3.5.1

Author: cboettig

X11/Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/r-ver:3.5.0
+FROM rocker/r-ver:3.5.1
 
 ## R's X11 runtime dependencies
 RUN apt-get update \

r-ver/Dockerfile

@@ -7,8 +7,8 @@ LABEL org.label-schema.license="GPL-2.0" \
 
 ARG R_VERSION
 ARG BUILD_DATE
-ENV BUILD_DATE ${BUILD_DATE:-2018-07-02}
-ENV R_VERSION=${R_VERSION:-3.5.0} \
+ENV BUILD_DATE ${BUILD_DATE:-2018-12-20}
+ENV R_VERSION=${R_VERSION:-3.5.1} \
     LC_ALL=en_US.UTF-8 \
     LANG=en_US.UTF-8 \
     TERM=xterm

rstudio/Dockerfile

@@ -1,8 +1,10 @@
-FROM rocker/r-ver:3.5.0
+FROM rocker/r-ver:3.5.1
 
 ARG RSTUDIO_VERSION
-## Comment the next line to use the latest RStudio Server version by default
-ENV RSTUDIO_VERSION=${RSTUDIO_VERSION:-1.1.447}
+ENV RSTUDIO_VERSION=${RSTUDIO_VERSION:-1.1.463}
+ARG S6_VERSION
+ENV S6_VERSION=${S6_VERSION:-v1.21.7.0}
+ENV S6_BEHAVIOUR_IF_STAGE2_FAILS=2
 ENV PATH=/usr/lib/rstudio-server/bin:$PATH
 
 ## Download and install RStudio server & dependencies
@@ -18,10 +20,10 @@ RUN apt-get update \
     libssl-dev \
     lsb-release \
     psmisc \
+    procps \
     python-setuptools \
     sudo \
     wget \
-    multiarch-support \
   && wget -O libssl1.0.0.deb http://ftp.debian.org/debian/pool/main/o/openssl/libssl1.0.0_1.0.1t-1+deb8u8_amd64.deb \
   && dpkg -i libssl1.0.0.deb \
   && rm libssl1.0.0.deb \
@@ -64,17 +66,23 @@ RUN apt-get update \
   && git config --system credential.helper 'cache --timeout=3600' \
   && git config --system push.default simple \
   ## Set up S6 init system
-  && wget -P /tmp/ https://github.com/just-containers/s6-overlay/releases/download/v1.11.0.1/s6-overlay-amd64.tar.gz \
+  && 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 / \
   && mkdir -p /etc/services.d/rstudio \
   && echo '#!/usr/bin/with-contenv bash \
-           \n## load /etc/environment vars first: \
-           \n for line in $( cat /etc/environment ) ; do export $line ; done \
-           \n exec /usr/lib/rstudio-server/bin/rserver --server-daemonize 0' \
-           > /etc/services.d/rstudio/run \
-   && echo '#!/bin/bash \
-           \n rstudio-server stop' \
-           > /etc/services.d/rstudio/finish
+          \n## load /etc/environment vars first: \
+  		  \n for line in $( cat /etc/environment ) ; do export $line ; done \
+          \n exec /usr/lib/rstudio-server/bin/rserver --server-daemonize 0' \
+          > /etc/services.d/rstudio/run \
+  && echo '#!/bin/bash \
+          \n rstudio-server stop' \
+          > /etc/services.d/rstudio/finish \
+  && 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
 
 COPY userconf.sh /etc/cont-init.d/userconf
 

tidyverse/Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/rstudio:3.5.0
+FROM rocker/rstudio:3.5.1
 
 RUN apt-get update -qq && apt-get -y --no-install-recommends install \
   libxml2-dev \
@@ -9,20 +9,14 @@ RUN apt-get update -qq && apt-get -y --no-install-recommends install \
   libpq-dev \
   libssh2-1-dev \
   unixodbc-dev \
-  && R -e "source('https://bioconductor.org/biocLite.R')" \
   && install2.r --error \
     --deps TRUE \
     tidyverse \
     dplyr \
-    ggplot2 \
     devtools \
     formatR \
     remotes \
     selectr \
-    caTools
+    caTools \
+    BiocManager
 
-## Notes: Above install2.r uses --deps TRUE to get Suggests dependencies as well,
-## dplyr and ggplot are already part of tidyverse, but listed explicitly to get their (many) suggested dependencies.
-## In addition to the the title 'tidyverse' packages, devtools is included for package development.
-## RStudio wants formatR for rmarkdown, even though it's not suggested.
-## remotes included for installation from heterogenous sources including git/svn, local, url, and specific cran versions

verse/Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/tidyverse:3.5.0
+FROM rocker/tidyverse:3.5.1
 ENV PATH=$PATH:/opt/TinyTeX/bin/x86_64-linux/
 
 ## Add LaTeX, rticles and bookdown support
@@ -52,8 +52,7 @@ RUN wget "https://travis-bin.yihui.name/texlive-local.deb" \
   && chmod -R g+w /opt/TinyTeX \
   && chmod -R g+wx /opt/TinyTeX/bin \
   && echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron \
-  ## Currently (2017-06-06) need devel PKI for ssl issue: https://github.com/s-u/PKI/issues/19
-  && install2.r --error --repo http://rforge.net PKI \
+  && install2.r --error PKI \
   ## And some nice R packages for publishing-related stuff
   && install2.r --error --deps TRUE \
     bookdown rticles rmdshower