Merge branch 'master' into freeze-version

731cb7a3 · Olivier Benz · d2f53e89 · b770b02f · 731cb7a3 · 731cb7a3
Verified Commit 731cb7a3 authored 2 years ago by Olivier Benz
--- a/.github/issue_template.md
+++ b/.github/issue_template.md
+---
+name: Tracking issue
+about: This repository is the source for R <= 3.6.3 images built before 2020-04; issues for R >= 4.0.0 images built after 2020-04 should be created in https://github.com/rocker-org/rocker-versioned2, not here.
+---
+
+<!-- This repository is the source for R <= 3.6.3 images built before 2020-04; issues for R >= 4.0.0 images built after 2020-04 should be created in https://github.com/rocker-org/rocker-versioned2, not here. -->
--- a/README.md
+++ b/README.md
-[![CircleCI](https://circleci.com/gh/rocker-org/rocker-versioned.svg?style=svg)](https://circleci.com/gh/rocker-org/rocker-versioned)
 [![license](https://img.shields.io/badge/license-GPLv2-blue.svg)](https://opensource.org/licenses/GPL-2.0)
-[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
+[![Project Status: Moved to https://github.com/rocker-org/rocker-versioned2 – The project has been moved to a new location, and the version at that location should be considered authoritative.](https://www.repostatus.org/badges/latest/moved.svg)](https://github.com/rocker-org/rocker-versioned2)
 [![DOI](https://zenodo.org/badge/25048007.svg)](https://zenodo.org/badge/latestdoi/25048007)


 Visit [rocker-project.org](https://rocker-project.org) for more about available Rocker images, configuration, and use. 

+# MOVED to [`rocker-versioned2`](https://github.com/rocker-org/rocker-versioned2)

-## Version-stable Rocker images
+This repository contains archived build scripts from the 3.x versioned series only.  Visit  [`rocker-versioned2`](https://github.com/rocker-org/rocker-versioned2) for current build scripts for 4.x versioned images.
+
+
+## Version-stable Rocker images for R 3.x

 ![rocker](https://avatars0.githubusercontent.com/u/9100160?v=3&s=200)

+***For documentation for R >= 4.0.0, for images `r-ver`, `rstudio`, `tidyverse`, `verse`, `geospatial`, `shiny`, and `binder`, please see the [`rocker-versioned2` repository](https://github.com/rocker-org/rocker-versioned2).*** 
+

 image            | description                               | size   | metrics | build status 
 ---------------- | ----------------------------------------- | ------ | ------- | --------------
 [r-ver](https://hub.docker.com/r/rocker/r-ver)            |  Version-stable base R & src build tools  | [![](https://images.microbadger.com/badges/image/rocker/r-ver.svg)](https://microbadger.com/images/rocker/r-ver) | [![](https://img.shields.io/docker/pulls/rocker/r-ver.svg)](https://hub.docker.com/r/rocker/r-ver) |  [![](https://img.shields.io/docker/automated/rocker/r-ver.svg)](https://hub.docker.com/r/rocker/r-ver/builds)
-[rstudio](https://hub.docker.com/r/rocker/rstudio)          |  Adds rstudio                             | [![](https://images.microbadger.com/badges/image/rocker/rstudio-stable.svg)](https://microbadger.com/) | [![](https://img.shields.io/docker/pulls/rocker/rstudio.svg)](https://hub.docker.com/r/rocker/rstudio)  |  [![](https://img.shields.io/docker/automated/rocker/rstudio.svg)](https://hub.docker.com/r/rocker/rstudio/builds)
+[rstudio](https://hub.docker.com/r/rocker/rstudio)          |  Adds rstudio                             | [![](https://images.microbadger.com/badges/image/rocker/rstudio-stable.svg)](https://microbadger.com/images/rocker/rstudio) | [![](https://img.shields.io/docker/pulls/rocker/rstudio.svg)](https://hub.docker.com/r/rocker/rstudio)  |  [![](https://img.shields.io/docker/automated/rocker/rstudio.svg)](https://hub.docker.com/r/rocker/rstudio/builds)
 [tidyverse](https://hub.docker.com/r/rocker/tidyverse)        |  Adds tidyverse & devtools                | [![](https://images.microbadger.com/badges/image/rocker/tidyverse.svg)](https://microbadger.com/images/rocker/tidyverse) | [![](https://img.shields.io/docker/pulls/rocker/tidyverse.svg)](https://hub.docker.com/r/rocker/tidyverse) |  [![](https://img.shields.io/docker/automated/rocker/tidyverse.svg)](https://hub.docker.com/r/rocker/tidyverse/builds) 
 [verse](https://hub.docker.com/r/rocker/verse)            |  Adds tex & publishing-related packages   | [![](https://images.microbadger.com/badges/image/rocker/verse.svg)](https://microbadger.com/images/rocker/verse) | [![](https://img.shields.io/docker/pulls/rocker/verse.svg)](https://hub.docker.com/r/rocker/verse) | [![](https://img.shields.io/docker/automated/rocker/verse.svg)](https://hub.docker.com/r/rocker/verse/builds)


