Cannot Install R Packages in Docker Image

Question

It seems because of legal reasons Java is not able to be installed separately in a docker image but rather we have to use a java image.

I am using a java image, with R installed as I need it, however when I am installing an R package I get an error

Here is my Dockerfile below:

FROM buildpack-deps:jessie-scm

# A few problems with compiling Java from source:
#  1. Oracle.  Licensing prevents us from redistributing the official JDK.
#  2. Compiling OpenJDK also requires the JDK to be installed, and it gets
#       really hairy.

RUN apt-get update && apt-get install -y --no-install-recommends \
        bzip2 \
        unzip \
        xz-utils \
    && rm -rf /var/lib/apt/lists/*

# Default to UTF-8 file.encoding
ENV LANG C.UTF-8

# add a simple script that can auto-detect the appropriate JAVA_HOME value
# based on whether the JDK or only the JRE is installed
RUN { \
        echo '#!/bin/sh'; \
        echo 'set -e'; \
        echo; \
        echo 'dirname "$(dirname "$(readlink -f "$(which javac || which java)")")"'; \
    } > /usr/local/bin/docker-java-home \
    && chmod +x /usr/local/bin/docker-java-home

ENV JAVA_HOME /usr/lib/jvm/java-7-openjdk-amd64

ENV JAVA_VERSION 7u111
ENV JAVA_DEBIAN_VERSION 7u111-2.6.7-2~deb8u1

RUN set -x \
    && apt-get update \
    && apt-get install -y \
        openjdk-7-jdk="$JAVA_DEBIAN_VERSION" \
    && rm -rf /var/lib/apt/lists/* \
    && [ "$JAVA_HOME" = "$(docker-java-home)" ]

# If you're reading this and have any feedback on how this image could be
#   improved, please open an issue or a pull request so we can discuss it!

# system libraries of general use
RUN apt-get update && apt-get install -y \
    sudo \
    pandoc \
    pandoc-citeproc \
    libcurl4-gnutls-dev \
    libcairo2-dev \
    libxt-dev \
    libssl-dev \
    libssh2-1-dev \
    libssl1.0.0

# system library dependency for the euler app
RUN apt-get update && apt-get install -y \
    libmpfr-dev

RUN sudo apt-get install -y \
    r-base r-base-dev

# basic shiny functionality
RUN R -e "install.packages(c('shiny', 'rmarkdown'), repos='https://cloud.r-project.org/')"

# install dependencies
RUN R -e "install.packages('Rmpfr', repos='https://cloud.r-project.org/')"

# Special Package
RUN R -e "install.packages('shiny')"
RUN R -e "install.packages('shinydashboard')"
RUN R -e "install.packages('plyr')"
RUN R -e "install.packages('dplyr')"
RUN R -e "install.packages('ggplot2')"
RUN R -e "install.packages('tm')"
RUN R -e "install.packages('SnowballC')"
RUN R -e "install.packages('wordcloud')"
RUN R -e "install.packages('RWeka')"
RUN R -e "install.packages('reshape2')"
RUN R -e "install.packages('igraph')"



# copy the app to the image
RUN mkdir /root/testapp1
COPY testapp1 /root/testapp1

COPY Rprofile.site /usr/lib/R/etc/

EXPOSE 3838

CMD ["R", "-e shiny::runApp('/root/testapp1')"]

When I try to install any R package I get this error below:

> install.packages('shiny')
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror
Calls: install.packages -> grep -> contrib.url
Execution halted
The command '/bin/sh -c R -e "install.packages('shiny')"' returned a non-zero code: 1

How can I resolve this headache of an issue.

Thanks.

Answer 1

When install.packages('shiny') is executed in R environment it hang asking you to select from what mirror you want to download.

> install.packages('shiny')

Installing package into ‘/Users/user/Library/R/3.3/library’
(as ‘lib’ is unspecified)

--- Please select a CRAN mirror for use in this session ---
HTTPS CRAN mirror

 1: 0-Cloud [https]                 
 2: Algeria [https]
 ... 
 55: (HTTP mirrors)

Selection: 

According to your error output seems that the command RUN R -e "install.packages(c('shiny', 'rmarkdown'), repos='https://cloud.r-project.org/')"

and the next one are executed, and then fails (error exit 1) when try to execute:

RUN R -e "install.packages('shiny')"

Providing instead install.packages('shiny', repos='https://cloud.r-project.org/') will probably do a silent install without asking anything.

Answer 2

Looks like the errors are you are getting are from the install.pacakges methods which don't have the repos argument specified.

Once I updated the install.packages with repos='http://cran.us.r-project.org/' in my local machine with your dockerfile, the image was building successfully.