • add a point on the format of packages_to_install.csv, and how we install it

In this part, we will described the specific Dockerfile for R.

Dockerfile.r

Here the content of the Dockefile.r

 1# Build image from base image `ubuntu`
 2FROM ubuntu:${UBUNTU_VERSION}
 3
 4# define geographic location during R installation
 5ENV TZ=Etc/UTC
 6ENV DEBIAN_FRONTEND=noninteractive
 7ENV SHINY_LOG_STDERR=1
 8
 9EXPOSE 3838
10CMD ["shiny-server"]
11
12# install dependencies
13RUN apt-get update \
14&& apt-get install -y \
15        nano \
16        wget \
17        curl \
18        lsb-release \
19        libcurl4-openssl-dev \
20        gcc \
21        gfortran \
22        g++ \
23        libreadline-dev \
24        zlib1g-dev \
25        libbz2-dev \
26        liblzma-dev \
27        libpcre2-dev \
28        libcairo-dev \
29        libpng-dev \
30        libicu-dev \
31        libxml2-dev \
32        libssl-dev \
33        make \
34        libtiff-dev \
35        xorg-dev \
36        libx11-dev \
37&& rm -rf /var/lib/apt/lists/*
38
39# Copy only this installation script so new R package won't invalidate it installation
40COPY ./scripts/install_r_cran.sh /opt/scripts/install_r_cran.sh
41
42# Copy the R archive is already present, otherwise it will be downloaded
43# COPY ./R*.tar.gz /tmp/
44
45ARG R_VERSION=latest
46# Install R, along with its dependencies
47RUN /opt/scripts/install_r_cran.sh
48# Test R in another layer
49RUN R -q -e "sessionInfo(); capabilities()"
50
51# Copy the remaining scripts
52COPY ./scripts /opt/scripts
53
54ARG SHINY_SERVER_VERSION=latest
55# Install R packages included Shiny, then install shiny server
56RUN /opt/scripts/configure_Rprofile.sh  \
57&& Rscript /opt/scripts/install_r_packages.R
58RUN /opt/scripts/install_shiny_server.sh
59
60# allows trafic from all ips
61RUN sed -i "s/3838/3838 0.0.0.0/g" /etc/shiny-server/shiny-server.conf
62
63# grant shiny to created bookmark state directory in /var/lib/
64# grant shiny to write logs in /var/log/
65# grant shiny to write in /srv/shiny-server/www/
66RUN chown shiny:shiny /var/lib/shiny-server \
67&& mkdir -p /var/log/shiny-server \
68&& chown shiny:shiny /var/log/shiny-server \
69&& mkdir -p /srv/shiny-server/www \
70&& chown shiny:shiny /srv/shiny-server/www

Line 2: The base image

1# Build image from base image `ubuntu`
2FROM ubuntu:focal

The FROM ... indicate which base image should be used, the image contains:

  • an OS, here ubuntu, either focal (LTS 20.04) or jammy (LTS 22.01)

  • R’s “shiny” package

  • the shiny-server

In the gitlab-ci.yml, we decide to provide selected version of R base image based on several R version and compatible with kubernetes architecture deployed at Pasteur. Actually (Sept. 2023), three versions are available and mentionned in the file gitlab-ci.yml`, as you can see extract below :

1...
2  - LANGUAGE: ["r"]
3    R_VERSION: [
4       "3.6.3",
5       "4.2.3",
6       "4.3.1",
7    ]
8
9...

For more details about gitlab-ci.yml, please see the dedicated pages for gitlab-ci.yml.

Lines 5-7 : Environment variables

4# Define geographic location during installation
5ENV TZ=Etc/UTC
6ENV DEBIAN_FRONTEND=noninteractive
7ENV SHINY_LOG_STDERR=1

Some environment variables need to be defined in the container and set parameters needed for shiny-server installation or configuration.

Here, we set :

  • line 5 : the System Timezone TZ to Etc/UT

  • line 6 : the debconf frontends (interaction with the debconf interface) DEBIAN_FRONTEND to noninteractive. noninteractive permit to have zero interaction while installing or upgrading the system via apt.

  • line 7 : the standard error output SHINY_LOG_STDERR to a non-empty value 1 . To saving individual process logs to disk, Shiny Server can also relay those logs to its own stderr (which, by default, is saved to /var/log/shiny-server.log).

Line 9 : Listen port for Shiny-server

9EXPOSE 3838

By default, Shiny Server listens on port 3838, so the default application will be available at http://<server-address>:3838. We decide to conserve the default port mentionned in the /etc/shiny-server/shiny-server.conf, configuration file of shiny-server.

