How DO you add RStudio?

[MarkEdmondson1234]

Hi, I've tried to add RStudio to the base R + TF + keras but have failed :) May I ask to take a look at my attempt? There is something about the $R_HOME folder that I don't understand - the pertinent bit is:

&& mkdir -p /etc/R \
  && mkdir -p /usr/local/lib/etc/R/ \
  ## Write config files in $R_HOME/etc
  && echo '\n\
    \n# Configure httr to perform out-of-band authentication if HTTR_LOCALHOST \
    \n# is not set since a redirect to localhost may not work depending upon \
    \n# where this Docker container is running. \
    \nif(is.na(Sys.getenv("HTTR_LOCALHOST", unset=NA))) { \
    \n  options(httr_oob_default = TRUE) \
    \n}' >> /usr/local/lib/etc/R/Rprofile.site \
  && echo "PATH=${PATH}" >> /usr/local/lib/etc/R/Renviron \

I added the && mkdir -p /usr/local/lib/etc/R/ \ as it was not finding the folder with the error: /bin/sh: 1: cannot create /usr/local/lib/R/etc/Rprofile.site: Directory nonexistent

And I changed /usr/local/lib/R/etc/ to /usr/local/lib/etc/R/ as it seemed a typo, but trying to change it back now.

so it at least finishes building, but when I start the container I can't connect to RStudio, the logs say:

rsession: no process found

.. which I guess is related.

Dockerfile below with comments

# I updated to most recent version, not got far enough in the build to see if this is a problem yet
FROM nvidia/cuda:9.0-cudnn7-runtime

## This handle reaches Carl and Dirk
MAINTAINER "Carl Boettiger and Dirk Eddelbuettel" rocker-maintainers@eddelbuettel.com

## Prepare R installation from 
RUN sh -c 'echo "deb http://cloud.r-project.org/bin/linux/ubuntu xenial/" >> /etc/apt/sources.list' \
    && gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 \
    && gpg -a --export E084DAB9 | apt-key add -

RUN apt-get update \
    && apt-get upgrade -y -q \
    && apt-get install -y --no-install-recommends \
           r-base \
           r-base-dev \
           r-cran-littler \
           libxml2-dev \
           libxt-dev \
           libssl-dev \
           libcurl4-openssl-dev \
           imagemagick \
           python-pip \
           libpython2.7 \
    && python -m pip install --upgrade pip \
    && pip install virtualenv \
    && echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' >> /etc/R/Rprofile.site \
    && /usr/lib/R/site-library/littler/examples/install.r tensorflow keras \
    && r -e "keras::install_keras(tensorflow = '1.4.1-gpu')"

# copied from rstudio dockerfile https://github.com/rocker-org/rocker-versioned/tree/master/rstudio/3.5.2
ARG RSTUDIO_VERSION
#ENV RSTUDIO_VERSION=${RSTUDIO_VERSION:0.1.463}
ARG S6_VERSION
ENV S6_VERSION=${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
## Attempts to get detect latest version, otherwise falls back to version given in $VER
## Symlink pandoc, pandoc-citeproc so they are available system-wide
RUN apt-get update \
  && apt-get install -y --no-install-recommends \
    file \
    git \
    libapparmor1 \
    libcurl4-openssl-dev \
    libedit2 \
    libssl-dev \
    lsb-release \
    psmisc \
    procps \
    python-setuptools \
    sudo \
    wget \
  && wget -O libssl1.0.0.deb http://ftp.debian.org/debian/pool/main/o/openssl/libssl1.0.0_1.0.1t-1+deb8u8_amd64.deb \
  && dpkg -i libssl1.0.0.deb \
  && rm libssl1.0.0.deb \
  && RSTUDIO_LATEST=$(wget --no-check-certificate -qO- https://s3.amazonaws.com/rstudio-server/current.ver) \
  && [ -z "$RSTUDIO_VERSION" ] && RSTUDIO_VERSION=$RSTUDIO_LATEST || true \
  && wget -q http://download2.rstudio.org/rstudio-server-${RSTUDIO_VERSION}-amd64.deb \
  && dpkg -i rstudio-server-${RSTUDIO_VERSION}-amd64.deb \
  && rm rstudio-server-*-amd64.deb \
  ## Symlink pandoc & standard pandoc templates for use system-wide
  && ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc /usr/local/bin \
  && ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc /usr/local/bin \
  && git clone https://github.com/jgm/pandoc-templates \
  && mkdir -p /opt/pandoc/templates \
  && cp -r pandoc-templates*/* /opt/pandoc/templates && rm -rf pandoc-templates* \
  && mkdir /root/.pandoc && ln -s /opt/pandoc/templates /root/.pandoc/templates \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/ \
  ## RStudio wants an /etc/R, will populate from $R_HOME/etc
  && mkdir -p /etc/R \
  && mkdir -p /usr/local/lib/etc/R/ \
  ## Write config files in $R_HOME/etc
  && echo '\n\
    \n# Configure httr to perform out-of-band authentication if HTTR_LOCALHOST \
    \n# is not set since a redirect to localhost may not work depending upon \
    \n# where this Docker container is running. \
    \nif(is.na(Sys.getenv("HTTR_LOCALHOST", unset=NA))) { \
    \n  options(httr_oob_default = TRUE) \
    \n}' >> /usr/local/lib/etc/R/Rprofile.site \
  && echo "PATH=${PATH}" >> /usr/local/lib/etc/R/Renviron \
  ## Need to configure non-root user for RStudio
  && useradd rstudio \
  && echo "rstudio:rstudio" | chpasswd \
    && mkdir /home/rstudio \
    && chown rstudio:rstudio /home/rstudio \
    && addgroup rstudio staff \
  ## Prevent rstudio from deciding to use /usr/bin/R if a user apt-get installs a package
  &&  echo 'rsession-which-r=/usr/local/bin/R' >> /etc/rstudio/rserver.conf \
  ## use more robust file locking to avoid errors when using shared volumes:
  && echo 'lock-type=advisory' >> /etc/rstudio/file-locks \
  ## configure git not to request password each time
  && 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/${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 \
  && 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

## running with "-e ADD=shiny" adds shiny server
COPY add_shiny.sh /etc/cont-init.d/add
COPY disable_auth_rserver.conf /etc/rstudio/disable_auth_rserver.conf
COPY pam-helper.sh /usr/lib/rstudio-server/bin/pam-helper

EXPOSE 8787

## automatically link a shared volume for kitematic users
VOLUME /home/rstudio/kitematic

CMD ["/init"]

[cboettig]

@MarkEdmondson1234 Can you take a look at https://github.com/rocker-org/ml/tree/master/gpu instead? RStudio should already work there out of the box, as documented in the README. That image should be available pre-built from Docker hub as rocker/gpu, and I'm just testing the tensorflow side of it now so your feedback would be timely! thanks

[MarkEdmondson1234]

Ah, its already built! Ok was waiting for a build but will try that one directly