--- a/VERSIONS.md
+++ b/VERSIONS.md
@@ -52,9 +52,9 @@ docker build --build-arg RSTUDIO_VERSION=1.1.414 -t rocker/rstudio:3.4.2 .
 | 3.5.1    | 2018-12-20 | 1.1.463         | stretch (9)    |
 | 3.5.2    | 2019-03-11 | 1.1.463         | stretch (9)    |
 | 3.5.3    | 2019-04-26 | 1.2.1335        | stretch (9)    |
-| 3.6.0    | 2019-07-05 |           | stretch (9)    |
-| 3.6.1    | 2019-12-12 |           | stretch (9)    |
-| 3.6.2    | 2020-02-29 |           | buster (10)    |
-| 3.6.3    | latest     | latest          | buster (10)    |
-
+| 3.6.0    | 2019-07-05 | 1.2.1335        | stretch (9)    |
+| 3.6.1    | 2019-12-12 | 1.2.5019        | stretch (9)    |
+| 3.6.2    | 2020-02-29 | 1.2.5033        | buster (10)    |
+| 3.6.3    | 2020-04-24 | 1.2.5042        | buster (10)    |

+Images starting with 4.0.0 are based on the stable Ubuntu release contemporary with the R version release (i.e. `ubuntu:focal` for 4.0.x and 4.1.x), and pin versions of RStudio, R packages and other software as defined in https://github.com/rocker-org/rocker-versioned2/tree/master/stacks
--- a/geospatial/.gitlab-ci.yml
+++ b/geospatial/.gitlab-ci.yml
@@ -5,27 +5,35 @@ services:
 variables:
  DOCKER_DRIVER: overlay2
  DOCKER_TLS_CERTDIR: "/certs"
+  R_VERSION: "4.2.0"
  UPDATE_MODE: "false"

 before_script:
-  - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-  - export VERSION_MAJ_MIN_PAT=`cat geospatial/latest.Dockerfile | head -n1 | sed 's/.*\([0-9].[0-9].[0-9]\)/\1/'`
-  - export VERSION_MAJ_MIN=`echo "${VERSION_MAJ_MIN_PAT:0:3}"`
-  - export VERSION_MAJ=`echo "${VERSION_MAJ_MIN_PAT:0:1}"`
+  - >
+    echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER
+    --password-stdin $CI_REGISTRY
+  - >
+    export VERSION_MAJ_MIN_PAT=$R_VERSION
+    
+    export VERSION_MAJ_MIN=`echo $VERSION_MAJ_MIN_PAT |
+    sed -n "s|\([[:digit:]]\+\.[[:digit:]]\+\).*|\1|p"`
+    
+    export VERSION_MAJ=`echo $VERSION_MAJ_MIN_PAT |
+    sed -n "s|\([[:digit:]]\+\).*|\1|p"`

 build-latest:
  stage: build
  script:
    - >
-      cd geospatial && docker build --pull --build-arg NCPUS=$((`nproc`/2+1))
-      -t $CI_REGISTRY_IMAGE:latest -f latest.Dockerfile .
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ
-    - docker push $CI_REGISTRY_IMAGE:latest
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ
+      docker build --pull
+      --build-arg R_VERSION
+      --build-arg NCPUS=$((`nproc`/2+1))
+      -t $CI_REGISTRY_IMAGE:latest
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ
+      -f geospatial/latest.Dockerfile .
+    - docker push -a $CI_REGISTRY_IMAGE
  rules:
    - if: $CI_COMMIT_BRANCH == "master" && $UPDATE_MODE != "true"
      changes:
@@ -35,10 +43,13 @@ build-version:
  stage: build
  script:
    - >
-      cd geospatial && docker build --pull --build-arg NCPUS=$((`nproc`/2+1))
-      -t $CI_REGISTRY_IMAGE:4.1.3 -f 4.1.3.Dockerfile .
-    - docker push $CI_REGISTRY_IMAGE:4.1.3
+      docker build --pull
+      --build-arg R_VERSION
+      --build-arg NCPUS=$((`nproc`/2+1))
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -f geospatial/$R_VERSION.Dockerfile .
+    - docker push -a $CI_REGISTRY_IMAGE
  rules:
-    - if: $CI_COMMIT_BRANCH == "freeze-version" && $UPDATE_MODE != "true"
+    - if: $CI_COMMIT_BRANCH == "freeze-version" && $CI_PIPELINE_TRIGGERED
      changes:
-        - geospatial/4.1.3.Dockerfile
+        - geospatial/$R_VERSION.Dockerfile
--- a/geospatial/latest.Dockerfile
+++ b/geospatial/latest.Dockerfile
-FROM registry.gitlab.b-data.ch/rocker/verse:4.1.3
+ARG R_VERSION
+
+FROM registry.gitlab.b-data.ch/rocker/verse:${R_VERSION}

