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" 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 ''' } 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. 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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. diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..a70d30a --- /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/\(ARG R_VERSION=\)[0-9]\+\.[0-9]\+\.[0-9]\+[^[:space:]]*/\1${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 ${IMAGES}; do \ + docker rmi inwt/$$img:${TAG} || true; \ + done diff --git a/README.md b/README.md index 5eefbe3..22021ec 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 && \ @@ -195,7 +196,7 @@ 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 $PWD:/app inwt/r-batch:4.5.1 check ``` diff --git a/r-base/Dockerfile b/r-base/Dockerfile index 9a3107c..6422485 100644 --- a/r-base/Dockerfile +++ b/r-base/Dockerfile @@ -1,20 +1,46 @@ -FROM rocker/r-ver:4.5.1 +# ------------------- +# Setup (Global Args) +# ------------------- +ARG R_VERSION=4.5.1 +ARG USER_NAME=user +ARG USER_UID=1000 +ARG USER_GID=1000 +ARG TZ="Europe/Berlin" +ARG LANG="en_US.UTF-8" + +# ---------------- +# Stage 1: builder +# ---------------- +FROM rocker/r-ver:${R_VERSION} AS builder + +# 1. User & Environment Setup +ARG USER_NAME +ARG USER_UID +ARG USER_GID +ARG TZ +ARG LANG -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 +ENV TZ=${TZ} +ENV LANG=${LANG} -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 ${USER_NAME} +WORKDIR /app +COPY . /includes/ + +# 2. System Dependencies, Timezone, and CA Certificates + # CA Certificates and Timezone Setup RUN mv -v /includes/*.crt /usr/local/share/ca-certificates/ \ && dpkg-reconfigure ca-certificates \ && rm /etc/localtime \ && ln -s /usr/share/zoneinfo/Europe/Berlin /etc/localtime \ - && echo "Europe/Berlin" > /etc/timezone \ + && echo "${TZ}" > /etc/timezone \ + # Install System Dependencies && apt-get -y update \ && apt-get -y upgrade \ && apt-get install -y --no-install-recommends \ @@ -42,7 +68,8 @@ 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 \ @@ -51,16 +78,76 @@ 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 \ - # 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 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 + +# -------------- +# Stage 2: final +# -------------- +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 +ARG USER_GID +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} \ + && useradd --uid ${USER_UID} --gid ${USER_GID} -m -G staff ${USER_NAME} + +# Set runtime environment variables +ENV HOME=/app +ENV TZ=${TZ} +ENV LANG=${LANG} + +# 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 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 ${HOME} + +CMD ["R"] diff --git a/r-base/get_mirror_date.R b/r-base/get_mirror_date.R index d4d9b4e..4deeb31 100644 --- a/r-base/get_mirror_date.R +++ b/r-base/get_mirror_date.R @@ -1,5 +1,9 @@ create_mirror_url <- function(date) { - sprintf("https://packagemanager.posit.co/cran/__linux__/jammy/%s", format(date, "%Y-%m-%d")) + os_info <- readLines("/etc/os-release") + os_codename_line <- grep("^VERSION_CODENAME=", os_info, value = TRUE) + os_codename <- gsub("VERSION_CODENAME=", "", os_codename_line) + + sprintf("https://packagemanager.posit.co/cran/__linux__/%s/%s", os_codename, format(date, "%Y-%m-%d")) } check_if_mirror_is_available <- function(date) { diff --git a/r-base/installAutomake.sh b/r-base/installAutomake.sh deleted file mode 100755 index 1873c24..0000000 --- a/r-base/installAutomake.sh +++ /dev/null @@ -1,28 +0,0 @@ -#!/bin/bash - -VERSION=${1} - -if echo $VERSION | grep -q '\..*\..*'; then - MAJOR_VERSION=${VERSION%.*} -else - MAJOR_VERSION=${VERSION} -fi - -function install_automake() { - wget http://ftp.gnu.org/gnu/automake/automake-$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 $VERSION" -} - -install_automake \ No newline at end of file diff --git a/r-batch/Dockerfile b/r-batch/Dockerfile index 128b632..5ec9402 100644 --- a/r-batch/Dockerfile +++ b/r-batch/Dockerfile @@ -1,46 +1,100 @@ -FROM inwt/r-base:4.5.1 +# ------------------- +# Setup (Global Args) +# ------------------- +ARG R_VERSION=4.5.1.non-root +ARG USER_NAME=user +ARG AWS_CLI_VERSION=2.25.13 -COPY aws.config /app/.aws/config +# ---------------- +# Stage 1: builder +# ---------------- +FROM inwt/r-base:${R_VERSION} AS batch-builder + +# 1. User and Environment Setup +ARG USER_NAME +ARG AWS_CLI_VERSION + +# 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 "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.25.13.zip" -o "awscliv2.zip" \ + 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-${AWS_CLI_VERSION}.