The EXPOSE instruction informs Docker that the container listens on the specified network ports at runtime. So, here we indicate the 3838 listen port.

Warning

If you change the default value of listen port, you must modify it also the /etc/shiny-server/shiny-server.conf.
More details below in the section line 61

Line 10 : Run Shiny-server

10CMD ["shiny-server"]

The main purpose of a CMD is to provide defaults for an executing container. Here, CMD ["shiny-server"] permits to launch the shiny-server, normally run by the command line shiny-server. Thanks to CMD, the shiny-server will be launch by default when the container will be run.

Note

Threre can only be one CMD instruction in a Dockerfile.

Lines 13-37 : The system dependencies

12# Install dependencies
13RUN apt-get update \
14&& apt-get install -y \
15    nano \
16    wget \
17    curl \
18    lsb-release \
19    libcurl4-openssl-dev \
20    gcc \
21    gfortran \
22    g++ \
23    libreadline-dev \
24    zlib1g-dev \
25    libbz2-dev \
26    liblzma-dev \
27    libpcre2-dev \
28    libcairo-dev \
29    libpng-dev \
30    libicu-dev \
31    libxml2-dev \
32    libssl-dev \
33    make \
34    libtiff-dev \
35    xorg-dev \
36    libx11-dev \
37 && rm -rf /var/lib/apt/lists/*

Shiny-server require some system dependencies. Here, we use the apt-get command line in order to install all dependencies requiered in the container.

Note

You can add system packages will be requiered by your future shiny app but don’t delete one in these previous list.

Lines 40-49 : Installation of R

41# Copy only this installation script so new R package won't invalidate it installation
42COPY ./scripts/install_r_cran.sh /opt/scripts/install_r_cran.sh
43
44# Copy the R archive is already present, otherwise it will be downloaded
45# COPY ./R*.tar.gz /tmp/
46
47ARG R_VERSION=latest
48# Install R, along with its dependencies
49RUN /opt/scripts/install_r_cran.sh
50# Test R in another layer
51RUN R -q -e "sessionInfo(); capabilities()"
Line 42 allow the copy of /opt/scripts/install_r_cran.sh file.
Line 49 run this script.
Line 51 permits to test if R session can be run inside the container.

More details about this bash script install_r_cran.sh in the helper script section

Lines 51-57 : Install R Packages

51# Copy the remaining scripts
52COPY ./scripts /opt/scripts
53
54ARG SHINY_SERVER_VERSION=latest
55# Install R packages included Shiny, then install shiny server
56RUN /opt/scripts/configure_Rprofile.sh  \
57&& Rscript /opt/scripts/install_r_packages.R
The line 52 allow the copy of content folder named scripts (files available in shiny-k8s gitlab project).
The line 54 set the variable SHINY_SERVER_VERSION to value latest.
The line 56-57 launch bash script configure_Rprofile.sh and R script install_r_packages.R.
More details about this bash script configure_Rprofile.sh in the helper script section
More details about this R script install_r_packages.R in the helper script section

Line 58 : Installation Shiny Server

58RUN /opt/scripts/install_shiny_server.sh

The instruction line 58 just run the bash script install_shiny_server.s

More details about the bash script in the helper scripts section

Line 61 : Custom Shiny-server configuration file

60# Allows trafic from all ips
61RUN sed -i "s/3838/3838 0.0.0.0/g" /etc/shiny-server/shiny-server.conf

In order to access correctly to your app, we set again the listen port in the specific configuration file of shiny-server. The line 61 permits to set the chosen values in the /etc/shiny-server/shiny-server.conf

Lines 66-70 : Permissions

63# Grant shiny to created bookmark state directory in /var/lib/
64# Grant shiny to write logs in /var/log/
65# Grant shiny to write in /srv/shiny-server/www/
66RUN chown shiny:shiny /var/lib/shiny-server \
67&& mkdir -p /var/log/shiny-server \
68&& chown shiny:shiny /var/log/shiny-server \
69&& mkdir -p /srv/shiny-server/www \
70&& chown shiny:shiny /srv/shiny-server/www

By default, Shiny Server will create and store data in /var/lib/shiny-server/. instruction line 57 permits to allow the user shiny to write in this dedicated folder.

All information related to Shiny Server itself, rather than a particular Shiny application, is logged in the global system log stored in /var/log/shiny-server.log. This log should be checked often to ensure Shiny Server is performing as expected. Any errors and warnings that Shiny Server needs to communicate will be written here. In order to access these log files, we grant the user shiny to write in the dedicated folder (lines 66-70).

In order to share easily data with the futur user of the shiny app, we add instruction to allow user shiny to access at /srv/shiny-server/www folder.

Note

More details about the content of Dockerfile in Dockerfile reference