I created a renv for my Shiny app. As you know that when you build a dockerfile, it has to install every package and its dependencies. If there are many packages, it takes long time.
I already installed packages my local machine. Also, the app will run on the remote machine. Is there any chance to copy the all libraries without restoring the renv? My local machine is macOS and my remote machine is Ubuntu. Due to the different Operating Systems might not work to use libraries. Probably, there are different dependencies between macOS and Ubuntu for the R packages.
Which is the best way to install R packages in a Dockerfile? Should I wait long docker building every time?
Directory
FROM openanalytics/r-base
# system libraries of general use
RUN apt-get update && apt-get install -y \
sudo \
nano \
automake \
pandoc \
pandoc-citeproc \
libcurl4-openssl-dev \
libcairo2-dev \
libxt-dev \
libssl-dev \
libssh2-1-dev \
libssl1.1 \
libmpfr-dev \
# RPostgres
libpq-dev \
libssl-dev \
# rvest
libxml2-dev \
libssl-dev
# Install Packages
# RUN R -e "install.packages(c('janitor','DBI','RPostgres','httr', 'rvest','xml2', 'shiny', 'rmarkdown', 'tidyverse', 'lubridate','shinyWidgets', 'shinyjs', 'shinycssloaders', 'openxlsx', 'DT'), repos='https://cloud.r-project.org/')"
# copy the app to the image
RUN mkdir /root/appfile
COPY appfile /root/appfile
# renv restore
RUN Rscript -e 'install.packages("renv")'
RUN Rscript -e "renv::restore(lockfile = '/root/appfile/renv.lock')"
EXPOSE 3838
CMD ["R", "-e", "shiny::runApp('/root/appfile')"]
Thanks.
Related
My Dockerfile contains the exact code as shown in the statworx website to build an image for a Shiny app. Whenever I run the following code however:
# Base image https://hub.docker.com/u/rocker/
FROM rocker/shiny:latest
# system libraries of general use
## install debian packages
RUN apt-get update -qq && apt-get -y --no-install-recommends install
libxml2-dev
libcairo2-dev
libsqlite3-dev
libmariadbd-dev
libpq-dev
libssh2-1-dev
unixodbc-dev
libcurl4-openssl-dev
libssl-dev
## update system libraries
RUN apt-get update &&
apt-get upgrade -y &&
apt-get clean
# copy necessary files
## app folder
COPY /example-app ./app
## renv.lock file
COPY /example-app/renv.lock ./renv.lock
# install renv & restore packages
RUN Rscript -e 'install.packages("renv")'
RUN Rscript -e 'renv::consent(provided = TRUE)'
RUN Rscript -e 'renv::restore()'
# expose port
EXPOSE 3838
# run app on container start
CMD ["R", "-e", "shiny::runApp('/app', host = '0.0.0.0', port = 3838)"]
docker build -t my-shinyapp-image .
I get the following error: failed to solve with frontend dockerfile.v0: failed to create LLB definition: dockerfile parse error line 7: unknown instruction: LIBXML2-DEV
If I remove the LIBXML2-DEV package it gives an error on the next one. Has anyone encountered this problem before?
Following the suggestion of #HubertL, here is the Dockerfile that will work:
# Base image https://hub.docker.com/u/rocker/
FROM rocker/shiny:latest
# system libraries of general use
## install Debian/Ubuntu packages
RUN apt-get update -qq && \
apt-get upgrade -y && \
apt-get -y --no-install-recommends install \
libxml2-dev \
libcairo2-dev \
libsqlite3-dev \
libmariadbd-dev \
libpq-dev \
libssh2-1-dev \
unixodbc-dev \
libcurl4-openssl-dev \
libssl-dev
## update system libraries
RUN apt-get update && \
apt-get upgrade -y && \
apt-get clean
# copy necessary files
## app folder
COPY /example-app ./app
## renv.lock file
COPY /example-app/renv.lock ./renv.lock
# install renv & restore packages
RUN Rscript -e 'install.packages("renv")'
RUN Rscript -e 'renv::consent(provided = TRUE)'
RUN Rscript -e 'renv::restore()'
# expose port
EXPOSE 3838
# run app on container start
CMD ["R", "-e", "shiny::runApp('/app', host = '0.0.0.0', port = 3838)"]
This is the first time I'm using Docker. I have tried a few times but this is the first time where I'm containerizing the project. The project generates reports using latex and officer. However, after building the container and running the image, Rstudio shows that none of the packages are installed and loaded.