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 ${USER_NAME} + +RUN installPackage \ + arrow \ + codetools \ + data.table \ + dplyr \ + futile.logger \ + gbm \ + ggplot2 \ + gridExtra \ + lintr \ + lme4 \ + mgcv \ + RClickhouse \ + rJava \ + RMySQL \ + roxygen2 \ + RPostgres \ + testthat \ + tidyr \ + dbtools \ + mctools \ && rm -rf /tmp/downloaded_packages/* + +# -------------- +# Stage 2: final +# -------------- +FROM inwt/r-base:${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-batch" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.version="${R_VERSION}" + +# 1. Enviroment and User Setup +ARG USER_NAME + +ENV HOME=/app + +# 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/ +# 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 ${HOME} + +CMD ["R"] diff --git a/r-batch/aws.config b/r-batch/aws.config deleted file mode 100644 index a5220e0..0000000 --- a/r-batch/aws.config +++ /dev/null @@ -1,2 +0,0 @@ -[default] -region = eu-central-1 diff --git a/r-geos/Dockerfile b/r-geos/Dockerfile index 69da132..440d873 100644 --- a/r-geos/Dockerfile +++ b/r-geos/Dockerfile @@ -1,15 +1,33 @@ -FROM inwt/r-batch:4.5.1 +# ------------------- +# Setup (Global Args) +# ------------------- +ARG R_VERSION=4.5.1.non-root +ARG USER_NAME=user +# ---------------- +# Stage 1: builder +# ---------------- +FROM inwt/r-batch:${R_VERSION} AS geos-builder + +# 1. User and Environment Setup +ARG USER_NAME + +# 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 ${USER_NAME} +RUN installPackage \ geojsonsf \ raster \ R.utils \ @@ -17,5 +35,32 @@ RUN apt-get -y update \ stars \ terra \ unix \ - && rm -rf /tmp/downloaded_packages/* + # Cleanup R build artifacts + && rm -rf /tmp/downloaded_packages/* + +# -------------- +# Stage 2: final +# -------------- +FROM inwt/r-batch:${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-geos" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.version="${R_VERSION}" + +# 1. Environment and User Setup +ARG USER_NAME +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 ${USER_NAME} +WORKDIR /app +CMD ["R"] diff --git a/r-model/Dockerfile b/r-model/Dockerfile index 518701d..891c6b2 100644 --- a/r-model/Dockerfile +++ b/r-model/Dockerfile @@ -1,11 +1,57 @@ -FROM inwt/r-batch:4.5.1 +# ------------------- +# Setup (Global Args) +# ------------------- +ARG R_VERSION=4.5.1.non-root +ARG USER_NAME=user +# ---------------- +# Stage 1: builder +# ---------------- +FROM inwt/r-batch:${R_VERSION} AS model-builder + +#1. User and Environment Setup +ARG USER_NAME + +# 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 ${USER_NAME} +RUN installPackage rstan \ + && installPackage prophet \ + # Cleanup R build artifacts + && rm -rf /tmp/downloaded_packages/* + +# -------------- +# Stage 2: final +# -------------- +FROM inwt/r-batch:${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-model" \ + org.opencontainers.image.vendor="INWT Statistics" \ + org.opencontainers.image.version="${R_VERSION}" + +# 1. Environment and User Setup +ARG USER_NAME +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 ${USER_NAME} +WORKDIR /app +CMD ["R"] diff --git a/r-shiny/Dockerfile b/r-shiny/Dockerfile index 60da7df..30e51cb 100644 --- a/r-shiny/Dockerfile +++ b/r-shiny/Dockerfile @@ -1,17 +1,40 @@ -FROM inwt/r-batch:4.5.1 +# ------------------- +# Setup (Global Args) +# ------------------- +ARG R_VERSION=4.5.1.non-root +ARG USER_NAME=user +ARG AUTOMAKE_VERSION=1.16.1 -EXPOSE 3838 +# ---------------- +# Stage 1: builder +# ---------------- +FROM inwt/r-batch:${R_VERSION} AS shiny-builder + +# 1. User and Environment Setup +ARG USER_NAME +ARG AUTOMAKE_VERSION -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 ${AUTOMAKE_VERSION} \ + # 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 ${USER_NAME} +RUN installPackage \ DT \ htmlwidgets \ leaflet \ @@ -22,4 +45,34 @@ RUN installAutomake 1.16.1 \ shinydashboard \ shinyjs \ shinythemes \ - plotly + plotly \ + && rm -rf /tmp/downloaded_packages/* + +# -------------- +# Stage 2: final +# -------------- +FROM inwt/r-batch:${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. Environment, Ports & User Setup +ARG USER_NAME +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 ${USER_NAME} +WORKDIR /app + +CMD ["R"] diff --git a/r-shiny/installAutomake.sh b/r-shiny/installAutomake.sh new file mode 100755 index 0000000..b30be30 --- /dev/null +++ b/r-shiny/installAutomake.sh @@ -0,0 +1,30 @@ +#!/bin/bash + +set -euo pipefail + +VERSION=${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 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