 ARG NCPUS=1

@@ -26,7 +28,6 @@ RUN apt-get update \
    unixodbc-dev \
  && install2.r --error --skipinstalled -n $NCPUS \
    RColorBrewer \
-    RandomFields \
    RNetCDF \
    classInt \
    deldir \
@@ -52,8 +53,11 @@ RUN apt-get update \
    terra \
    tidync \
    tmap \
-    geoR \
    geosphere \
+  ## Archived on 2022-05-04 as check problems were not corrected in time.
+  && Rscript -e "devtools::install_version('RandomFields', version = '3.3.14')" \
+  ## Archived on 2022-05-04 as requires archived package 'RandomFields'.
+  && Rscript -e "devtools::install_version('geoR', version = '1.8-1')" \
  ## from bioconductor
  && R -e "BiocManager::install('rhdf5', update = FALSE, ask = FALSE)" \
  ## Clean up

--- a/r-ver/.gitlab-ci.yml
+++ b/r-ver/.gitlab-ci.yml
@@ -9,7 +9,7 @@
    if [[ $CI_COMMIT_BRANCH == "master" ]]; then
      export CI_APP_TAG=${CI_APP_TAG:-latest}
    elif [[ $CI_COMMIT_BRANCH == "freeze-version" ]]; then
-      export CI_APP_TAG=${CI_APP_TAG:-4.1.3}
+      export CI_APP_TAG=${CI_APP_TAG:-$R_VERSION}
    else
      export CI_APP_TAG=${CI_APP_TAG:-$CI_COMMIT_SHA}
    fi
@@ -17,9 +17,7 @@
    echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER
    --password-stdin $CI_REGISTRY
  - >
-    export VERSION_MAJ_MIN_PAT=`sed -n
-    "s|.*R_VERSION=\([[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\).*|\1|p"
-    r-ver/$CI_APP_TAG.Dockerfile | head -1`
+    export VERSION_MAJ_MIN_PAT=$R_VERSION
    
    export VERSION_MAJ_MIN=`echo $VERSION_MAJ_MIN_PAT |
    sed -n "s|\([[:digit:]]\+\.[[:digit:]]\+\).*|\1|p"`
@@ -35,8 +33,8 @@
  variables:
    DOCKER_DRIVER: overlay2
    DOCKER_TLS_CERTDIR: "/certs"
-    CRAN: https://cloud.r-project.org
-    UPDATE_MODE: "false"
+    R_VERSION: "4.2.0"
+    CRAN: "https://cloud.r-project.org"
  before_script:
    - *before-script-build

