From 6b6a380aa6f0564cb15c3966bcb81279e39331f8 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 9 Oct 2025 11:32:06 +0200 Subject: [PATCH 01/31] gnu: switch to ftpmirror and https --- r-base/installAutomake.sh | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/r-base/installAutomake.sh b/r-base/installAutomake.sh index 1873c24..c3bd189 100755 --- a/r-base/installAutomake.sh +++ b/r-base/installAutomake.sh @@ -2,27 +2,27 @@ VERSION=${1} -if echo $VERSION | grep -q '\..*\..*'; then - MAJOR_VERSION=${VERSION%.*} -else - MAJOR_VERSION=${VERSION} +if echo $VERSION | grep -q '\..*\..*'; then + MAJOR_VERSION=${VERSION%.*} +else + MAJOR_VERSION=${VERSION} fi function install_automake() { - wget http://ftp.gnu.org/gnu/automake/automake-$VERSION.tar.gz \ - && tar -xvf automake-$VERSION.tar.gz \ - && cd automake-$VERSION \ - && ./configure --prefix=/usr/local/automake-$VERSION \ - && make \ - && make install \ - && cd .. \ - && rm automake-$VERSION.tar.gz \ - && rm -rf automake-$VERSION \ - && rm -f /usr/local/bin/aclocal-$VERSION \ - && rm -f /usr/local/bin/automake-$VERSION \ - && ln -s /usr/local/automake-$VERSION/bin/aclocal-$MAJOR_VERSION /usr/local/bin/aclocal-$MAJOR_VERSION \ - && ln -s /usr/local/automake-$VERSION/bin/automake-$MAJOR_VERSION /usr/local/bin/automake-$MAJOR_VERSION \ - && echo "Installed automake in version $VERSION" + wget https://ftpmirror.gnu.org/gnu/automake/automake-$VERSION.tar.gz && + tar -xvf automake-$VERSION.tar.gz && + cd automake-$VERSION && + ./configure --prefix=/usr/local/automake-$VERSION && + make && + make install && + cd .. && + rm automake-$VERSION.tar.gz && + rm -rf automake-$VERSION && + rm -f /usr/local/bin/aclocal-$VERSION && + rm -f /usr/local/bin/automake-$VERSION && + ln -s /usr/local/automake-$VERSION/bin/aclocal-$MAJOR_VERSION /usr/local/bin/aclocal-$MAJOR_VERSION && + ln -s /usr/local/automake-$VERSION/bin/automake-$MAJOR_VERSION /usr/local/bin/automake-$MAJOR_VERSION && + echo "Installed automake in version $VERSION" } -install_automake \ No newline at end of file +install_automake From 5b1035734002a154b107854565e2b130156134de Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Wed, 15 Oct 2025 17:27:54 +0200 Subject: [PATCH 02/31] change tag name (temporary) --- r-batch/Dockerfile | 2 +- r-geos/Dockerfile | 2 +- r-model/Dockerfile | 2 +- r-shiny/Dockerfile | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/r-batch/Dockerfile b/r-batch/Dockerfile index 128b632..0e1cca4 100644 --- a/r-batch/Dockerfile +++ b/r-batch/Dockerfile @@ -1,4 +1,4 @@ -FROM inwt/r-base:4.5.1 +FROM inwt/r-base:4.5.1.non-root COPY aws.config /app/.aws/config diff --git a/r-geos/Dockerfile b/r-geos/Dockerfile index 69da132..dd8a8fc 100644 --- a/r-geos/Dockerfile +++ b/r-geos/Dockerfile @@ -1,4 +1,4 @@ -FROM inwt/r-batch:4.5.1 +FROM inwt/r-batch:4.5.1.non-root RUN apt-get -y update \ && apt-get install -y --no-install-recommends \ diff --git a/r-model/Dockerfile b/r-model/Dockerfile index 518701d..2b38d97 100644 --- a/r-model/Dockerfile +++ b/r-model/Dockerfile @@ -1,4 +1,4 @@ -FROM inwt/r-batch:4.5.1 +FROM inwt/r-batch:4.5.1.non-root RUN apt-get -y update \ && apt-get install -y --no-install-recommends \ diff --git a/r-shiny/Dockerfile b/r-shiny/Dockerfile index 60da7df..4412c1a 100644 --- a/r-shiny/Dockerfile +++ b/r-shiny/Dockerfile @@ -1,4 +1,4 @@ -FROM inwt/r-batch:4.5.1 +FROM inwt/r-batch:4.5.1.non-root EXPOSE 3838 From 7d6f81948110928277a8eaaf86ad3767734bbd31 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Wed, 15 Oct 2025 18:29:26 +0200 Subject: [PATCH 03/31] r-base - introduce a multi stage build with a non-root user --- r-base/Dockerfile | 79 ++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 72 insertions(+), 7 deletions(-) diff --git a/r-base/Dockerfile b/r-base/Dockerfile index 9a3107c..ad0c534 100644 --- a/r-base/Dockerfile +++ b/r-base/Dockerfile @@ -1,20 +1,35 @@ -FROM rocker/r-ver:4.5.1 +# ---------------- +# Stage 1: builder +# ---------------- + +FROM rocker/r-ver:4.5.1 AS builder + +# 1. User and Environment Setup +ARG USER_NAME=user +ARG USER_UID=1000 +ARG USER_GID=1000 -WORKDIR /app -ENV HOME=/app ENV DEBIAN_FRONTEND=noninteractive ENV OPENBLAS_NUM_THREADS=1 ENV _R_CHECK_TESTS_NLINES_=0 ENV TZ="Europe/Berlin" ENV LANG=en_US.UTF-8 -ADD . /includes/ +# Create the non-root user (UID 1000:GID 1000) +RUN groupadd --gid ${USER_GID} ${USER_NAME} \ + && useradd --uid ${USER_UID} --gid ${USER_GID} -m -G staff ${USER_NAME} +WORKDIR /app +COPY . /includes/ + +# 2. System Dependencies, Timezone, and CA Certificates + # CA Certificates and Timezone Setup RUN mv -v /includes/*.crt /usr/local/share/ca-certificates/ \ && dpkg-reconfigure ca-certificates \ && rm /etc/localtime \ && ln -s /usr/share/zoneinfo/Europe/Berlin /etc/localtime \ && echo "Europe/Berlin" > /etc/timezone \ + # Install System Dependencies && apt-get -y update \ && apt-get -y upgrade \ && apt-get install -y --no-install-recommends \ @@ -42,7 +57,8 @@ RUN mv -v /includes/*.crt /usr/local/share/ca-certificates/ \ && apt-get autoclean -y \ && rm -rf /var/lib/apt/lists/* - # R things +# 3. R Environment Setup and Package Installation + # Link scripts RUN chmod +x /includes/*.R \ && ln -s /usr/local/lib/R/site-library/littler/examples/dratInsert.r /usr/local/bin/dratInsert.r \ && ln -s /includes/check.R /usr/local/bin/check \ @@ -52,15 +68,64 @@ RUN chmod +x /includes/*.R \ && ln -s /includes/installGithub.R /usr/local/bin/installGithub \ && ln -s /includes/installPackage.R /usr/local/bin/installPackage \ && ln -s /includes/installAutomake.sh /usr/local/bin/installAutomake \ + # Set Posit Package Manager as CRAN Mirror && echo "options(repos = c(CRAN = '$(Rscript /includes/get_mirror_date.R)'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \ - # temporary fix for stringr & libicu lib + # Install R Packages (stringi needs to be recompiled) && Rscript -e "options(warn = 2); install.packages('https://github.com/gagolews/stringi/releases/download/v1.8.7/stringi_1.8.7.tar.gz', repos = NULL, type = 'source')" \ && Rscript -e "options(warn = 2); install.packages(c('devtools', 'docopt', 'drat', 'modules'), Ncpus = parallel::detectCores())" \ && rm -rf /tmp/downloaded_packages/* \ + # Setup local repository && mkdir -p /r-repo/src/contrib \ && touch /r-repo/src/contrib/PACKAGES \ && echo "options(repos = c(getOption('repos'), LOCAL = 'file:////r-repo/'))" >> /usr/local/lib/R/etc/Rprofile.site \ && echo "options(repos = c(getOption('repos'), INWT = 'https://r-repo.core.cld.htz.int.inwt.de'))" >> /usr/local/lib/R/etc/Rprofile.site \ && echo "options(repos = c(getOption('repos'), INWTLab = 'https://inwtlab.github.io/drat/'))" >> /usr/local/lib/R/etc/Rprofile.site \ && echo "options(dratRepo = '/r-repo/')" >> /usr/local/lib/R/etc/Rprofile.site \ - && chmod --recursive o+w /usr/local/lib/R/site-library + # Set ownership for site-library, local r-repo & R scriüts + && chown -R ${USER_NAME}:${USER_NAME} /usr/local/lib/R/site-library/ \ + && chown -R ${USER_NAME}:${USER_NAME} /r-repo \ + && chown -R ${USER_NAME}:${USER_NAME} /includes + +# -------------- +# Stage 2: final +# -------------- +FROM rocker/r-ver:4.5.1 + +# 1. Environment and User Setup +ARG USER_NAME=user +ARG USER_UID=1000 +ARG USER_GID=1000 + +# Re-create the non-root user in the final stage (since this is a new base layer) +RUN groupadd --gid ${USER_GID} ${USER_NAME} \ + && useradd --uid ${USER_UID} --gid ${USER_GID} -m -G staff ${USER_NAME} + +# Set runtime environment variables +ENV HOME=/app +ENV TZ="Europe/Berlin" +ENV LANG=en_US.UTF-8 + +# 2. Copy Artifacts from the builder stage +COPY --from=builder /usr/local/bin/ /usr/local/bin/ +COPY --from=builder /usr/local/lib/R/site-library/ /usr/local/lib/R/site-library/ +COPY --from=builder /usr/local/lib/R/etc/Rprofile.site /usr/local/lib/R/etc/Rprofile.site +COPY --from=builder /r-repo/ /r-repo/ + +# 3. Add all utility scripts +RUN mkdir -p /includes/check-lib + +COPY --from=builder /includes/build.R /includes/build.R +COPY --from=builder /includes/check.R /includes/check.R +COPY --from=builder /includes/installPackage.R /includes/installPackage.R +COPY --from=builder /includes/installGithub.R /includes/installGithub.R +COPY --from=builder /includes/register-dependencies.R /includes/register-dependencies.R +COPY --from=builder /includes/validate-settings.R /includes/validate-settings.R +COPY --from=builder /includes/check-lib/ /includes/check-lib/ + +RUN chown -R ${USER_NAME}:${USER_NAME} /includes + +# 3. Set User and Workdir +USER ${USER_NAME} +WORKDIR ${HOME} + +CMD ["R"] From 6205327bb794859480958b9d999f5894184e5faa Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 12:03:41 +0200 Subject: [PATCH 04/31] r-batch - remove aws config --- r-batch/aws.config | 2 -- 1 file changed, 2 deletions(-) delete mode 100644 r-batch/aws.config diff --git a/r-batch/aws.config b/r-batch/aws.config deleted file mode 100644 index a5220e0..0000000 --- a/r-batch/aws.config +++ /dev/null @@ -1,2 +0,0 @@ -[default] -region = eu-central-1 From cdf071cb3a980c7b0597225c31252520f0907675 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 12:03:57 +0200 Subject: [PATCH 05/31] r-batch - introduce a multi stage build with a non-root user --- r-batch/Dockerfile | 110 +++++++++++++++++++++++++++++---------------- 1 file changed, 72 insertions(+), 38 deletions(-) diff --git a/r-batch/Dockerfile b/r-batch/Dockerfile index 0e1cca4..6e75c16 100644 --- a/r-batch/Dockerfile +++ b/r-batch/Dockerfile @@ -1,46 +1,80 @@ -FROM inwt/r-base:4.5.1.non-root +# ---------------- +# Stage 1: builder +# ---------------- +FROM inwt/r-base:4.5.1.non-root AS batch-builder + +# 1. User and Enviroment Setup +ARG USER_NAME=user -COPY aws.config /app/.aws/config +# 2. System Dependencies +USER root RUN apt-get -y update \ + && apt-get -y upgrade \ && apt-get install -y --no-install-recommends \ - curl \ - openjdk-8-jdk \ - libbz2-dev \ - liblzma-dev \ - libpcre3-dev \ - libpcre2-dev \ - libmysqlclient-dev \ - libpq-dev \ - && apt-get autoremove -y \ - && apt-get autoclean -y \ - && rm -rf /var/lib/apt/lists/* \ + curl \ + openjdk-8-jdk \ + libbz2-dev \ + liblzma-dev \ + libmysqlclient-dev \ + libpcre3-dev \ + libpcre2-dev \ + libpq-dev \ + # AWS CLI && curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.25.13.zip" -o "awscliv2.zip" \ && unzip awscliv2.zip \ && ./aws/install \ - && rm -rf aws awscliv2.zip - -# R things -RUN R CMD javareconf \ - && installPackage \ - arrow \ - codetools \ - data.table \ - dplyr \ - futile.logger \ - gbm \ - ggplot2 \ - gridExtra \ - lintr \ - lme4 \ - mgcv \ - RClickhouse \ - rJava \ - RMySQL \ - roxygen2 \ - RPostgres \ - testthat \ - tidyr \ - dbtools \ - mctools \ + # Cleanup + && apt-get autoremove -y \ + && apt-get autoclean -y \ + && rm -rf /var/lib/apt/lists/* aws awscliv2.zip + +# 3. Configure Java & R Packages Installation +RUN R CMD javareconf +USER ${USER_NAME} +RUN installPackage \ + arrow \ + codetools \ + data.table \ + dplyr \ + futile.logger \ + gbm \ + ggplot2 \ + gridExtra \ + lintr \ + lme4 \ + mgcv \ + RClickhouse \ + rJava \ + RMySQL \ + roxygen2 \ + RPostgres \ + testthat \ + tidyr \ + dbtools \ + mctools \ && rm -rf /tmp/downloaded_packages/* + +# -------------- +# Stage 2: final +# -------------- +FROM inwt/r-base:4.5.1.non-root + +# 1. Enviroment and User Setup +ARG USER_NAME=user + +ENV HOME=/app + +# 2. Copy Artifacts (R libaries & aws cli) from builder stage +COPY --from=batch-builder /usr/local/lib/R/site-library/ /usr/local/lib/R/site-library/ +USER root +COPY --from=batch-builder /usr/local/aws-cli/ /usr/local/aws-cli/ +# create symlinks for aws cli +RUN ln -s /usr/local/aws-cli/v2/current/bin/aws /usr/local/bin/aws \ + && ln -s /usr/local/aws-cli/v2/current/bin/aws_completer /usr/local/bin/aws_completer + +# 3. Set User and Workdir +USER ${USER_NAME} +WORKDIR ${HOME} + +CMD ["R"] From ade12c28ae0566711019968f1a251ba8de364872 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 12:53:43 +0200 Subject: [PATCH 06/31] r-shiny - add installAutomake.sh to r-shiny --- r-shiny/installAutomake.sh | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100755 r-shiny/installAutomake.sh diff --git a/r-shiny/installAutomake.sh b/r-shiny/installAutomake.sh new file mode 100755 index 0000000..c3bd189 --- /dev/null +++ b/r-shiny/installAutomake.sh @@ -0,0 +1,28 @@ +#!/bin/bash + +VERSION=${1} + +if echo $VERSION | grep -q '\..*\..*'; then + MAJOR_VERSION=${VERSION%.*} +else + MAJOR_VERSION=${VERSION} +fi + +function install_automake() { + wget https://ftpmirror.gnu.org/gnu/automake/automake-$VERSION.tar.gz && + tar -xvf automake-$VERSION.tar.gz && + cd automake-$VERSION && + ./configure --prefix=/usr/local/automake-$VERSION && + make && + make install && + cd .. && + rm automake-$VERSION.tar.gz && + rm -rf automake-$VERSION && + rm -f /usr/local/bin/aclocal-$VERSION && + rm -f /usr/local/bin/automake-$VERSION && + ln -s /usr/local/automake-$VERSION/bin/aclocal-$MAJOR_VERSION /usr/local/bin/aclocal-$MAJOR_VERSION && + ln -s /usr/local/automake-$VERSION/bin/automake-$MAJOR_VERSION /usr/local/bin/automake-$MAJOR_VERSION && + echo "Installed automake in version $VERSION" +} + +install_automake From f03fe067b97c9028f6dca7e9bf0064d819c2010c Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 12:53:57 +0200 Subject: [PATCH 07/31] r-shiny - introduce a multi stage build with a non-root user --- r-shiny/Dockerfile | 77 +++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 69 insertions(+), 8 deletions(-) diff --git a/r-shiny/Dockerfile b/r-shiny/Dockerfile index 4412c1a..a07482f 100644 --- a/r-shiny/Dockerfile +++ b/r-shiny/Dockerfile @@ -1,17 +1,32 @@ -FROM inwt/r-batch:4.5.1.non-root +# ---------------- +# Stage 1: builder +# ---------------- +FROM inwt/r-batch:4.5.1.non-root AS shiny-builder -EXPOSE 3838 +# 1. User and Enviroment Setup +ARG USER_NAME=user -RUN installAutomake 1.16.1 \ - && apt-get update \ - && apt-get install -y \ +# 2. System Dependencies +COPY installAutomake.sh /tmp/installAutomake.sh +USER root +RUN apt-get -y update \ + && apt-get -y upgrade \ + && apt-get install -y --no-install-recommends \ + wget \ libudunits2-dev \ libgdal-dev \ xdg-utils \ + # installAutomake + && chmod +x /tmp/installAutomake.sh \ + && /tmp/installAutomake.sh 1.16.1 \ + # Cleanup && apt-get autoremove -y \ && apt-get autoclean -y \ - && rm -rf /var/lib/apt/lists/* \ - && installPackage \ + && rm -rf /var/lib/apt/lists/* /tmp/installAutomake.sh + +# 3. Install R Packages Installation +USER ${USER_NAME} +RUN installPackage \ DT \ htmlwidgets \ leaflet \ @@ -22,4 +37,50 @@ RUN installAutomake 1.16.1 \ shinydashboard \ shinyjs \ shinythemes \ - plotly + plotly \ + && rm -rf /tmp/downloaded_packages/* + +# -------------- +# Stage 2: final +# -------------- +FROM inwt/r-batch:4.5.1.non-root + +# 1. Enviroment, Ports & User Setup +ARG USER_NAME=user +EXPOSE 3838 +ENV HOME=/app + +# 2. Copy Artifacts from builder stage +COPY --from=shiny-builder /usr/local/lib/R/site-library/ /usr/local/lib/R/site-library/ + +# 3. Set User and Workdir +USER ${USER_NAME} +WORKDIR /app + +CMD ["R"] + +# FROM inwt/r-batch:4.5.1.non-root +# +# EXPOSE 3838 +# +# RUN installAutomake 1.16.1 \ +# && apt-get update \ +# && apt-get install -y \ +# libudunits2-dev \ +# libgdal-dev \ +# xdg-utils \ +# && apt-get autoremove -y \ +# && apt-get autoclean -y \ +# && rm -rf /var/lib/apt/lists/* \ +# && installPackage \ +# DT \ +# htmlwidgets \ +# leaflet \ +# sf \ +# shiny \ +# shinyalert \ +# shinybusy \ +# shinydashboard \ +# shinyjs \ +# shinythemes \ +# plotly From 954a141c4172d37e3ec962130e7f075d674cba3a Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 12:55:30 +0200 Subject: [PATCH 08/31] r-base - remove automake --- r-base/Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/r-base/Dockerfile b/r-base/Dockerfile index ad0c534..d1d7bf9 100644 --- a/r-base/Dockerfile +++ b/r-base/Dockerfile @@ -67,7 +67,6 @@ RUN chmod +x /includes/*.R \ && ln -s /includes/main.R /usr/local/bin/main \ && ln -s /includes/installGithub.R /usr/local/bin/installGithub \ && ln -s /includes/installPackage.R /usr/local/bin/installPackage \ - && ln -s /includes/installAutomake.sh /usr/local/bin/installAutomake \ # Set Posit Package Manager as CRAN Mirror && echo "options(repos = c(CRAN = '$(Rscript /includes/get_mirror_date.R)'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \ # Install R Packages (stringi needs to