Merge branch 'master' into freeze-version

geospatial/latest.Dockerfile

-FROM registry.gitlab.b-data.ch/rocker/verse:4.1.1
+FROM registry.gitlab.b-data.ch/rocker/verse:4.1.2
 
 ARG DEBIAN_FRONTEND=noninteractive
 

r-ver/latest.Dockerfile

 ARG IMAGE=debian:bullseye
-ARG R_VERSION=4.1.1
+ARG R_VERSION=4.1.2
 
 FROM registry.gitlab.b-data.ch/r/rsi/${R_VERSION}/${IMAGE} as rsi
 
@@ -14,7 +14,7 @@ ARG IMAGE=debian:bullseye
 ARG DEBIAN_FRONTEND=noninteractive
 
 ARG LAPACK=libopenblas-dev
-ARG R_VERSION=4.1.1
+ARG R_VERSION=4.1.2
 ARG BUILD_DATE
 ARG CRAN=https://cran.rstudio.com
 ## Setting a BUILD_DATE will set CRAN to the matching MRAN date
@@ -46,12 +46,12 @@ RUN apt-get update \
     '^libjpeg.*-turbo.*-dev$' \
     liblzma-dev \
     ${LAPACK} \
-    libpangocairo-* \
+    libpangocairo-1.0.0 \
     libpaper-utils \
     '^libpcre[2|3]-dev$' \
     libpng-dev \
     libreadline-dev \
-    libtiff* \
+    libtiff5 \
     locales \
     pkg-config \
     unzip \

rstudio/add_shiny.sh

@@ -2,21 +2,28 @@
 
 ADD=${ADD:=none}
 
+SHINY_SERVER_VERSION=${1:-${SHINY_SERVER_VERSION:-latest}}
+
+NCPUS=${NCPUS:--1}
+
 ## A script to add shiny to an rstudio-based rocker image.
 
+if [ "$SHINY_SERVER_VERSION" = "latest" ]; then
+  SHINY_SERVER_VERSION=$(wget -qO- https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION)
+fi
+
 if [ "$ADD" == "shiny" ]; then
   echo "Adding shiny server to container..."
   apt-get update && apt-get -y install \
     gdebi-core \
     libxt-dev && \
-    wget --no-verbose https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/VERSION -O "version.txt" && \
-    VERSION=$(cat version.txt)  && \
-    wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
+    wget --no-verbose "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-${SHINY_SERVER_VERSION}-amd64.deb" -O ss-latest.deb && \
     gdebi -n ss-latest.deb && \
-    rm -f version.txt ss-latest.deb && \
-    install2.r -e --skipinstalled shiny rmarkdown && \
+    rm -f ss-latest.deb && \
+    install2.r --error --skipinstalled -n $NCPUS shiny rmarkdown && \
     cp -R /usr/local/lib/R/site-library/shiny/examples/* /srv/shiny-server/ && \
     rm -rf /var/lib/apt/lists/* && \
+    rm -rf /tmp/downloaded_packages && \
     mkdir -p /var/log/shiny-server && \
     chown shiny.shiny /var/log/shiny-server && \
     mkdir -p /etc/services.d/shiny-server && \

rstudio/latest.Dockerfile

-ARG BASE_IMAGE=debian:bullseye
-ARG GIT_VERSION=2.32.0
+ARG IMAGE=debian:bullseye
+ARG GIT_VERSION=2.34.1
 
-FROM registry.gitlab.b-data.ch/git/gsi/${GIT_VERSION}/${BASE_IMAGE} as gsi
+FROM registry.gitlab.b-data.ch/git/gsi/${GIT_VERSION}/${IMAGE} as gsi
 
-FROM registry.gitlab.b-data.ch/r/r-ver:4.1.1
+FROM registry.gitlab.b-data.ch/r/r-ver:4.1.2
 
 ARG DEBIAN_FRONTEND=noninteractive
 
-ARG RSTUDIO_VERSION=1.4.1717
-ARG S6_VERSION=v1.21.7.0
-ARG GIT_VERSION=2.32.0
-ARG PANDOC_TEMPLATES_VERSION=2.14.2
+ARG GIT_VERSION=2.34.1
+ARG PANDOC_TEMPLATES_VERSION=2.14.1
+ARG RSTUDIO_VERSION=2021.09.2+382
+ARG S6_VERSION=v2.2.0.3
 