@@ -47,12 +45,13 @@ build:latest-linux-amd64:
    - os:linux
  script:
    - >
-      docker build --build-arg CRAN=$CRAN --pull -t $CI_APP_REPO:$CI_APP_TAG-linux-amd64
+      docker build --pull
+      --build-arg CRAN
+      --build-arg R_VERSION
+      -t $CI_APP_REPO:$CI_APP_TAG-linux-amd64
      -t $CI_APP_REPO:$VERSION_MAJ_MIN_PAT-linux-amd64
-      -f r-ver/$CI_APP_TAG.Dockerfile .
-    - |
-      docker push $CI_APP_REPO:$CI_APP_TAG-linux-amd64
-      docker push $CI_APP_REPO:$VERSION_MAJ_MIN_PAT-linux-amd64
+      -f r-ver/latest.Dockerfile .
+    - docker push -a $CI_APP_REPO
  rules:
    - if: $CI_COMMIT_BRANCH == "master" && $CI_BUILD_PLATFORMS =~ /(linux\/amd64)/
      changes:
@@ -65,12 +64,13 @@ build:latest-linux-arm64v8:
    - os:linux
  script:
    - >
-      docker build --build-arg CRAN=$CRAN --pull -t $CI_APP_REPO:$CI_APP_TAG-linux-arm64v8
+      docker build --pull
+      --build-arg CRAN
+      --build-arg R_VERSION
+      -t $CI_APP_REPO:$CI_APP_TAG-linux-arm64v8
      -t $CI_APP_REPO:$VERSION_MAJ_MIN_PAT-linux-arm64v8
-      -f r-ver/$CI_APP_TAG.Dockerfile .
-    - |
-      docker push $CI_APP_REPO:$CI_APP_TAG-linux-arm64v8
-      docker push $CI_APP_REPO:$VERSION_MAJ_MIN_PAT-linux-arm64v8
+      -f r-ver/latest.Dockerfile .
+    - docker push -a $CI_APP_REPO
  rules:
    - if: $CI_COMMIT_BRANCH == "master" && $CI_BUILD_PLATFORMS =~ /(linux\/arm64\/v8)/
      changes:
@@ -83,13 +83,16 @@ build:version-linux-amd64:
    - os:linux
  script:
    - >
-      docker build --build-arg CRAN=$CRAN --pull -t $CI_APP_REPO:$CI_APP_TAG-linux-amd64
-      -f r-ver/$CI_APP_TAG.Dockerfile .
+      docker build --pull
+      --build-arg CRAN
+      --build-arg R_VERSION
+      -t $CI_APP_REPO:$CI_APP_TAG-linux-amd64
+      -f r-ver/$R_VERSION.Dockerfile .
    - docker push $CI_APP_REPO:$CI_APP_TAG-linux-amd64
  rules:
    - if: $CI_COMMIT_BRANCH == "freeze-version" && $CI_BUILD_PLATFORMS =~ /(linux\/amd64)/
      changes:
-        - r-ver/4.1.3.Dockerfile
+        - r-ver/$R_VERSION.Dockerfile

 build:version-linux-arm64v8:
  extends: .build
@@ -98,13 +101,16 @@ build:version-linux-arm64v8:
    - os:linux
  script:
    - >
-      docker build --build-arg CRAN=$CRAN --pull -t $CI_APP_REPO:$CI_APP_TAG-linux-arm64v8
-      -f r-ver/$CI_APP_TAG.Dockerfile .
+      docker build --pull
+      --build-arg CRAN
+      --build-arg R_VERSION
+      -t $CI_APP_REPO:$CI_APP_TAG-linux-arm64v8
+      -f r-ver/$R_VERSION.Dockerfile .
    - docker push $CI_APP_REPO:$CI_APP_TAG-linux-arm64v8
  rules:
    - if: $CI_COMMIT_BRANCH == "freeze-version" && $CI_BUILD_PLATFORMS =~ /(linux\/arm64\/v8)/
      changes:
-        - r-ver/4.1.3.Dockerfile
+        - r-ver/$R_VERSION.Dockerfile

 build-manifest:latest-linux-multiarch:
  extends: .build
@@ -165,21 +171,7 @@ build-manifest:version-linux-multiarch:
  rules:
    - if: $CI_COMMIT_BRANCH == "freeze-version"
      changes:
-        - r-ver/4.1.3.Dockerfile
-
-trigger-latest-build-foreign:
-  extends: .build
-  stage: .post
-  before_script:
-    - apk upgrade --no-cache
-    - apk add --update --no-cache curl
-  script:
-    - curl -X POST -F token=$R_TIDYVERSE -F ref=master https://gitlab.b-data.ch/api/v4/projects/173/trigger/pipeline
-    - curl -X POST -F token=$R_PLUMBER -F ref=master https://gitlab.b-data.ch/api/v4/projects/176/trigger/pipeline
-  rules:
-    - if: $CI_COMMIT_BRANCH == "master" && $UPDATE_MODE != "true"
-      changes:
-        - r-ver/latest.Dockerfile
+        - r-ver/$R_VERSION.Dockerfile

 trigger-latest-build:
  extends: .build
@@ -205,4 +197,4 @@ trigger-version-build:
  rules:
    - if: $CI_COMMIT_BRANCH == "freeze-version"
      changes:
-        - r-ver/4.1.3.Dockerfile
+        - r-ver/$R_VERSION.Dockerfile
--- a/r-ver/latest.Dockerfile
+++ b/r-ver/latest.Dockerfile
 ARG IMAGE=debian:bullseye
-ARG R_VERSION=4.1.3
+ARG BLAS=libopenblas-dev
+ARG R_VERSION
+ARG CRAN=https://cran.rstudio.com

 FROM registry.gitlab.b-data.ch/r/rsi/${R_VERSION}/${IMAGE} as rsi

 FROM ${IMAGE}

 LABEL org.opencontainers.image.licenses="GPL-2.0" \
-      org.opencontainers.image.source="https://gitlab.b-data.ch/r/docker-stack" \
+      org.opencontainers.image.source="https://gitlab.b-data.ch/rocker/docker-stack" \
      org.opencontainers.image.vendor="b-data GmbH" \
      org.opencontainers.image.authors="Olivier Benz <olivier.benz@b-data.ch>"