be recompiled) From 8b97fdeb6834e3c42e8653d2c21e94dca6852312 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 13:04:33 +0200 Subject: [PATCH 09/31] r-model - introduce a multi stage build with a non-root user --- r-model/Dockerfile | 48 +++++++++++++++++++++++++++++++++++++--------- 1 file changed, 39 insertions(+), 9 deletions(-) diff --git a/r-model/Dockerfile b/r-model/Dockerfile index 2b38d97..59a065e 100644 --- a/r-model/Dockerfile +++ b/r-model/Dockerfile @@ -1,11 +1,41 @@ -FROM inwt/r-batch:4.5.1.non-root +# ---------------- +# Stage 1: builder +# ---------------- +FROM inwt/r-batch:4.5.1.non-root AS model-builder + +#1. User and Environment Setup +ARG USER_NAME=user +# 2. System Dependencies (Run as root) +USER root RUN apt-get -y update \ - && apt-get install -y --no-install-recommends \ - libnode-dev \ - && apt-get autoremove -y \ - && apt-get autoclean -y \ - && rm -rf /var/lib/apt/lists/* \ - && installPackage rstan \ - && installPackage prophet \ - && rm -rf /tmp/downloaded_packages/* + && apt-get install -y --no-install-recommends \ + libnode-dev \ + # Cleanup APT after install + && apt-get autoremove -y \ + && apt-get autoclean -y \ + && rm -rf /var/lib/apt/lists/* + +# 3. Install R Packages Installation +USER ${USER_NAME} +RUN installPackage rstan \ + && installPackage prophet \ + # Cleanup R build artifacts + && rm -rf /tmp/downloaded_packages/* + +# -------------- +# Stage 2: final +# -------------- +FROM inwt/r-batch:4.5.1.non-root + +# 1. Environment and User Setup +ARG USER_NAME=user +ENV HOME=/app + +# 2. Copy Artifacts from builder stage +COPY --from=model-builder /usr/local/lib/R/site-library/ /usr/local/lib/R/site-library/ + +# 3. Set User and Workdir +USER ${USER_NAME} +WORKDIR /app +CMD ["R"] From ab200ffeef783d77ee959a0b63816b3a984d0bda Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 13:12:43 +0200 Subject: [PATCH 10/31] r-geos - introduce a multi stage build with a non-root user --- r-geos/Dockerfile | 51 +++++++++++++++++++++++++++++++++++++---------- 1 file changed, 40 insertions(+), 11 deletions(-) diff --git a/r-geos/Dockerfile b/r-geos/Dockerfile index dd8a8fc..37310ae 100644 --- a/r-geos/Dockerfile +++ b/r-geos/Dockerfile @@ -1,15 +1,27 @@ -FROM inwt/r-batch:4.5.1.non-root +# ---------------- +# Stage 1: builder +# ---------------- +FROM inwt/r-batch:4.5.1.non-root AS geos-builder + +# 1. User and Environment Setup +ARG USER_NAME=user +# 2. System Dependencies (Run as root) +USER root RUN apt-get -y update \ - && apt-get install -y --no-install-recommends \ - libgdal-dev \ - libgeos-dev \ - libproj-dev \ - libudunits2-dev \ - && apt-get autoremove -y \ - && apt-get autoclean -y \ - && rm -rf /var/lib/apt/lists/* \ - && installPackage \ + && apt-get install -y --no-install-recommends \ + libgdal-dev \ + libgeos-dev \ + libproj-dev \ + libudunits2-dev \ + # Cleanup APT after install + && apt-get autoremove -y \ + && apt-get autoclean -y \ + && rm -rf /var/lib/apt/lists/* + +# 3. Install R Packages Installation +USER ${USER_NAME} +RUN installPackage \ geojsonsf \ raster \ R.utils \ @@ -17,5 +29,22 @@ RUN apt-get -y update \ stars \ terra \ unix \ - && rm -rf /tmp/downloaded_packages/* + # Cleanup R build artifacts + && rm -rf /tmp/downloaded_packages/* + +# -------------- +# Stage 2: final +# -------------- +FROM inwt/r-batch:4.5.1.non-root + +# 1. Environment and User Setup +ARG USER_NAME=user +ENV HOME=/app + +# 2. Copy Artifacts from builder stage +COPY --from=geos-builder /usr/local/lib/R/site-library/ /usr/local/lib/R/site-library/ +# 3. Set User and Workdir +USER ${USER_NAME} +WORKDIR /app +CMD ["R"] From 98b18f436e13058fc4de05f6d3d60a3ead2ae3af Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 14:24:21 +0200 Subject: [PATCH 11/31] add Makefile to change R-Version and Build Images --- Makefile | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 Makefile diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..8f43e55 --- /dev/null +++ b/Makefile @@ -0,0 +1,28 @@ +R_VERSION := 4.5.1 +TAG := ${R_VERSION} +IMAGES := r-base r-batch r-model r-geos r-shiny + +.PHONY: update-version +update-version: + @echo "--- Updating R version tags to ${R_VERSION} in Dockerfiles ---" + @for image in ${IMAGES}; do \ + file="$$image/Dockerfile"; \ + sed -i "s/\(FROM \)\(rocker\/r-ver\|inwt\/r-base\|inwt\/r-batch\):[0-9]\+\.[0-9]\+\.[0-9]\+/\1\2:${R_VERSION}/g" "$$file" \ + && echo "Updated $$file"; \ + done + @echo "--- All Dockerfiles updated successfully! ---" + +.PHONY: all $(IMAGES) clean +all: $(IMAGES) + @echo "--- Successfully built all Docker images with tag: $(TAG) ---" + +$(IMAGES): + @echo "Building Docker image: inwt/$@:$(TAG) from folder: $@" + docker build -t inwt/$@:$(TAG) $@ + +.PHONY: clean +clean: + @echo "Removing locally tagged images for version ${TAG}..." + @for img in ${ALL_IMAGES}; do \ + docker rmi inwt/$$img:${TAG} || true; \ + done From c736967f9b4f0d076e1844a9940a5bcff4ab6380 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 15:01:58 +0200 Subject: [PATCH 12/31] add global arguments --- r-base/Dockerfile | 46 ++++++++++++++++++++++++++++++---------------- r-batch/Dockerfile | 20 +++++++++++++++----- r-geos/Dockerfile | 14 ++++++++++---- r-model/Dockerfile | 14 ++++++++++---- r-shiny/Dockerfile | 44 +++++++++++++------------------------------- 5 files changed, 78 insertions(+), 60 deletions(-) diff --git a/r-base/Dockerfile b/r-base/Dockerfile index d1d7bf9..3c58d07 100644 --- a/r-base/Dockerfile +++ b/r-base/Dockerfile @@ -1,19 +1,31 @@ -# ---------------- -# Stage 1: builder -# ---------------- +# ------------------- +# Setup (Global Args) +# ------------------- -FROM rocker/r-ver:4.5.1 AS builder - -# 1. User and Environment Setup +ARG R_VERSION=4.5.1 ARG USER_NAME=user ARG USER_UID=1000 ARG USER_GID=1000 +ARG GLOBAL_TZ="Europe/Berlin" +ARG GLOBAL_LANG="en_US.UTF-8" + +# ---------------- +# Stage 1: builder +# ---------------- +FROM rocker/r-ver:${R_VERSION} AS builder + +# 1. User & Environment Setup +ARG USER_NAME +ARG USER_UID +ARG USER_GID +ARG GLOBAL_TZ +ARG GLOBAL_LANG ENV DEBIAN_FRONTEND=noninteractive ENV OPENBLAS_NUM_THREADS=1 ENV _R_CHECK_TESTS_NLINES_=0 -ENV TZ="Europe/Berlin" -ENV LANG=en_US.UTF-8 +ENV TZ=${GLOBAL_TZ} +ENV LANG=${GLOBAL_LANG} # Create the non-root user (UID 1000:GID 1000) RUN groupadd --gid ${USER_GID} ${USER_NAME} \ @@ -88,12 +100,14 @@ RUN chmod +x /includes/*.R \ # -------------- # Stage 2: final # -------------- -FROM rocker/r-ver:4.5.1 +FROM rocker/r-ver:${R_VERSION} -# 1. Environment and User Setup -ARG USER_NAME=user -ARG USER_UID=1000 -ARG USER_GID=1000 +# 1. User Setup +ARG USER_NAME +ARG USER_UID +ARG USER_GID +ARG GLOBAL_TZ +ARG GLOBAL_LANG # Re-create the non-root user in the final stage (since this is a new base layer) RUN groupadd --gid ${USER_GID} ${USER_NAME} \ @@ -101,8 +115,8 @@ RUN groupadd --gid ${USER_GID} ${USER_NAME} \ # Set runtime environment variables ENV HOME=/app -ENV TZ="Europe/Berlin" -ENV LANG=en_US.UTF-8 +ENV TZ=${GLOBAL_TZ} +ENV LANG=${GLOBAL_LANG} # 2. Copy Artifacts from the builder stage COPY --from=builder /usr/local/bin/ /usr/local/bin/ @@ -110,7 +124,7 @@ COPY --from=builder /usr/local/lib/R/site-library/ /usr/local/lib/R/site-library COPY --from=builder /usr/local/lib/R/etc/Rprofile.site /usr/local/lib/R/etc/Rprofile.site COPY --from=builder /r-repo/ /r-repo/ -# 3. Add all utility scripts +# 3. Add utility scripts RUN mkdir -p /includes/check-lib COPY --from=builder /includes/build.R /includes/build.R diff --git a/r-batch/Dockerfile b/r-batch/Dockerfile index 6e75c16..181d697 100644 --- a/r-batch/Dockerfile +++ b/r-batch/Dockerfile @@ -1,10 +1,18 @@ +# ------------------- +# Setup (Global Args) +# ------------------- +ARG R_VERSION=4.5.1.non-root +ARG USER_NAME=user +ARG AWS_CLI_VERSION=2.25.13 + # ---------------- # Stage 1: builder # ---------------- -FROM inwt/r-base:4.5.1.non-root AS batch-builder +FROM inwt/r-base:${R_VERSION} AS batch-builder # 1. User and Enviroment Setup -ARG USER_NAME=user +ARG USER_NAME +ARG AWS_CLI_VERSION # 2. System Dependencies USER root @@ -21,7 +29,7 @@ RUN apt-get -y update \ libpcre2-dev \ libpq-dev \ # AWS CLI - && curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.25.13.zip" -o "awscliv2.zip" \ + && curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-${AWS_CLI_VERSION}.zip" -o "awscliv2.zip" \ && unzip awscliv2.zip \ && ./aws/install \ # Cleanup @@ -31,7 +39,9 @@ RUN apt-get -y update \ # 3. Configure Java & R Packages Installation RUN R CMD javareconf + USER ${USER_NAME} + RUN installPackage \ arrow \ codetools \ @@ -58,10 +68,10 @@ RUN installPackage \ # -------------- # Stage 2: final # -------------- -FROM inwt/r-base:4.5.1.non-root +FROM inwt/r-base:${R_VERSION} # 1. Enviroment and User Setup -ARG USER_NAME=user +ARG USER_NAME ENV HOME=/app diff --git a/r-geos/Dockerfile b/r-geos/Dockerfile index 37310ae..3ed5979 100644 --- a/r-geos/Dockerfile +++ b/r-geos/Dockerfile @@ -1,10 +1,16 @@ +# ------------------- +# Setup (Global Args) +# ------------------- +ARG R_VERSION=4.5.1.non-root +ARG USER_NAME=user + # ---------------- # Stage 1: builder # ---------------- -FROM inwt/r-batch:4.5.1.non-root AS geos-builder +FROM inwt/r-batch:${R_VERSION} AS geos-builder # 1. User and Environment Setup -ARG USER_NAME=user +ARG USER_NAME # 2. System Dependencies (Run as root) USER root @@ -35,10 +41,10 @@ RUN installPackage \ # -------------- # Stage 2: final # -------------- -FROM inwt/r-batch:4.5.1.non-root +FROM inwt/r-batch:${R_VERSION} # 1. Environment and User Setup -ARG USER_NAME=user +ARG USER_NAME ENV HOME=/app # 2. Copy Artifacts from builder stage diff --git a/r-model/Dockerfile b/r-model/Dockerfile index 59a065e..daa1e7c 100644 --- a/r-model/Dockerfile +++ b/r-model/Dockerfile @@ -1,10 +1,16 @@ +# ------------------- +# Setup (Global Args) +# ------------------- +ARG R_VERSION=4.5.1.non-root +ARG USER_NAME=user + # ---------------- # Stage 1: builder # ---------------- -FROM inwt/r-batch:4.5.1.non-root AS model-builder +FROM inwt/r-batch:${R_VERSION} AS model-builder #1. User and Environment Setup -ARG USER_NAME=user +ARG USER_NAME # 2. System Dependencies (Run as root) USER root @@ -26,10 +32,10 @@ RUN installPackage rstan \ # -------------- # Stage 2: final # -------------- -FROM inwt/r-batch:4.5.1.non-root +FROM inwt/r-batch:${R_VERSION} # 1. Environment and User Setup -ARG USER_NAME=user +ARG USER_NAME ENV HOME=/app # 2. Copy Artifacts from builder stage diff --git a/r-shiny/Dockerfile b/r-shiny/Dockerfile index a07482f..c42f249 100644 --- a/r-shiny/Dockerfile +++ b/r-shiny/Dockerfile @@ -1,10 +1,18 @@ +# ------------------- +# Setup (Global Args) +# ------------------- +ARG R_VERSION=4.5.1.non-root +ARG USER_NAME=user +ARG AUTOMAKE_VERSION=1.16.1 + # ---------------- # Stage 1: builder # ---------------- -FROM inwt/r-batch:4.5.1.non-root AS shiny-builder +FROM inwt/r-batch:${R_VERSION} AS shiny-builder # 1. User and Enviroment Setup -ARG USER_NAME=user +ARG USER_NAME +ARG AUTOMAKE_VERSION # 2. System Dependencies COPY installAutomake.sh /tmp/installAutomake.sh @@ -18,7 +26,7 @@ RUN apt-get -y update \ xdg-utils \ # installAutomake && chmod +x /tmp/installAutomake.sh \ - && /tmp/installAutomake.sh 1.16.1 \ + && /tmp/installAutomake.sh ${AUTOMAKE_VERSION} \ # Cleanup && apt-get autoremove -y \ && apt-get autoclean -y \ @@ -43,10 +51,10 @@ RUN installPackage \ # -------------- # Stage 2: final # -------------- -FROM inwt/r-batch:4.5.1.non-root +FROM inwt/r-batch:${R_VERSION} # 1. Enviroment, Ports & User Setup -ARG USER_NAME=user +ARG USER_NAME EXPOSE 3838 ENV HOME=/app @@ -58,29 +66,3 @@ USER ${USER_NAME} WORKDIR /app CMD ["R"] - -# FROM inwt/r-batch:4.5.1.non-root -# -# EXPOSE 3838 -# -# RUN installAutomake 1.16.1 \ -# && apt-get update \ -# && apt-get install -y \ -# libudunits2-dev \ -# libgdal-dev \ -# xdg-utils \ -# && apt-get autoremove -y \ -# && apt-get autoclean -y \ -# && rm -rf /var/lib/apt/lists/* \ -# && installPackage \ -# DT \ -# htmlwidgets \ -# leaflet \ -# sf \ -# shiny \ -# shinyalert \ -# shinybusy \ -# shinydashboard \ -# shinyjs \ -# shinythemes \ -# plotly From f2e07aa68b93f0dd2e65f498c0c59ca1565861b8 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 15:02:12 +0200 Subject: [PATCH 13/31] adjust sed command --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 8f43e55..aa40eef 100644 --- a/Makefile +++ b/Makefile @@ -7,7 +7,7 @@ update-version: @echo "--- Updating R version tags to ${R_VERSION} in Dockerfiles ---" @for image in ${IMAGES}; do \ file="$$image/Dockerfile"; \ - sed -i "s/\(FROM \)\(rocker\/r-ver\|inwt\/r-base\|inwt\/r-batch\):[0-9]\+\.[0-9]\+\.[0-9]\+/\1\2:${R_VERSION}/g" "$$file" \ + sed -i "s/\(ARG R_VERSION=\)[0-9]\+\.[0-9]\+\.[0-9]\+/\1${R_VERSION}/g" "$$file" \ && echo "Updated $$file"; \ done @echo "--- All Dockerfiles updated successfully! ---" From 14276b60ad0ead56748b78bb4ba5bc93043fe4a9 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 15:31:37 +0200 Subject: [PATCH 14/31] add opencontainer Lables --- r-base/Dockerfile | 9 ++++++++- r-batch/Dockerfile | 8 ++++++++ r-geos/Dockerfile | 8 ++++++++ r-model/Dockerfile | 8 ++++++++ r-shiny/Dockerfile | 8 ++++++++ 5 files changed, 40 insertions(+), 1 deletion(-) diff --git a/r-base/Dockerfile b/r-base/Dockerfile index 3c58d07..d70cd7f 100644 --- a/r-base/Dockerfile +++ b/r-base/Dockerfile @@ -1,7 +1,6 @@ # ------------------- # Setup (Global Args) # ------------------- - ARG R_VERSION=4.5.1 ARG USER_NAME=user ARG USER_UID=1000 @@ -9,6 +8,14 @@ ARG USER_GID=1000 ARG GLOBAL_TZ="Europe/Berlin" ARG GLOBAL_LANG="en_US.UTF-8" +LABEL org.opencontainers.image.title="INWT - R Base Image" \ + org.opencontainers.image.description="Multi-stage R environment based on Rocker" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ + org.opencontainers.image.version="${R_VERSION}" \ + org.opencontainers.image.url="https://github.com/INWTlab/r-docker" \ + org.opencontainers.image.source="https://github.com/INWTlab/r-docker" + # ---------------- # Stage 1: builder # ---------------- diff --git a/r-batch/Dockerfile b/r-batch/Dockerfile index 181d697..861c105 100644 --- a/r-batch/Dockerfile +++ b/r-batch/Dockerfile @@ -5,6 +5,14 @@ ARG R_VERSION=4.5.1.non-root ARG USER_NAME=user ARG AWS_CLI_VERSION=2.25.13 +LABEL org.opencontainers.image.title="INWT - R Batch Image" \ + org.opencontainers.image.description="Build Upon inwt/r-base with AWS CLI, Java and R Packages" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ + org.opencontainers.image.version="${R_VERSION}" \ + org.opencontainers.image.url="https://github.com/INWTlab/r-docker" \ + org.opencontainers.image.source="https://github.com/INWTlab/r-docker" + # ---------------- # Stage 1: builder # ---------------- diff --git a/r-geos/Dockerfile b/r-geos/Dockerfile index 3ed5979..2eb10b1 100644 --- a/r-geos/Dockerfile +++ b/r-geos/Dockerfile @@ -4,6 +4,14 @@ ARG R_VERSION=4.5.1.non-root ARG USER_NAME=user +LABEL org.opencontainers.image.title="INWT - R Geos Image" \ + org.opencontainers.image.description="Build upon inwt/r-batch for geospatial data processing with GDAL" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ + org.opencontainers.image.version="${R_VERSION}" \ + org.opencontainers.image.url="https://github.com/INWTlab/r-docker" \ + org.opencontainers.image.source="https://github.com/INWTlab/r-docker" + # ---------------- # Stage 1: builder # ---------------- diff --git a/r-model/Dockerfile b/r-model/Dockerfile index daa1e7c..71bf6ea 100644 --- a/r-model/Dockerfile +++ b/r-model/Dockerfile @@ -4,6 +4,14 @@ ARG R_VERSION=4.5.1.non-root ARG USER_NAME=user +LABEL org.opencontainers.image.title="INWT - R Model Image" \ + org.opencontainers.image.description="Build upon inwt/r-batch with rstan and prophet for modeling" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ + org.opencontainers.image.version="${R_VERSION}" \ + org.opencontainers.image.url="https://github.com/INWTlab/r-docker" \ + org.opencontainers.image.source="https://github.com/INWTlab/r-docker" + # ---------------- # Stage 1: builder # ---------------- diff --git a/r-shiny/Dockerfile b/r-shiny/Dockerfile index c42f249..808b133 100644 --- a/r-shiny/Dockerfile +++ b/r-shiny/Dockerfile @@ -5,6 +5,14 @@ ARG R_VERSION=4.5.1.non-root ARG USER_NAME=user ARG AUTOMAKE_VERSION=1.16.1 +LABEL org.opencontainers.image.title="INWT - R Shiny Image" \ + org.opencontainers.image.description="Build