Dockerfile
FROM rocker/verse:4.0.5
ENV RENV_VERSION 0.15.1
RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
RUN R -e "remotes::install_github('rstudio/renv#${RENV_VERSION}')"
WORKDIR /REAL
COPY . .
RUN apt-get -y update --fix-missing
#RUN apt-get -y install build-essential \
# libssl-dev \
# libcurl4-openssl-dev \
# libxml2-dev \
# libfontconfig1-dev \
# libcairo2-dev
RUN R -e 'options(renv.consent = TRUE); renv::restore(lockfile = "/REAL/renv.lock"); renv::activate()'
Building Docker image
docker build -t reports/real .
Running docker with rstudio support
docker run --rm -d -p 8787:8787 --name real_report -e ROOT=TRUE -e DISABLE_AUTH=TRUE -v C:/Users/test/sources/REAL_Reports:/home/rstudio/REAL_Reports reports/real:latest
What am I doing wrong and how do I fix it so that all packages that renv has discovered are installed and loaded?
RUN R -e 'options(renv.consent = TRUE); renv::restore(lockfile = "/REAL/renv.lock"); renv::activate()'
You likely need to activate / load your project before calling restore(), or just forego using a project-local library altogether.
https://rstudio.github.io/renv/articles/docker.html may also be useful here.
I am installing several R packages from CRAN via docker file. Below is my docker file:
FROM r-base:4.0.2
RUN apt-get update \
&& apt-get install -y --auto-remove \
build-essential \
libcurl4-openssl-dev \
libpq-dev \
libssl-dev \
libxml2-dev \
&& R -e "system.time(install.packages(c('shiny', 'rmarkdown', 'Hmisc', 'rjson', 'caret','DBI', 'RPostgres','curl', 'httr', 'xml2', 'aws.s3'), repos='https://cloud.r-project.org/'))"
RUN mkdir /shinyapp
COPY . /shinyapp
EXPOSE 5000
CMD ["R", "-e", "shiny::runApp('/shinyapp/src/shiny', port = 5000, host = '0.0.0.0')"]
The docker build process is taking too much time (25 to 30 minutes). Below are the execution time details after completion of build.
user system elapsed
1306.268 232.438 1361.374
Is there any way to optimize above Dockerfile? Any way to install packages in parallel manner?
Note: I have also tried rocker/r-base, but didn't find any luck in installation speed.
‘pak’ performs package download and installation in parallel.
Unfortunately the current CRAN version of ‘pak’ (0.1.2.1) is arguably broken: it has tons of dependencies. By contrast, the development version on GitHub has no external dependencies, as it should. So we need to install that one.
So you could change your Dockerfile as follows:
…
&& Rscript -e "install.packages('pak', repos = 'https://r-lib.github.io/p/pak/dev/'); pak::pkg_install(c('shiny', 'rmarkdown', 'Hmisc', 'rjson', 'caret','DBI', 'RPostgres','curl', 'httr', 'xml2', 'aws.s3'))"
…
But, frankly, that’s quite unreadable. A better approach would be to use ARG or ENV to supply the packages to be installed (this is regardless of whether we use ‘pak’ to install packages):
FROM r-base:4.0.2
ARG PKGS="shiny, rmarkdown, Hmisc, rjson, caret, DBI, RPostgres, curl, httr, xml2, aws.s3"
RUN apt-get update \
&& apt-get install -y --auto-remove \
build-essential \
libcurl4-openssl-dev \
libpq-dev \
libssl-dev \
libxml2-dev
RUN Rscript -e 'install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")' \
&& echo "$PKGS" \
| Rscript -e 'pak::pkg_install(strsplit(readLines("stdin"), ", ?")[[1L]])'
RUN mkdir /shinyapp
COPY . /shinyapp
EXPOSE 5000
CMD ["Rscript", "-e", "shiny::runApp('/shinyapp/src/shiny', port = 5000, host = '0.0.0.0')"]
Also note that R shouldn’t be invoked via the R binary for scripted use — that’s what Rscript is for. Amongst other things it handles stdout better.