-ARG IMAGE=debian:bullseye
+ARG IMAGE
 ARG DEBIAN_FRONTEND=noninteractive

-ARG BLAS=libopenblas-dev
-ARG R_VERSION=4.1.3
+ARG BLAS
+ARG R_VERSION
+ARG CRAN
 ARG BUILD_DATE
-ARG CRAN=https://cran.rstudio.com
 ## Setting a BUILD_DATE will set CRAN to the matching MRAN date
 ## No BUILD_DATE means that CRAN will default to latest 
 ENV BASE_IMAGE=${IMAGE} \
@@ -46,7 +48,7 @@ RUN apt-get update \
    liblapack-dev \
    liblzma-dev \
    ${BLAS} \
-    libpangocairo-1.0.0 \
+    libpangocairo-1.0-0 \
    libpaper-utils \
    '^libpcre[2|3]-dev$' \
    libpng-dev \
@@ -72,15 +74,13 @@ RUN apt-get update \
  && mkdir -p /usr/local/lib/R/site-library \
  && chown root:staff /usr/local/lib/R/site-library \
  && chmod g+ws /usr/local/lib/R/site-library \
-  ## Fix library path
-  && echo "R_LIBS_SITE=\${R_LIBS_SITE-'/usr/local/lib/R/site-library'}" >> /usr/local/lib/R/etc/Renviron.site \
  ## Set configured CRAN mirror
  && if [ -z "$BUILD_DATE" ]; then MRAN=$CRAN; \
   else MRAN=https://mran.microsoft.com/snapshot/${BUILD_DATE}; fi \
-   && echo MRAN=$MRAN >> /etc/environment \
+  && echo MRAN=$MRAN >> /etc/environment \
  && echo "options(repos = c(CRAN='$MRAN'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \
  ## Use littler installation scripts
-  && Rscript -e "install.packages(c('littler', 'docopt'), repos = '$CRAN')" \
+  && Rscript -e "install.packages(c('littler', 'docopt'), repos = '$MRAN')" \
  && ln -s /usr/local/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
  && ln -s /usr/local/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
  && ln -s /usr/local/lib/R/site-library/littler/bin/r /usr/local/bin/r \

--- a/rstudio/.gitlab-ci.yml
+++ b/rstudio/.gitlab-ci.yml
@@ -5,25 +5,34 @@ services:
 variables:
  DOCKER_DRIVER: overlay2
  DOCKER_TLS_CERTDIR: "/certs"
+  R_VERSION: "4.2.0"
  UPDATE_MODE: "false"

 before_script:
-  - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-  - export VERSION_MAJ_MIN_PAT=`sed -n "s|.*r-ver:\([0-9]\.[0-9]\.[0-9]\).*|\1|p" rstudio/latest.Dockerfile`
-  - export VERSION_MAJ_MIN=`echo "${VERSION_MAJ_MIN_PAT:0:3}"`
-  - export VERSION_MAJ=`echo "${VERSION_MAJ_MIN_PAT:0:1}"`
+  - >
+    echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER
+    --password-stdin $CI_REGISTRY
+  - >
+    export VERSION_MAJ_MIN_PAT=$R_VERSION
+    
+    export VERSION_MAJ_MIN=`echo $VERSION_MAJ_MIN_PAT |
+    sed -n "s|\([[:digit:]]\+\.[[:digit:]]\+\).*|\1|p"`
+    
+    export VERSION_MAJ=`echo $VERSION_MAJ_MIN_PAT |
+    sed -n "s|\([[:digit:]]\+\).*|\1|p"`

 build-latest:
  stage: build
  script:
-    - cd rstudio && docker build --pull -t $CI_REGISTRY_IMAGE:latest -f latest.Dockerfile .
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ
-    - docker push $CI_REGISTRY_IMAGE:latest
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ
+    - >
+      cd rstudio && docker build --pull
+      --build-arg R_VERSION
+      -t $CI_REGISTRY_IMAGE:latest
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ
+      -f latest.Dockerfile .
+    - docker push -a $CI_REGISTRY_IMAGE
  rules:
    - if: $CI_COMMIT_BRANCH == "master" && $UPDATE_MODE != "true"
      changes:
@@ -32,12 +41,16 @@ build-latest:
 build-version:
  stage: build
  script:
-    - cd rstudio && docker build --pull -t $CI_REGISTRY_IMAGE:4.1.3 -f 4.1.3.Dockerfile .
-    - docker push $CI_REGISTRY_IMAGE:4.1.3
+    - >
+      cd rstudio && docker build --pull
+      --build-arg R_VERSION
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -f $R_VERSION.Dockerfile .
+    - docker push -a $CI_REGISTRY_IMAGE
  rules:
-    - if: $CI_COMMIT_BRANCH == "freeze-version" && $UPDATE_MODE != "true"
+    - if: $CI_COMMIT_BRANCH == "freeze-version" && $CI_PIPELINE_TRIGGERED
      changes:
-        - rstudio/4.1.3.Dockerfile
+        - rstudio/$R_VERSION.Dockerfile