upon inwt/r-batch with Shiny & deps for web applications" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ + org.opencontainers.image.version="${R_VERSION}" \ + org.opencontainers.image.url="https://github.com/INWTlab/r-docker" \ + org.opencontainers.image.source="https://github.com/INWTlab/r-docker" + # ---------------- # Stage 1: builder # ---------------- From ea76724b064725804ba5ba8343376307b1c444a7 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 15:42:33 +0200 Subject: [PATCH 15/31] add revision and created lables to image builds --- Jenkinsfile | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/Jenkinsfile b/Jenkinsfile index 59c3fa0..12f010c 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -21,7 +21,10 @@ pipeline { steps { withDockerRegistry([ credentialsId: "jenkins-docker-hub", url: "" ]) { sh ''' - docker build -t inwt/r-base:$LABEL r-base + docker build \ + --label org.opencontainers.image.revision=$(git rev-parse HEAD) \ + --label org.opencontainers.image.created=$(date -u +%Y-%m-%dT%H:%M:%SZ) \ + -t inwt/r-base:$LABEL r-base docker push inwt/r-base:$LABEL ''' } @@ -31,7 +34,10 @@ pipeline { steps { withDockerRegistry([ credentialsId: "jenkins-docker-hub", url: "" ]) { sh ''' - docker build -t inwt/r-batch:$LABEL r-batch + docker build \ + --label org.opencontainers.image.revision=$(git rev-parse HEAD) \ + --label org.opencontainers.image.created=$(date -u +%Y-%m-%dT%H:%M:%SZ) \ + -t inwt/r-batch:$LABEL r-batch docker push inwt/r-batch:$LABEL ''' } @@ -41,7 +47,10 @@ pipeline { steps { withDockerRegistry([ credentialsId: "jenkins-docker-hub", url: "" ]) { sh ''' - docker build -t inwt/r-shiny:$LABEL r-shiny + docker build \ + --label org.opencontainers.image.revision=$(git rev-parse HEAD) \ + --label org.opencontainers.image.created=$(date -u +%Y-%m-%dT%H:%M:%SZ) \ + -t inwt/r-shiny:$LABEL r-shiny docker push inwt/r-shiny:$LABEL ''' } @@ -51,7 +60,10 @@ pipeline { steps { withDockerRegistry([ credentialsId: "jenkins-docker-hub", url: "" ]) { sh ''' - docker build -t inwt/r-model:$LABEL r-model + docker build \ + --label org.opencontainers.image.revision=$(git rev-parse HEAD) \ + --label org.opencontainers.image.created=$(date -u +%Y-%m-%dT%H:%M:%SZ) \ + -t inwt/r-model:$LABEL r-model docker push inwt/r-model:$LABEL ''' } @@ -61,7 +73,10 @@ pipeline { steps { withDockerRegistry([ credentialsId: "jenkins-docker-hub", url: "" ]) { sh ''' - docker build -t inwt/r-geos:$LABEL r-geos + docker build \ + --label org.opencontainers.image.revision=$(git rev-parse HEAD) \ + --label org.opencontainers.image.created=$(date -u +%Y-%m-%dT%H:%M:%SZ) \ + -t inwt/r-geos:$LABEL r-geos docker push inwt/r-geos:$LABEL ''' } From 2db420ed8656f706f32fd028c64509aeddab0337 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 16:03:47 +0200 Subject: [PATCH 16/31] adjust Lables --- r-base/Dockerfile | 18 ++++++++++-------- r-batch/Dockerfile | 18 ++++++++++-------- r-geos/Dockerfile | 18 ++++++++++-------- r-model/Dockerfile | 18 ++++++++++-------- r-shiny/Dockerfile | 18 ++++++++++-------- 5 files changed, 50 insertions(+), 40 deletions(-) diff --git a/r-base/Dockerfile b/r-base/Dockerfile index d70cd7f..755ff62 100644 --- a/r-base/Dockerfile +++ b/r-base/Dockerfile @@ -8,14 +8,6 @@ ARG USER_GID=1000 ARG GLOBAL_TZ="Europe/Berlin" ARG GLOBAL_LANG="en_US.UTF-8" -LABEL org.opencontainers.image.title="INWT - R Base Image" \ - org.opencontainers.image.description="Multi-stage R environment based on Rocker" \ - org.opencontainers.image.vendor="INWT Statistics" \ - org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ - org.opencontainers.image.version="${R_VERSION}" \ - org.opencontainers.image.url="https://github.com/INWTlab/r-docker" \ - org.opencontainers.image.source="https://github.com/INWTlab/r-docker" - # ---------------- # Stage 1: builder # ---------------- @@ -109,6 +101,16 @@ RUN chmod +x /includes/*.R \ # -------------- FROM rocker/r-ver:${R_VERSION} +LABEL org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ + org.opencontainers.image.created="BUILD_DATE_TIME_PLACEHOLDER" \ + org.opencontainers.image.description="Multi-stage R environment based on Rocker" \ + org.opencontainers.image.licenses="GPL-2.0-or-later" \ + org.opencontainers.image.revision="GIT_SHA_PLACEHOLDER" \ + org.opencontainers.image.source="https://github.com/INWTlab/r-docker" \ + org.opencontainers.image.title="inwt/r-base" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.version="${R_VERSION}" + # 1. User Setup ARG USER_NAME ARG USER_UID diff --git a/r-batch/Dockerfile b/r-batch/Dockerfile index 861c105..39949dd 100644 --- a/r-batch/Dockerfile +++ b/r-batch/Dockerfile @@ -5,14 +5,6 @@ ARG R_VERSION=4.5.1.non-root ARG USER_NAME=user ARG AWS_CLI_VERSION=2.25.13 -LABEL org.opencontainers.image.title="INWT - R Batch Image" \ - org.opencontainers.image.description="Build Upon inwt/r-base with AWS CLI, Java and R Packages" \ - org.opencontainers.image.vendor="INWT Statistics" \ - org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ - org.opencontainers.image.version="${R_VERSION}" \ - org.opencontainers.image.url="https://github.com/INWTlab/r-docker" \ - org.opencontainers.image.source="https://github.com/INWTlab/r-docker" - # ---------------- # Stage 1: builder # ---------------- @@ -78,6 +70,16 @@ RUN installPackage \ # -------------- FROM inwt/r-base:${R_VERSION} +LABEL org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ + org.opencontainers.image.created="BUILD_DATE_TIME_PLACEHOLDER" \ + org.opencontainers.image.description="Build Upon inwt/r-base with AWS CLI, Java and R Packages" \ + org.opencontainers.image.licenses="GPL-2.0-or-later" \ + org.opencontainers.image.revision="GIT_SHA_PLACEHOLDER" \ + org.opencontainers.image.source="https://github.com/INWTlab/r-docker" \ + org.opencontainers.image.title="inwt/r-base" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.version="${R_VERSION}" + # 1. Enviroment and User Setup ARG USER_NAME diff --git a/r-geos/Dockerfile b/r-geos/Dockerfile index 2eb10b1..ab1c559 100644 --- a/r-geos/Dockerfile +++ b/r-geos/Dockerfile @@ -4,14 +4,6 @@ ARG R_VERSION=4.5.1.non-root ARG USER_NAME=user -LABEL org.opencontainers.image.title="INWT - R Geos Image" \ - org.opencontainers.image.description="Build upon inwt/r-batch for geospatial data processing with GDAL" \ - org.opencontainers.image.vendor="INWT Statistics" \ - org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ - org.opencontainers.image.version="${R_VERSION}" \ - org.opencontainers.image.url="https://github.com/INWTlab/r-docker" \ - org.opencontainers.image.source="https://github.com/INWTlab/r-docker" - # ---------------- # Stage 1: builder # ---------------- @@ -51,6 +43,16 @@ RUN installPackage \ # -------------- FROM inwt/r-batch:${R_VERSION} +LABEL org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ + org.opencontainers.image.created="BUILD_DATE_TIME_PLACEHOLDER" \ + org.opencontainers.image.description="Build upon inwt/r-batch for geospatial data processing with GDAL" \ + org.opencontainers.image.licenses="GPL-2.0-or-later" \ + org.opencontainers.image.revision="GIT_SHA_PLACEHOLDER" \ + org.opencontainers.image.source="https://github.com/INWTlab/r-docker" \ + org.opencontainers.image.title="inwt/r-base" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.version="${R_VERSION}" + # 1. Environment and User Setup ARG USER_NAME ENV HOME=/app diff --git a/r-model/Dockerfile b/r-model/Dockerfile index 71bf6ea..b106eaa 100644 --- a/r-model/Dockerfile +++ b/r-model/Dockerfile @@ -4,14 +4,6 @@ ARG R_VERSION=4.5.1.non-root ARG USER_NAME=user -LABEL org.opencontainers.image.title="INWT - R Model Image" \ - org.opencontainers.image.description="Build upon inwt/r-batch with rstan and prophet for modeling" \ - org.opencontainers.image.vendor="INWT Statistics" \ - org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ - org.opencontainers.image.version="${R_VERSION}" \ - org.opencontainers.image.url="https://github.com/INWTlab/r-docker" \ - org.opencontainers.image.source="https://github.com/INWTlab/r-docker" - # ---------------- # Stage 1: builder # ---------------- @@ -42,6 +34,16 @@ RUN installPackage rstan \ # -------------- FROM