I am a beginner in docker, my question can be considered somewhat obvious but where do I save and write the dockerfile?
example:
FROM openanalytics/r-base
LABEL maintainer "Tobias Verbeke <tobias.verbeke#openanalytics.eu>"
# 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
# basic shiny functionality
RUN R -e "install.packages(c('shiny', 'rmarkdown'), repos='https://cloud.r-project.org/')"
# install dependencies of the euler app
RUN R -e "install.packages('Rmpfr', repos='https://cloud.r-project.org/')"
# copy the app to the image
RUN mkdir /root/euler
COPY euler /root/euler
COPY Rprofile.site /usr/lib/R/etc/
EXPOSE 3838
CMD ["R", "-e", "shiny::runApp('/root/euler')"]
where specifically does this file have to be written? Where specifically does he have to be saved? what format does it have to be saved?
The pattern I follow is to include the Dockerfile in the root of the project directory.
I also store it in the same repo as the project.
I'm trying to build a docker image for my shiny app. Below is my dockerfile. When I build my images, everything else seems fine, except I got error message Error in library(devtools) : there is no package called ‘devtools’ Execution halted. I also tried devtools::install_github('nik01010/dashboardthemes') with no success. I have non clue why? What could go wrong? Do anyone know what is wrong with my dockerfile? Thanks a lot.
# Install R version 3.6
FROM r-base:3.6.0
# Install Ubuntu packages
RUN apt-get update && apt-get install -y \
sudo \
gdebi-core \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev/unstable \
libxt-dev \
libssl-dev
# Download and install ShinyServer (latest version)
RUN wget --no-verbose https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/VERSION -O "version.txt" && \
VERSION=$(cat version.txt) && \
wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
gdebi -n ss-latest.deb && \
rm -f version.txt ss-latest.deb
# Install R packages that are required
RUN R -e "install.packages(c('devtools', 'shiny','shinythemes','shinydashboard','shinyWidgets','shinyjs', 'tidyverse', 'dplyr', 'ggplot2','rlang','DT','lubridate', 'plotly', 'leaflet', 'mapview', 'tigris', 'rgdal', 'visNetwork', 'wordcloud2', 'arules'), repos='http://cran.rstudio.com/')"
RUN R -e "library(devtools)"
RUN R -e "install_github('nik01010/dashboardthemes')"
# Copy configuration files into the Docker image
COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
COPY /app /srv/shiny-server/
# Make the ShinyApp available at port 80
EXPOSE 80
# Copy further configuration files into the Docker image
COPY shiny-server.sh /usr/bin/shiny-server.sh
CMD ["/usr/bin/shiny-server.sh"]
There are a few approaches you might try.
Easiest:
Use remotes::install_github instead of devtools. remotes has many fewer dependencies if you don't need the other functionality.
Second Easiest:
Use rocker/tidyverse image from Docker Hub instead of baseR image.
docker pull rocker/tidyverse
Change line 2:
FROM rocker/verse
Hardest:
Otherwise, you will need to figure out which dependencies you need to install inside your docker image before you can install devtools. It will likely be obvious if you try to install it interactively.
Make sure the container is running
Get the container name using docker ps
Start a shell with docker exec -it <container name> /bin/bash
Start R and try to install devtools interactively