use bioclite

r-ver/3.3.3/Dockerfile

-FROM debian:jessie
-
-ARG R_VERSION
-ARG BUILD_DATE
-ENV BUILD_DATE ${BUILD_DATE:-2017-04-21}
-ENV R_VERSION ${R_VERSION:-3.3.3}
-ENV LC_ALL en_US.UTF-8
-ENV LANG en_US.UTF-8
-ENV TERM xterm
-
-## dependencies
-RUN apt-get update \
-  && apt-get install -y --no-install-recommends \
-    bash-completion \
-    ca-certificates \
-    file \
-    fonts-texgyre \
-    g++ \
-    gfortran \
-    gsfonts \
-    libbz2-1.0 \
-    libcurl3 \
-    libicu52 \
-    libjpeg62-turbo \
-    libopenblas-dev \
-    libpangocairo-1.0-0 \
-    libpcre3 \
-    libpng12-0 \
-    libtiff5 \
-    liblzma5 \
-    locales \
-    make \
-    unzip \
-    zip \
-    zlib1g \
-  && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
-  && locale-gen en_US.utf8 \
-  && /usr/sbin/update-locale LANG=en_US.UTF-8 \
-  && BUILDDEPS="curl \
-    default-jdk \
-    libbz2-dev \
-    libcairo2-dev \
-    libcurl4-openssl-dev \
-    libpango1.0-dev \
-    libjpeg-dev \
-    libicu-dev \
-    libpcre3-dev \
-    libpng-dev \
-    libreadline-dev \
-    libtiff5-dev \
-    liblzma-dev \
-    libx11-dev \
-    libxt-dev \
-    perl \
-    tcl8.5-dev \
-    tk8.5-dev \
-    texinfo \
-    texlive-extra-utils \
-    texlive-fonts-recommended \
-    texlive-fonts-extra \
-    texlive-latex-recommended \
-    x11proto-core-dev \
-    xauth \
-    xfonts-base \
-    xvfb \
-    zlib1g-dev" \
-  && apt-get install -y --no-install-recommends $BUILDDEPS \
-  && cd tmp/ \
-  ## Download source code
-  && curl -O https://cran.r-project.org/src/base/R-3/R-${R_VERSION}.tar.gz \
-  ## Extract source code
-  && tar -xf R-${R_VERSION}.tar.gz \
-  && cd R-${R_VERSION} \
-  ## Set compiler flags
-  && R_PAPERSIZE=letter \
-    R_BATCHSAVE="--no-save --no-restore" \
-    R_BROWSER=xdg-open \
-    PAGER=/usr/bin/pager \
-    PERL=/usr/bin/perl \
-    R_UNZIPCMD=/usr/bin/unzip \
-    R_ZIPCMD=/usr/bin/zip \
-    R_PRINTCMD=/usr/bin/lpr \
-    LIBnn=lib \
-    AWK=/usr/bin/awk \
-    CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \
-    CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \
-  ## Configure options
-  ./configure --enable-R-shlib \
-               --enable-memory-profiling \
-               --with-readline \
-               --with-blas="-lopenblas" \
-               --disable-nls \
-               --without-recommended-packages \
-  ## Build and install
-  && make \
-  && make install \
-  ## Add a default CRAN mirror
-  && echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \
-  ## Add a library directory (for user-installed packages)
-  && mkdir -p /usr/local/lib/R/site-library \
-  && chown root:staff /usr/local/lib/R/site-library \
-  && chmod g+wx /usr/local/lib/R/site-library \
-  ## Fix library path
-  && echo "R_LIBS_USER='/usr/local/lib/R/site-library'" >> /usr/local/lib/R/etc/Renviron \
-  && echo "R_LIBS=\${R_LIBS-'/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library'}" >> /usr/local/lib/R/etc/Renviron \
-  ## install packages from date-locked MRAN snapshot of CRAN
-  && [ -z "$BUILD_DATE" ] && BUILD_DATE=$(TZ="America/Los_Angeles" date -I) || true \
-  && MRAN=https://mran.microsoft.com/snapshot/${BUILD_DATE} \
-  && echo MRAN=$MRAN >> /etc/environment \
-  && export MRAN=$MRAN \
-  && echo "options(repos = c(CRAN='$MRAN'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \
-  ## Use littler installation scripts
-  && Rscript -e "install.packages(c('littler', 'docopt'), repo = '$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 \
-  ## Clean up from R source install
-  && cd / \
-  && rm -rf /tmp/* \
-  && apt-get remove --purge -y $BUILDDEPS \
-  && apt-get autoremove -y \
-  && apt-get autoclean -y \
-  && rm -rf /var/lib/apt/lists/*
-
-CMD ["R"]
-