inwt/r-batch:${R_VERSION} +LABEL org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ + org.opencontainers.image.created="BUILD_DATE_TIME_PLACEHOLDER" \ + org.opencontainers.image.description="Build upon inwt/r-batch with rstan and prophet for modeling" \ + org.opencontainers.image.licenses="GPL-2.0-or-later" \ + org.opencontainers.image.revision="GIT_SHA_PLACEHOLDER" \ + org.opencontainers.image.source="https://github.com/INWTlab/r-docker" \ + org.opencontainers.image.title="inwt/r-base" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.version="${R_VERSION}" + # 1. Environment and User Setup ARG USER_NAME ENV HOME=/app diff --git a/r-shiny/Dockerfile b/r-shiny/Dockerfile index 808b133..90c23ff 100644 --- a/r-shiny/Dockerfile +++ b/r-shiny/Dockerfile @@ -5,14 +5,6 @@ ARG R_VERSION=4.5.1.non-root ARG USER_NAME=user ARG AUTOMAKE_VERSION=1.16.1 -LABEL org.opencontainers.image.title="INWT - R Shiny Image" \ - org.opencontainers.image.description="Build upon inwt/r-batch with Shiny & deps for web applications" \ - org.opencontainers.image.vendor="INWT Statistics" \ - org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ - org.opencontainers.image.version="${R_VERSION}" \ - org.opencontainers.image.url="https://github.com/INWTlab/r-docker" \ - org.opencontainers.image.source="https://github.com/INWTlab/r-docker" - # ---------------- # Stage 1: builder # ---------------- @@ -61,6 +53,16 @@ RUN installPackage \ # -------------- FROM inwt/r-batch:${R_VERSION} +LABEL org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ + org.opencontainers.image.created="BUILD_DATE_TIME_PLACEHOLDER" \ + org.opencontainers.image.description="Build upon inwt/r-batch with Shiny & deps for web applications" \ + org.opencontainers.image.licenses="GPL-2.0-or-later" \ + org.opencontainers.image.revision="GIT_SHA_PLACEHOLDER" \ + org.opencontainers.image.source="https://github.com/INWTlab/r-docker" \ + org.opencontainers.image.title="inwt/r-base" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.version="${R_VERSION}" + # 1. Enviroment, Ports & User Setup ARG USER_NAME EXPOSE 3838 From bdb05a264cf76b32538e4af9f09ac093ddaca9ed Mon Sep 17 00:00:00 2001 From: Jan Abel <106665518+jan-abel-inwt@users.noreply.github.com> Date: Thu, 16 Oct 2025 16:08:23 +0200 Subject: [PATCH 17/31] Create LICENSE --- LICENSE | 339 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 339 insertions(+) create mode 100644 LICENSE diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..d159169 --- /dev/null +++ b/LICENSE @@ -0,0 +1,339 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Lesser General Public License instead.) You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +this service if you wish), that you receive source code or can get it +if you want it, that you can change the software or use pieces of it +in new free programs; and that you know you can do these things. + + To protect your rights, we need to make restrictions that forbid +anyone to deny you these rights or to ask you to surrender the rights. +These restrictions translate to certain responsibilities for you if you +distribute copies of the software, or if you modify it. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must give the recipients all the rights that +you have. You must make sure that they, too, receive or can get the +source code. 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To prevent this, we have made it clear that any +patent must be licensed for everyone's free use or not licensed at all. + + The precise terms and conditions for copying, distribution and +modification follow. + + GNU GENERAL PUBLIC LICENSE + TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION + + 0. This License applies to any program or other work which contains +a notice placed by the copyright holder saying it may be distributed +under the terms of this General Public License. The "Program", below, +refers to any such program or work, and a "work based on the Program" +means either the Program or any derivative work under copyright law: +that is to say, a work containing the Program or a portion of it, +either verbatim or with modifications and/or translated into another +language. (Hereinafter, translation is included without limitation in +the term "modification".) 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You may copy and distribute verbatim copies of the Program's +source code as you receive it, in any medium, provided that you +conspicuously and appropriately publish on each copy an appropriate +copyright notice and disclaimer of warranty; keep intact all the +notices that refer to this License and to the absence of any warranty; +and give any other recipients of the Program a copy of this License +along with the Program. + +You may charge a fee for the physical act of transferring a copy, and +you may at your option offer warranty protection in exchange for a fee. + + 2. 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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR +REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING +OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED +TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY +YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER +PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGES. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + 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, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision 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, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This 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. From 21c929c7983293bb0541e9ea728f9aefc326ce3b Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 16:23:45 +0200 Subject: [PATCH 18/31] adjust Readme --- README.md | 40 ++++++++++++++++++++++------------------ 1 file changed, 22 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index 5eefbe3..c811b5d 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# Container for R Applications +# Multi Stage Container for R Applications In this project we keep our configuration for INWT projects. If you are not working with us you can see what we think is a good way to bring R applications into production. If you need a clean docker @@ -13,44 +13,45 @@ The container from this project can be found at: ## Featured images +All images now use a multi-stage build for minimal size and enforce execution as a non-root user + ### r-base -- Starts from rocker/r-ver:4.1.2 -- Includes basic build tools +- Starts from rocker/r-ver +- Includes basic build tools and core R packages (`devtools`, `drat`) +- Enforces non-root user execution as `user` + - Adds INWT network settings: certificate and r-repo ### r-batch - Starts from r-base -- Adds database connectors (MySQL) +- Adds database connectors (MySQL, Postgres) +- Includes `AWS CLI v2` - Basic packages for modelling (lme4, mgcv, gbm) -- Packages for data manipulation (data.table, dplyr, tidyr) -- Home-brewed and open source (dbtools, mctools) +- Packages for data manipulation (`data.table`, `dplyr`, `tidyr`) +- Home-brewed and open source (`dbtools`, `mctools`) ### r-geos - Starts from r-batch -- Installs Linux libraries necessary for running geo/gis related operations. -- Adds geo/gis related r packages (sf, stars, terra, etc.) +- Installs Linux libraries for GIS/geo related operations. +- Adds geo/gis related r packages (`sf`, `stars`, `terra`, etc.) ### r-shiny - Starts from r-batch -- Adds shiny related packages (shiny, shinyjs, etc.) - -### r-ver-ubuntu (deprecated) - -- Based on Ubuntu -- R in given version with fixed MRAN -- Based on the rocker r-ver project +- Installs `Automake` +- Adds shiny related packages (`shiny`, `shinyjs`, `leaflet` etc.) +- Exposes port `3838` ## Simplest use of an image Example for `r-base` image: ``` -docker pull inwt/r-base:3.4.4 -docker run -it inwt/r-base:3.4.4 +docker pull inwt/r-base:4.5.1 +docker run -it inwt/r-base:4.5.1 ``` ## Why using docker @@ -88,7 +89,7 @@ make use of the predefined images introduced above. Therefore, a possible Docker the following code: ``` -FROM inwt/r-batch:3.4.4 +FROM inwt/r-batch:4.5.1 ADD . . RUN rm -vf .Rprofile && \ @@ -197,5 +198,8 @@ directory of the container. Be aware that with `-v` we are granting write access cd /path/to/your/package docker run --rm -v $PWD:/app --user `id -u`:`id -g` inwt/r-batch:3.4.4 check docker run --rm -v $PWD:/app --user `id -u`:`id -g` inwt/r-batch:3.5.1 check + +docker run --rm -v $PWD:/app inwt/r-batch:4.4.3 check +docker run --rm -v $PWD:/app inwt/r-batch:4.5.1 check ``` From c8e8ea642c08f4c962958509ab1448b829d9d833 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 16:31:37 +0200 Subject: [PATCH 19/31] add dependabot --- .github/dependabot.yml | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..d7c438c --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,8 @@ +version: 2 +updates: + - package-ecosystem: "docker" + directory: "/r-base/" + schedule: + interval: "monthly" + assignees: + - "jan-abel-inwt" From 0a669f3aec2b2ea7969771e19197a7e2cdef3060 Mon Sep 17 00:00:00 2001 From: Jan Abel <106665518+jan-abel-inwt@users.noreply.github.com> Date: Thu, 16 Oct 2025 16:48:20 +0200 Subject: [PATCH 20/31] Update Makefile Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index aa40eef..3a41867 100644 --- a/Makefile +++ b/Makefile @@ -23,6 +23,6 @@ $(IMAGES): .PHONY: clean clean: @echo "Removing locally tagged images for version ${TAG}..." - @for img in ${ALL_IMAGES}; do \ + @for img in ${IMAGES}; do \ docker rmi inwt/$$img:${TAG} || true; \ done From c55d0b562085e7c88a76d51fbfc5d24f1aecdebb Mon Sep 17 00:00:00 2001 From: Jan Abel <106665518+jan-abel-inwt@users.noreply.github.com> Date: Thu, 16 Oct 2025 16:48:44 +0200 Subject: [PATCH 21/31] Update Makefile Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 3a41867..a70d30a 100644 --- a/Makefile +++ b/Makefile @@ -7,7 +7,7 @@ update-version: @echo "--- Updating R version tags to ${R_VERSION} in Dockerfiles ---" @for image in ${IMAGES}; do \ file="$$image/Dockerfile"; \ - sed -i "s/\(ARG R_VERSION=\)[0-9]\+\.[0-9]\+\.[0-9]\+/\1${R_VERSION}/g" "$$file" \ + sed -i "s/\(ARG R_VERSION=\)[0-9]\+\.[0-9]\+\.[0-9]\+[^[:space:]]*/\1${R_VERSION}/g" "$$file" \ && echo "Updated $$file"; \ done @echo "--- All Dockerfiles updated successfully! ---" From 0d329ac94cc82fb55adf453ab1959936ce149d30 Mon Sep 17 00:00:00 2001 From: Jan Abel <106665518+jan-abel-inwt@users.noreply.github.com> Date: Thu, 16 Oct 2025 16:52:10 +0200 Subject: [PATCH 22/31] Update r-batch/Dockerfile Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- r-batch/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/r-batch/Dockerfile b/r-batch/Dockerfile index 39949dd..7aca412 100644 --- a/r-batch/Dockerfile +++ b/r-batch/Dockerfile @@ -76,7 +76,7 @@ LABEL org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ org.opencontainers.image.licenses="GPL-2.0-or-later" \ org.opencontainers.image.revision="GIT_SHA_PLACEHOLDER" \ org.opencontainers.image.source="https://github.com/INWTlab/r-docker" \ - org.opencontainers.image.title="inwt/r-base" \ + org.opencontainers.image.title="inwt/r-batch" \ org.opencontainers.image.vendor="INWT Statistics" \ org.opencontainers.image.version="${R_VERSION}" From 12b9eb9679eee91cf9ff90c656be92914896d7e9 Mon Sep 17 00:00:00 2001 From: Jan Abel <106665518+jan-abel-inwt@users.noreply.github.com> Date: Thu, 16 Oct 2025 16:52:47 +0200 Subject: [PATCH 23/31] Update r-geos/Dockerfile Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- r-geos/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/r-geos/Dockerfile b/r-geos/Dockerfile index ab1c559..440d873 100644 --- a/r-geos/Dockerfile +++ b/r-geos/Dockerfile @@ -49,7 +49,7 @@ LABEL org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ org.opencontainers.image.licenses="GPL-2.0-or-later" \ org.opencontainers.image.revision="GIT_SHA_PLACEHOLDER" \ org.opencontainers.image.source="https://github.com/INWTlab/r-docker" \ - org.opencontainers.image.title="inwt/r-base" \ + org.opencontainers.image.title="inwt/r-geos" \ org.opencontainers.image.vendor="INWT Statistics" \ org.opencontainers.image.version="${R_VERSION}" From 281589bc8a86edf07e37fadb54595113c23edd0c Mon Sep 17 00:00:00 2001 From: Jan Abel <106665518+jan-abel-inwt@users.noreply.github.com> Date: Thu, 16 Oct 2025 16:53:11 +0200 Subject: [PATCH 24/31] Update r-model/Dockerfile Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- r-model/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/r-model/Dockerfile b/r-model/Dockerfile index b106eaa..891c6b2 100644 --- a/r-model/Dockerfile +++ b/r-model/Dockerfile @@ -40,7 +40,7 @@ LABEL org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ org.opencontainers.image.licenses="GPL-2.0-or-later" \ org.opencontainers.image.revision="GIT_SHA_PLACEHOLDER" \ org.opencontainers.image.source="https://github.com/INWTlab/r-docker" \ - org.opencontainers.image.title="inwt/r-base" \ + org.opencontainers.image.title="inwt/r-model" \ org.opencontainers.image.vendor="INWT Statistics" \ org.opencontainers.image.version="${R_VERSION}" From 097ac05617ce02b2f32f83e079bf537df665e4fe Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 16:58:36 +0200 Subject: [PATCH 25/31] fix typos --- README.md | 5 +---- r-base/Dockerfile | 2 +- r-batch/Dockerfile | 4 ++-- r-shiny/Dockerfile | 4 ++-- 4 files changed, 6 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index c811b5d..22021ec 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# Multi Stage Container for R Applications +# Multi-Stage Container for R Applications In this project we keep our configuration for INWT projects. If you are not working with us you can see what we think is a good way to bring R applications into production. If you need a clean docker @@ -196,9 +196,6 @@ directory of the container. Be aware that with `-v` we are granting write access ``` cd /path/to/your/package -docker run --rm -v $PWD:/app --user `id -u`:`id -g` inwt/r-batch:3.4.4 check -docker run --rm -v $PWD:/app --user `id -u`:`id -g` inwt/r-batch:3.5.1 check - docker run --rm -v $PWD:/app inwt/r-batch:4.4.3 check docker run --rm -v $PWD:/app inwt/r-batch:4.5.1 check ``` diff --git a/r-base/Dockerfile b/r-base/Dockerfile index 755ff62..7fcd563 100644 --- a/r-base/Dockerfile +++ b/r-base/Dockerfile @@ -91,7 +91,7 @@ RUN chmod +x /includes/*.R \ && echo "options(repos = c(getOption('repos'), INWT = 'https://r-repo.core.cld.htz.int.inwt.de'))" >> /usr/local/lib/R/etc/Rprofile.site \ && echo "options(repos = c(getOption('repos'), INWTLab = 'https://inwtlab.github.io/drat/'))" >> /usr/local/lib/R/etc/Rprofile.site \ && echo "options(dratRepo = '/r-repo/')" >> /usr/local/lib/R/etc/Rprofile.site \ - # Set ownership for site-library, local r-repo & R scriüts + # Set ownership for site-library, local r-repo & R scripts && chown -R ${USER_NAME}:${USER_NAME} /usr/local/lib/R/site-library/ \ && chown -R ${USER_NAME}:${USER_NAME} /r-repo \ && chown -R ${USER_NAME}:${USER_NAME} /includes diff --git a/r-batch/Dockerfile b/r-batch/Dockerfile index 7aca412..5ec9402 100644 --- a/r-batch/Dockerfile +++ b/r-batch/Dockerfile @@ -10,7 +10,7 @@ ARG AWS_CLI_VERSION=2.25.13 # ---------------- FROM inwt/r-base:${R_VERSION} AS batch-builder -# 1. User and Enviroment Setup +# 1. User and Environment Setup ARG USER_NAME ARG AWS_CLI_VERSION @@ -85,7 +85,7 @@ ARG USER_NAME ENV HOME=/app -# 2. Copy Artifacts (R libaries & aws cli) from builder stage +# 2. Copy Artifacts (R libraries & aws cli) from builder stage COPY --from=batch-builder /usr/local/lib/R/site-library/ /usr/local/lib/R/site-library/ USER root COPY --from=batch-builder /usr/local/aws-cli/ /usr/local/aws-cli/ diff --git a/r-shiny/Dockerfile b/r-shiny/Dockerfile index 90c23ff..30e51cb 100644 --- a/r-shiny/Dockerfile +++ b/r-shiny/Dockerfile @@ -10,7 +10,7 @@ ARG AUTOMAKE_VERSION=1.16.1 # ---------------- FROM inwt/r-batch:${R_VERSION} AS shiny-builder -# 1. User and Enviroment Setup +# 1. User and Environment Setup ARG USER_NAME ARG AUTOMAKE_VERSION @@ -63,7 +63,7 @@ LABEL org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ org.opencontainers.image.vendor="INWT Statistics" \ org.opencontainers.image.version="${R_VERSION}" -# 1. Enviroment, Ports & User Setup +# 1. Environment, Ports & User Setup ARG USER_NAME EXPOSE 3838 ENV HOME=/app From b011a26cc949d8f1b3c24b103204f5994936949b Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 17:05:13 +0200 Subject: [PATCH 26/31] ShellCheck InstallAutomake Script --- r-shiny/installAutomake.sh | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/r-shiny/installAutomake.sh b/r-shiny/installAutomake.sh index c3bd189..b30be30 100755 --- a/r-shiny/installAutomake.sh +++ b/r-shiny/installAutomake.sh @@ -1,27 +1,29 @@ #!