 trigger-latest-build:
  stage: deploy
@@ -59,6 +72,6 @@ trigger-version-build:
  script:
    - curl -X POST -F token=$ROCKER_TIDYVERSE -F ref=freeze-version https://gitlab.b-data.ch/api/v4/projects/186/trigger/pipeline
  rules:
-    - if: $CI_COMMIT_BRANCH == "freeze-version" && $UPDATE_MODE != "true"
+    - if: $CI_COMMIT_BRANCH == "freeze-version" && $CI_PIPELINE_TRIGGERED
      changes:
-        - rstudio/4.1.3.Dockerfile
+        - rstudio/$R_VERSION.Dockerfile
--- a/rstudio/README.md
+++ b/rstudio/README.md
@@ -52,19 +52,18 @@ Navigate to <http://localhost:8787> and you should be logged into RStudio as
 the `rstudio` user without needing a password.


-### Add shiny server on start up with `e ADD=shiny`
+### Add shiny server 

-    docker run -d -p 3838:3838 -p 8787:8787 -e ADD=shiny -e PASSWORD=yourpasswordhere rocker/rstudio
-
-shiny server is now running on `localhost:3838` and RStudio on `localhost:8787`.  
+If you are building your own Dockerfiles on top of this stack, you should simply include the RUN command:

+    RUN /rocker_scripts/install_shiny_server.sh

-Note: this triggers shiny install at runtime, which may require a few minutes to execute before services come up.
-If you are building your own Dockerfiles on top of this stack, you should simply include the RUN command:
+This works on any rocker-versioned image with R >= 4.0.0. 
+NOTE: older images tagged with R version 3.x.x will need to do:

    RUN export ADD=shiny && bash /etc/cont-init.d/add

-Then omit the `-e ADD=shiny` when running your image and shiny should be installed and waiting on port 3838.
+Run your image and shiny should be installed and waiting on port 3838.

 **Note**: Please see the `rocker/shiny` and `rocker/shiny-verse` images for
 setting up a shiny server in a separate container from RStudio. 

--- a/rstudio/latest.Dockerfile
+++ b/rstudio/latest.Dockerfile
 ARG IMAGE=debian:bullseye
-ARG GIT_VERSION=2.35.1
+ARG R_VERSION
+ARG GIT_VERSION=2.36.1
+ARG RSTUDIO_VERSION=2022.02.3+492
+ARG S6_VERSION=v2.2.0.3

 FROM registry.gitlab.b-data.ch/git/gsi/${GIT_VERSION}/${IMAGE} as gsi

-FROM registry.gitlab.b-data.ch/r/r-ver:4.1.3
+FROM registry.gitlab.b-data.ch/r/r-ver:${R_VERSION}

 ARG DEBIAN_FRONTEND=noninteractive

-ARG GIT_VERSION=2.35.1
-ARG RSTUDIO_VERSION=2022.02.1+461
-ARG S6_VERSION=v2.2.0.3
+ARG GIT_VERSION
+ARG RSTUDIO_VERSION
+ARG S6_VERSION

 ENV GIT_VERSION=${GIT_VERSION} \
    RSTUDIO_VERSION=${RSTUDIO_VERSION} \
@@ -21,7 +24,7 @@ COPY --from=gsi /usr/local /usr/local
 COPY --from=gsi /etc/bash_completion.d /etc/bash_completion.d

 ## Download and install RStudio server & dependencies
-## Attempts to get detect latest version, otherwise falls back to version given in $VER
+## Attempts to detect latest version, otherwise falls back to $RSTUDIO_VERSION
 RUN apt-get update \
  && apt-get install -y --no-install-recommends \
    curl \