tidyverse/3.3.1/Dockerfile

@@ -7,12 +7,15 @@ RUN apt-get update -qq && apt-get -y --no-install-recommends install \
   libmariadbd-dev \
   libmariadb-client-lgpl-dev \
   libpq-dev \
-  && . /etc/environment \
+  && R -e "source('https://bioconductor.org/biocLite.R')" \
   && install2.r --error \
-    --repos 'http://www.bioconductor.org/packages/release/bioc' \
-    --repos $MRAN \ 
     --deps TRUE \
-    tidyverse devtools dplyr ggplot2 profvis formatR remotes
+    tidyverse \
+    dplyr \
+    ggplot2 \
+    devtools \
+    formatR \
+    remotes
 
 ## 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.

tidyverse/3.3.2/Dockerfile

@@ -7,12 +7,15 @@ RUN apt-get update -qq && apt-get -y --no-install-recommends install \
   libmariadbd-dev \
   libmariadb-client-lgpl-dev \
   libpq-dev \
-  && . /etc/environment \
+  && R -e "source('https://bioconductor.org/biocLite.R')" \
   && install2.r --error \
-    --repos 'http://www.bioconductor.org/packages/release/bioc' \
-    --repos $MRAN \ 
     --deps TRUE \
-    tidyverse devtools dplyr ggplot2 profvis formatR remotes
+    tidyverse \
+    dplyr \
+    ggplot2 \
+    devtools \
+    formatR \
+    remotes
 
 ## 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.

tidyverse/3.3.3/Dockerfile

@@ -7,12 +7,15 @@ RUN apt-get update -qq && apt-get -y --no-install-recommends install \
   libmariadbd-dev \
   libmariadb-client-lgpl-dev \
   libpq-dev \
-  && . /etc/environment \
+  && R -e "source('https://bioconductor.org/biocLite.R')" \
   && install2.r --error \
-    --repos 'http://www.bioconductor.org/packages/release/bioc' \
-    --repos $MRAN \ 
     --deps TRUE \
-    tidyverse devtools dplyr ggplot2 profvis formatR remotes
+    tidyverse \
+    dplyr \
+    ggplot2 \
+    devtools \
+    formatR \
+    remotes
 
 ## 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.

tidyverse/3.4.0/Dockerfile

@@ -7,12 +7,15 @@ RUN apt-get update -qq && apt-get -y --no-install-recommends install \
   libmariadbd-dev \
   libmariadb-client-lgpl-dev \
   libpq-dev \
-  && . /etc/environment \
+  && R -e "source('https://bioconductor.org/biocLite.R')" \
   && install2.r --error \
-    --repos 'http://www.bioconductor.org/packages/release/bioc' \
-    --repos $MRAN \ 
     --deps TRUE \
-    tidyverse devtools dplyr ggplot2 profvis formatR remotes
+    tidyverse \
+    dplyr \
+    ggplot2 \
+    devtools \
+    formatR \
+    remotes
 
 ## 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.

tidyverse/Dockerfile

@@ -7,12 +7,15 @@ RUN apt-get update -qq && apt-get -y --no-install-recommends install \
   libmariadbd-dev \
   libmariadb-client-lgpl-dev \
   libpq-dev \
-  && . /etc/environment \
+  && R -e "source('https://bioconductor.org/biocLite.R')" \
   && install2.r --error \
-    --repos 'http://www.bioconductor.org/packages/release/bioc' \
-    --repos $MRAN \ 
     --deps TRUE \
-    tidyverse devtools dplyr ggplot2 profvis formatR remotes
+    tidyverse \
+    dplyr \
+    ggplot2 \
+    devtools \
+    formatR \
+    remotes
 
 ## 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.

tidyverse/devel/Dockerfile

@@ -7,12 +7,15 @@ RUN apt-get update -qq && apt-get -y --no-install-recommends install \
   libmariadbd-dev \
   libmariadb-client-lgpl-dev \
   libpq-dev \
-  && . /etc/environment \
+  && R -e "source('https://bioconductor.org/biocLite.R')" \
   && install2.r --error \
-    --repos 'http://www.bioconductor.org/packages/release/bioc' \
-    --repos $MRAN \ 
     --deps TRUE \
-    tidyverse devtools dplyr ggplot2 profvis formatR remotes
+    tidyverse \
+    dplyr \
+    ggplot2 \
+    devtools \
+    formatR \
+    remotes
 
 ## 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.