/bin/bash +set -euo pipefail + VERSION=${1} -if echo $VERSION | grep -q '\..*\..*'; then +if echo "$VERSION" | grep -q '\..*\..*'; then MAJOR_VERSION=${VERSION%.*} else MAJOR_VERSION=${VERSION} fi function install_automake() { - wget https://ftpmirror.gnu.org/gnu/automake/automake-$VERSION.tar.gz && - tar -xvf automake-$VERSION.tar.gz && - cd automake-$VERSION && - ./configure --prefix=/usr/local/automake-$VERSION && + wget "https://ftpmirror.gnu.org/gnu/automake/automake-$VERSION.tar.gz" && + tar -xvf "automake-$VERSION.tar.gz" && + cd "automake-$VERSION" && + ./configure --prefix="/usr/local/automake-$VERSION" && make && make install && cd .. && - rm automake-$VERSION.tar.gz && - rm -rf automake-$VERSION && - rm -f /usr/local/bin/aclocal-$VERSION && - rm -f /usr/local/bin/automake-$VERSION && - ln -s /usr/local/automake-$VERSION/bin/aclocal-$MAJOR_VERSION /usr/local/bin/aclocal-$MAJOR_VERSION && - ln -s /usr/local/automake-$VERSION/bin/automake-$MAJOR_VERSION /usr/local/bin/automake-$MAJOR_VERSION && + rm "automake-$VERSION.tar.gz" && + rm -rf "automake-$VERSION" && + rm -f "/usr/local/bin/aclocal-$VERSION" && + rm -f "/usr/local/bin/automake-$VERSION" && + ln -s "/usr/local/automake-$VERSION/bin/aclocal-$MAJOR_VERSION" "/usr/local/bin/aclocal-$MAJOR_VERSION" && + ln -s "/usr/local/automake-$VERSION/bin/automake-$MAJOR_VERSION" "/usr/local/bin/automake-$MAJOR_VERSION" && echo "Installed automake in version $VERSION" } From 4da1ece78f04184f06b71a5b50f608b213c24664 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 17:19:21 +0200 Subject: [PATCH 27/31] remove install automake script from r-base --- r-base/installAutomake.sh | 28 ---------------------------- 1 file changed, 28 deletions(-) delete mode 100755 r-base/installAutomake.sh diff --git a/r-base/installAutomake.sh b/r-base/installAutomake.sh deleted file mode 100755 index c3bd189..0000000 --- a/r-base/installAutomake.sh +++ /dev/null @@ -1,28 +0,0 @@ -#!/bin/bash - -VERSION=${1} - -if echo $VERSION | grep -q '\..*\..*'; then - MAJOR_VERSION=${VERSION%.*} -else - MAJOR_VERSION=${VERSION} -fi - -function install_automake() { - wget https://ftpmirror.gnu.org/gnu/automake/automake-$VERSION.tar.gz && - tar -xvf automake-$VERSION.tar.gz && - cd automake-$VERSION && - ./configure --prefix=/usr/local/automake-$VERSION && - make && - make install && - cd .. && - rm automake-$VERSION.tar.gz && - rm -rf automake-$VERSION && - rm -f /usr/local/bin/aclocal-$VERSION && - rm -f /usr/local/bin/automake-$VERSION && - ln -s /usr/local/automake-$VERSION/bin/aclocal-$MAJOR_VERSION /usr/local/bin/aclocal-$MAJOR_VERSION && - ln -s /usr/local/automake-$VERSION/bin/automake-$MAJOR_VERSION /usr/local/bin/automake-$MAJOR_VERSION && - echo "Installed automake in version $VERSION" -} - -install_automake From a366303b2e32afd153ecaee2478602eb0dc8fcae Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 17:33:31 +0200 Subject: [PATCH 28/31] use TZ envvar --- r-base/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/r-base/Dockerfile b/r-base/Dockerfile index 7fcd563..a9ca3be 100644 --- a/r-base/Dockerfile +++ b/r-base/Dockerfile @@ -39,7 +39,7 @@ RUN mv -v /includes/*.crt /usr/local/share/ca-certificates/ \ && dpkg-reconfigure ca-certificates \ && rm /etc/localtime \ && ln -s /usr/share/zoneinfo/Europe/Berlin /etc/localtime \ - && echo "Europe/Berlin" > /etc/timezone \ + && echo "${GLOBAL_TZ}" > /etc/timezone \ # Install System Dependencies && apt-get -y update \ && apt-get -y upgrade \ From 54a45450d74c54508484d27147feeb6175fd4d35 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Thu, 16 Oct 2025 17:46:12 +0200 Subject: [PATCH 29/31] use TZ envvar II --- r-base/Dockerfile | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/r-base/Dockerfile b/r-base/Dockerfile index a9ca3be..6422485 100644 --- a/r-base/Dockerfile +++ b/r-base/Dockerfile @@ -5,8 +5,8 @@ ARG R_VERSION=4.5.1 ARG USER_NAME=user ARG USER_UID=1000 ARG USER_GID=1000 -ARG GLOBAL_TZ="Europe/Berlin" -ARG GLOBAL_LANG="en_US.UTF-8" +ARG TZ="Europe/Berlin" +ARG LANG="en_US.UTF-8" # ---------------- # Stage 1: builder @@ -17,14 +17,14 @@ FROM rocker/r-ver:${R_VERSION} AS builder ARG USER_NAME ARG USER_UID ARG USER_GID -ARG GLOBAL_TZ -ARG GLOBAL_LANG +ARG TZ +ARG LANG ENV DEBIAN_FRONTEND=noninteractive ENV OPENBLAS_NUM_THREADS=1 ENV _R_CHECK_TESTS_NLINES_=0 -ENV TZ=${GLOBAL_TZ} -ENV LANG=${GLOBAL_LANG} +ENV TZ=${TZ} +ENV LANG=${LANG} # Create the non-root user (UID 1000:GID 1000) RUN groupadd --gid ${USER_GID} ${USER_NAME} \ @@ -39,7 +39,7 @@ RUN mv -v /includes/*.crt /usr/local/share/ca-certificates/ \ && dpkg-reconfigure ca-certificates \ && rm /etc/localtime \ && ln -s /usr/share/zoneinfo/Europe/Berlin /etc/localtime \ - && echo "${GLOBAL_TZ}" > /etc/timezone \ + && echo "${TZ}" > /etc/timezone \ # Install System Dependencies && apt-get -y update \ && apt-get -y upgrade \ @@ -115,8 +115,8 @@ LABEL org.opencontainers.image.authors="Sebastian Warnholz, Jan Abel" \ ARG USER_NAME ARG USER_UID ARG USER_GID -ARG GLOBAL_TZ -ARG GLOBAL_LANG +ARG TZ +ARG LANG # Re-create the non-root user in the final stage (since this is a new base layer) RUN groupadd --gid ${USER_GID} ${USER_NAME} \ @@ -124,8 +124,8 @@ RUN groupadd --gid ${USER_GID} ${USER_NAME} \ # Set runtime environment variables ENV HOME=/app -ENV TZ=${GLOBAL_TZ} -ENV LANG=${GLOBAL_LANG} +ENV TZ=${TZ} +ENV LANG=${LANG} # 2. Copy Artifacts from the builder stage COPY --from=builder /usr/local/bin/ /usr/local/bin/ From 5697902951f2f350d04ad361e732710bc4589351 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Wed, 17 Dec 2025 14:16:31 +0100 Subject: [PATCH 30/31] test pak --- use-pak.md | 48 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 use-pak.md diff --git a/use-pak.md b/use-pak.md new file mode 100644 index 0000000..7a3616f --- /dev/null +++ b/use-pak.md @@ -0,0 +1,48 @@ +# Install pak in rbase + +better instpak need to be pinned to a specific version (0.9.0) + +``` +&& Rscript -e "options(warn = 2); install.packages(c('devtools', 'drat', modules', 'pak'))"\ +``` + +doctop is aleready installed in rocker/r-base + +## Utility Scripts + +### installPackages + +- validate-settings +- register-dependencies +- `install.packages()` + +### installGithub + +- validate-settings +- register-dependencies +- `devtools::install_github` + +### build + +- `source("/includes/validate-settings.R")` +- `source("/includes/register-dependencies.R")` +- `devtools::install(dependencies = TRUE)` +- `devtools::build(".", ".")` + +### check + +- `source("/includes/validate-settings.R")` +- `source("/includes/register-dependencies.R")` +- `devtools::install(PKG, dependencies = TRUE)` +- `devtools::check(PKG, error_on = "never")` + +### test + +- `source("/includes/validate-settings.R")` +- `source("/includes/register-dependencies.R")` +- `devtools::install()` +- `devtools::test()` + +### validate-settings + +### register-dependencies From c28460f46b4da157366027e6de7cac400fe344a5 Mon Sep 17 00:00:00 2001 From: Jan Abel Date: Wed, 17 Dec 2025 14:23:51 +0100 Subject: [PATCH 31/31] adjust os codename for ppm url --- r-base/get_mirror_date.R | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/r-base/get_mirror_date.R b/r-base/get_mirror_date.R index d4d9b4e..4deeb31 100644 --- a/r-base/get_mirror_date.R +++ b/r-base/get_mirror_date.R @@ -1,5 +1,9 @@ create_mirror_url <- function(date) { - sprintf("https://packagemanager.posit.co/cran/__linux__/jammy/%s", format(date, "%Y-%m-%d")) + os_info <- readLines("/etc/os-release") + os_codename_line <- grep("^VERSION_CODENAME=", os_info, value = TRUE) + os_codename <- gsub("VERSION_CODENAME=", "", os_codename_line) + + sprintf("https://packagemanager.posit.co/cran/__linux__/%s/%s", os_codename, format(date, "%Y-%m-%d")) } check_if_mirror_is_available <- function(date) {