--- a/tidyverse/.gitlab-ci.yml
+++ b/tidyverse/.gitlab-ci.yml
@@ -5,27 +5,35 @@ services:
 variables:
  DOCKER_DRIVER: overlay2
  DOCKER_TLS_CERTDIR: "/certs"
+  R_VERSION: "4.2.0"
  UPDATE_MODE: "false"

 before_script:
-  - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-  - export VERSION_MAJ_MIN_PAT=`cat tidyverse/latest.Dockerfile | head -n1 | sed 's/.*\([0-9].[0-9].[0-9]\)/\1/'`
-  - export VERSION_MAJ_MIN=`echo "${VERSION_MAJ_MIN_PAT:0:3}"`
-  - export VERSION_MAJ=`echo "${VERSION_MAJ_MIN_PAT:0:1}"`
+  - >
+    echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER
+    --password-stdin $CI_REGISTRY
+  - >
+    export VERSION_MAJ_MIN_PAT=$R_VERSION
+    
+    export VERSION_MAJ_MIN=`echo $VERSION_MAJ_MIN_PAT |
+    sed -n "s|\([[:digit:]]\+\.[[:digit:]]\+\).*|\1|p"`
+    
+    export VERSION_MAJ=`echo $VERSION_MAJ_MIN_PAT |
+    sed -n "s|\([[:digit:]]\+\).*|\1|p"`

 build-latest:
  stage: build
  script:
    - >
-      cd tidyverse && docker build --pull --build-arg NCPUS=$((`nproc`/2+1))
-      -t $CI_REGISTRY_IMAGE:latest -f latest.Dockerfile .
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ
-    - docker push $CI_REGISTRY_IMAGE:latest
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ
+      docker build --pull
+      --build-arg R_VERSION
+      --build-arg NCPUS=$((`nproc`/2+1))
+      -t $CI_REGISTRY_IMAGE:latest
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ
+      -f tidyverse/latest.Dockerfile .
+    - docker push -a $CI_REGISTRY_IMAGE
  rules:
    - if: $CI_COMMIT_BRANCH == "master" && $UPDATE_MODE != "true"
      changes:
@@ -35,13 +43,16 @@ build-version:
  stage: build
  script:
    - >
-      cd tidyverse && docker build --pull --build-arg NCPUS=$((`nproc`/2+1))
-      -t $CI_REGISTRY_IMAGE:4.1.3 -f 4.1.3.Dockerfile .
-    - docker push $CI_REGISTRY_IMAGE:4.1.3
+      docker build --pull
+      --build-arg R_VERSION
+      --build-arg NCPUS=$((`nproc`/2+1))
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -f tidyverse/$R_VERSION.Dockerfile .
+    - docker push -a $CI_REGISTRY_IMAGE
  rules:
-    - if: $CI_COMMIT_BRANCH == "freeze-version" && $UPDATE_MODE != "true"
+    - if: $CI_COMMIT_BRANCH == "freeze-version" && $CI_PIPELINE_TRIGGERED
      changes:
-        - tidyverse/4.1.3.Dockerfile
+        - tidyverse/$R_VERSION.Dockerfile

 trigger-latest-build:
  stage: deploy
@@ -63,6 +74,6 @@ trigger-version-build:
  script:
    - curl -X POST -F token=$ROCKER_VERSE -F ref=freeze-version https://gitlab.b-data.ch/api/v4/projects/187/trigger/pipeline
  rules:
-    - if: $CI_COMMIT_BRANCH == "freeze-version" && $UPDATE_MODE != "true"
+    - if: $CI_COMMIT_BRANCH == "freeze-version" && $CI_PIPELINE_TRIGGERED
      changes:
-        - tidyverse/4.1.3.Dockerfile
+        - tidyverse/$R_VERSION.Dockerfile
--- a/tidyverse/latest.Dockerfile
+++ b/tidyverse/latest.Dockerfile
-FROM registry.gitlab.b-data.ch/rocker/rstudio:4.1.3
+ARG R_VERSION
+
+FROM registry.gitlab.b-data.ch/rocker/rstudio:${R_VERSION}

 ARG NCPUS=1


--- a/verse/.gitlab-ci.yml
+++ b/verse/.gitlab-ci.yml
@@ -5,27 +5,35 @@ services:
 variables:
  DOCKER_DRIVER: overlay2
  DOCKER_TLS_CERTDIR: "/certs"
+  R_VERSION: "4.2.0"
  UPDATE_MODE: "false"

 before_script:
-  - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-  - export VERSION_MAJ_MIN_PAT=`cat verse/latest.Dockerfile | head -n1 | sed 's/.*\([0-9].[0-9].[0-9]\)/\1/'`
-  - export VERSION_MAJ_MIN=`echo "${VERSION_MAJ_MIN_PAT:0:3}"`
-  - export VERSION_MAJ=`echo "${VERSION_MAJ_MIN_PAT:0:1}"`
+  - >
+    echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER
+    --password-stdin $CI_REGISTRY
+  - >
+    export VERSION_MAJ_MIN_PAT=$R_VERSION
+    
+    export VERSION_MAJ_MIN=`echo $VERSION_MAJ_MIN_PAT |
+    sed -n "s|\([[:digit:]]\+\.[[:digit:]]\+\).*|\1|p"`
+    
+    export VERSION_MAJ=`echo $VERSION_MAJ_MIN_PAT |
+    sed -n "s|\([[:digit:]]\+\).*|\1|p"`

