jq missing as bionic dependency (compared to r-core)

[aronatkins]

Dockerfile showing the lack of jq when using the r-builds bionic installer.

FROM ubuntu:bionic-20190912.1

RUN export DEBIAN_FRONTEND=noninteractive && \
    apt-get update && \
    apt-get install -y \
    curl && \
    rm -rf /var/lib/apt/lists/*

# Install R and make it default.
ARG R_VERSION=3.4.4
ARG OS_IDENTIFIER=ubuntu-1804
RUN curl -L -O https://cdn.rstudio.com/r/${OS_IDENTIFIER}/pkgs/r-${R_VERSION}_1_amd64.deb && \
    export DEBIAN_FRONTEND=noninteractive && \
    apt-get update && \
    apt-get install -f -y ./r-${R_VERSION}_1_amd64.deb && \
    ln -s /opt/R/${R_VERSION}/bin/R /usr/bin/R && \
    ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/bin/Rscript && \
    ln -s /opt/R/${R_VERSION}/lib/R /usr/lib/R && \
    rm r-${R_VERSION}_1_amd64.deb && \
    rm -rf /var/lib/apt/lists/*

RUN jq --help

When building this Dockerfile, we get the error:

Step 6/6 : RUN jq --help
 ---> Running in c70358551411
/bin/sh: 1: jq: not found
The command '/bin/sh -c jq --help' returned a non-zero code: 127

Compare this against the result of installing r-base from the Ubuntu repository.

FROM ubuntu:bionic-20190912.1

RUN export DEBIAN_FRONTEND=noninteractive && \
    apt-get update && \
    apt-get install -y \
    curl && \
    rm -rf /var/lib/apt/lists/*

RUN export DEBIAN_FRONTEND=noninteractive && \
    apt-get update && \
    apt-get install -y \
    r-base && \
    rm -rf /var/lib/apt/lists/*

RUN jq --help

This Dockerfile successfully builds. The jq utility is installed as a consequence of installing r-base.

Workaround:

Explicitly install jq.

# Install jq as a standalone step. Also fine as an addition to the earlier apt-get install.
RUN export DEBIAN_FRONTEND=noninteractive && \
    apt-get update && \
    apt-get install -y \
    jq

[aronatkins]

A post about adding the jq dependency to trusty / xenial, as it's a build dependency for some packages.

https://rubuntu.netlify.com/post/2018-05-23-adding-jq-trusty-xenial/

It's probably OK to not automatically pull in jq (how do we decide what dependencies are worth having?), but should document this difference from the Ubuntu-supplied package.

[jonyoder]

In some of our other docker images, we've been installing jq this way:

# Install jq
RUN wget -O /usr/local/bin/jq https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64 && \
    chmod +x /usr/local/bin/jq