-ENV RSTUDIO_VERSION=${RSTUDIO_VERSION}
-ENV PATH=/usr/lib/rstudio-server/bin:$PATH
-ENV S6_VERSION=${S6_VERSION}
-ENV S6_BEHAVIOUR_IF_STAGE2_FAILS=2
-ENV GIT_VERSION=${GIT_VERSION}
-ENV PANDOC_TEMPLATES_VERSION=${PANDOC_TEMPLATES_VERSION}
+ENV GIT_VERSION=${GIT_VERSION} \
+    PANDOC_TEMPLATES_VERSION=${PANDOC_TEMPLATES_VERSION} \
+    RSTUDIO_VERSION=${RSTUDIO_VERSION} \
+    S6_VERSION=${S6_VERSION} \
+    S6_BEHAVIOUR_IF_STAGE2_FAILS=2 \
+    PATH=/usr/lib/rstudio-server/bin:$PATH
 
 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 $VER
@@ -48,9 +49,8 @@ RUN apt-get update \
     less \
     ssh-client \
   && if [ -z "$RSTUDIO_VERSION" ]; \
-    then RSTUDIO_URL="https://www.rstudio.org/download/latest/stable/server/bionic/rstudio-server-latest-amd64.deb"; \
-    else RSTUDIO_URL="http://download2.rstudio.org/server/bionic/amd64/rstudio-server-${RSTUDIO_VERSION}-amd64.deb"; fi \
-  && wget -q $RSTUDIO_URL \
+    then wget "https://www.rstudio.org/download/latest/stable/server/bionic/rstudio-server-latest-amd64.deb"; \
+    else /bin/bash -c 'wget "http://download2.rstudio.org/server/bionic/amd64/rstudio-server-${RSTUDIO_VERSION/'+'/'-'}-amd64.deb"'; fi \
   && dpkg -i rstudio-server-*-amd64.deb \
   && rm rstudio-server-*-amd64.deb \
   ## https://github.com/rocker-org/rocker-versioned2/issues/137
@@ -68,6 +68,7 @@ RUN apt-get update \
   && rm -rf /var/lib/apt/lists/* \
   ## RStudio wants an /etc/R, will populate from $R_HOME/etc
   && mkdir -p /etc/R \
+  && echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron.site \
   ## Need to configure non-root user for RStudio
   && useradd rstudio \
   && echo "rstudio:rstudio" | chpasswd \
@@ -88,7 +89,9 @@ RUN apt-get update \
   && git config --system push.default simple \
   ## Set up S6 init system
   && wget -P /tmp/ https://github.com/just-containers/s6-overlay/releases/download/${S6_VERSION}/s6-overlay-amd64.tar.gz \
-  && tar xzf /tmp/s6-overlay-amd64.tar.gz -C / \
+  ## need the modified double tar now, see https://github.com/just-containers/s6-overlay/issues/288
+  && tar hzxf /tmp/s6-overlay-amd64.tar.gz -C / --exclude=usr/bin/execlineb \
+  && tar hzxf /tmp/s6-overlay-amd64.tar.gz -C /usr ./bin/execlineb && $_clean \
   && mkdir -p /etc/services.d/rstudio \
   && echo '#!/usr/bin/with-contenv bash \
           \n## load /etc/environment vars first: \
@@ -100,14 +103,17 @@ RUN apt-get update \
           > /etc/services.d/rstudio/finish \
   && echo '[*] \
           \nlog-level=warn \
-          \nlogger-type=stderr' \
+          \nlogger-type=syslog' \
           > /etc/rstudio/logging.conf \
   && mkdir -p /home/rstudio/.rstudio/monitored/user-settings \
   && echo 'alwaysSaveHistory="0" \
           \nloadRData="0" \
           \nsaveAction="0"' \
           > /home/rstudio/.rstudio/monitored/user-settings/user-settings \
-  && chown -R rstudio:rstudio /home/rstudio/.rstudio
+  && chown -R rstudio:rstudio /home/rstudio/.rstudio \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/*
 
 COPY userconf.sh /etc/cont-init.d/userconf
 

tidyverse/latest.Dockerfile

-FROM registry.gitlab.b-data.ch/rocker/rstudio:4.1.1
+FROM registry.gitlab.b-data.ch/rocker/rstudio:4.1.2
 
 ARG DEBIAN_FRONTEND=noninteractive
 

verse/latest.Dockerfile

-FROM registry.gitlab.b-data.ch/rocker/tidyverse:4.1.1
+FROM registry.gitlab.b-data.ch/rocker/tidyverse:4.1.2
 
 ARG DEBIAN_FRONTEND=noninteractive