 build-latest:
  stage: build
  script:
    - >
-      cd verse && docker build --pull --build-arg NCPUS=$((`nproc`/2+1))
-      -t $CI_REGISTRY_IMAGE:latest -f latest.Dockerfile .
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
-    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$VERSION_MAJ
-    - docker push $CI_REGISTRY_IMAGE:latest
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
-    - docker push $CI_REGISTRY_IMAGE:$VERSION_MAJ
+      docker build --pull
+      --build-arg R_VERSION
+      --build-arg NCPUS=$((`nproc`/2+1))
+      -t $CI_REGISTRY_IMAGE:latest
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ
+      -f verse/latest.Dockerfile .
+    - docker push -a $CI_REGISTRY_IMAGE
  rules:
    - if: $CI_COMMIT_BRANCH == "master" && $UPDATE_MODE != "true"
      changes:
@@ -35,13 +43,16 @@ build-version:
  stage: build
  script:
    - >
-      cd verse && docker build --pull --build-arg NCPUS=$((`nproc`/2+1))
-      -t $CI_REGISTRY_IMAGE:4.1.3 -f 4.1.3.Dockerfile .
-    - docker push $CI_REGISTRY_IMAGE:4.1.3
+      docker build --pull
+      --build-arg R_VERSION
+      --build-arg NCPUS=$((`nproc`/2+1))
+      -t $CI_REGISTRY_IMAGE:$VERSION_MAJ_MIN_PAT
+      -f verse/$R_VERSION.Dockerfile .
+    - docker push -a $CI_REGISTRY_IMAGE
  rules:
-    - if: $CI_COMMIT_BRANCH == "freeze-version" && $UPDATE_MODE != "true"
+    - if: $CI_COMMIT_BRANCH == "freeze-version" && $CI_PIPELINE_TRIGGERED
      changes:
-        - verse/4.1.3.Dockerfile
+        - verse/$R_VERSION.Dockerfile

 trigger-latest-build:
  stage: deploy
@@ -63,6 +74,6 @@ trigger-version-build:
  script:
    - curl -X POST -F token=$ROCKER_GEOSPATIAL -F ref=freeze-version https://gitlab.b-data.ch/api/v4/projects/188/trigger/pipeline
  rules:
-    - if: $CI_COMMIT_BRANCH == "freeze-version" && $UPDATE_MODE != "true"
+    - if: $CI_COMMIT_BRANCH == "freeze-version" && $CI_PIPELINE_TRIGGERED
      changes:
-        - verse/4.1.3.Dockerfile
+        - verse/$R_VERSION.Dockerfile
--- a/verse/latest.Dockerfile
+++ b/verse/latest.Dockerfile
-FROM registry.gitlab.b-data.ch/rocker/tidyverse:4.1.3
+ARG R_VERSION
+ARG CTAN_REPO=https://mirror.ctan.org/systems/texlive/tlnet
+
+FROM registry.gitlab.b-data.ch/rocker/tidyverse:${R_VERSION}

 ARG NCPUS=1

 ARG DEBIAN_FRONTEND=noninteractive

-ARG CTAN_REPO=${CTAN_REPO:-https://mirror.ctan.org/systems/texlive/tlnet}
-ENV CTAN_REPO=${CTAN_REPO}
+ARG CTAN_REPO

-ENV PATH=/opt/TinyTeX/bin/x86_64-linux:$PATH
+ENV CTAN_REPO=${CTAN_REPO} \
+    PATH=/opt/TinyTeX/bin/linux:$PATH

 ## Add LaTeX, rticles and bookdown support
 RUN wget "https://travis-bin.yihui.name/texlive-local.deb" \
@@ -57,11 +60,15 @@ RUN wget "https://travis-bin.yihui.name/texlive-local.deb" \
  && wget -qO- "https://yihui.org/tinytex/install-unx.sh" \
    | sh -s - --admin --no-path \
  && mv ~/.TinyTeX /opt/TinyTeX \
-  && /opt/TinyTeX/bin/*/tlmgr path add \
+  && ln -rs /opt/TinyTeX/bin/$(uname -m)-linux \
+    /opt/TinyTeX/bin/linux \
+  && /opt/TinyTeX/bin/linux/tlmgr path add \
  && tlmgr update --self \
  && tlmgr install \
    ae \
+    cm-super \
    context \
+    dvipng \
    listings \
    makeindex \
    parskip \