diff --git a/X11/Dockerfile b/X11/Dockerfile index d35df24..9db7fb6 100644 --- a/X11/Dockerfile +++ b/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 \ diff --git a/r-ver/Dockerfile b/r-ver/Dockerfile index 2ba8baf..a33c500 100644 --- a/r-ver/Dockerfile +++ b/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 diff --git a/rstudio/Dockerfile b/rstudio/Dockerfile index 0213d83..5df3f44 100644 --- a/rstudio/Dockerfile +++ b/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 $line ; done \ + \n exec /usr/lib/rstudio-server/bin/rserver --server-daemonize 0' \ + > /etc/services.d/rstudio/run \ + && echo '#!/bin/bash \ + \n rstudio-server stop' \ + > /etc/services.d/rstudio/finish \ + && mkdir -p /home/rstudio/.rstudio/monitored/user-settings \ + && echo 'alwaysSaveHistory="0" \ + \nloadRData="0" \ + \nsaveAction="0"' \ + > /home/rstudio/.rstudio/monitored/user-settings/user-settings \ + && chown -R rstudio:rstudio /home/rstudio/.rstudio COPY userconf.sh /etc/cont-init.d/userconf diff --git a/tidyverse/Dockerfile b/tidyverse/Dockerfile index 146699d..35f8169 100644 --- a/tidyverse/Dockerfile +++ b/tidyverse/Dockerfile @@ -1,4 +1,4 @@ -FROM rocker/rstudio:3.5.0 +FROM rocker/rstudio:3.5.1 RUN apt-get update -qq && apt-get -y --no-install-recommends install \ libxml2-dev \ @@ -9,20 +9,14 @@ RUN apt-get update -qq && apt-get -y --no-install-recommends install \ libpq-dev \ libssh2-1-dev \ unixodbc-dev \ - && R -e "source('https://bioconductor.org/biocLite.R')" \ && install2.r --error \ --deps TRUE \ tidyverse \ dplyr \ - ggplot2 \ devtools \ formatR \ remotes \ selectr \ - caTools + caTools \ + BiocManager -## Notes: Above install2.r uses --deps TRUE to get Suggests dependencies as well, -## dplyr and ggplot are already part of tidyverse, but listed explicitly to get their (many) suggested dependencies. -## In addition to the the title 'tidyverse' packages, devtools is included for package development. -## RStudio wants formatR for rmarkdown, even though it's not suggested. -## remotes included for installation from heterogenous sources including git/svn, local, url, and specific cran versions diff --git a/verse/Dockerfile b/verse/Dockerfile index 1d1ede9..63c7fcc 100644 --- a/verse/Dockerfile +++ b/verse/Dockerfile @@ -1,4 +1,4 @@ -FROM rocker/tidyverse:3.5.0 +FROM rocker/tidyverse:3.5.1 ENV PATH=$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