I have created an R Plumber API, and deploy it in a Docker image.
Dockerfile:
ARG R_VERSION=latest
FROM rocker/r-ver:${R_VERSION}
# install the linux libraries needed for plumber
RUN apt-get update -qq && apt-get install -y \
libssl-dev \
libcurl4-gnutls-dev
COPY / /
# Making home & test folders
RUN Rscript required-packages/required-packages.R
# Giving permission to tests to run
RUN chmod +x tests/run_tests.sh
# Run Tests
RUN tests/run_tests.sh
# open port 7575 to traffic
EXPOSE 7575
# when the container starts, start the main.R script
ENTRYPOINT ["Rscript", "./main.R"]
main.R
library(plumber)
r <- plumb("./plumber.R")
r$run(port = 7575, host = "0.0.0.0")
I run the container with the following command.
docker run --rm -p 7575:7575 'container-name'
On the machine, http://localhost:7575/echo works perfectly fine. However, I cannot call the API from an external computer with http://ip_address:7575/echo.
What could be the problem? As far as I know, the 7575 port is open.
Related
I am deploying Shiny-server in container. By default Shiny-server listens on port 3838, here is piece from shiny-server.conf
# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;
# Define a server that listens on port 3838
server {
listen 3838;
I would like to change this port to 80. I obviously can launch container instance, login to it, and change it, but I would like to change it in Dockerfile.
FROM rocker/shiny:3.5.1
RUN apt-get update && apt-get install libcurl4-openssl-dev libv8-3.14-dev -y &&\
mkdir -p /var/lib/shiny-server/bookmarks/shiny
# Download and install library
RUN R -e "install.packages(c('shinydashboard', 'shinyjs', 'V8'))"
# copy the app to the image COPY shinyapps /srv/shiny-server/
COPY "reports" "/srv/shiny-server/sample-apps/reports/"
# make all app files readable (solves issue when dev in Windows, but building in Ubuntu)
RUN chmod -R 755 /srv/shiny-server/
EXPOSE 80
CMD ["/usr/bin/shiny-server.sh"]
Is there command line option for final line in Dockerfile?
Add
RUN sed -i -e 's/\blisten 3838\b/listen 80/g' /path/to/shiny-server.conf
So perhaps ending up with:
FROM rocker/shiny:3.5.1
RUN apt-get update && apt-get install libcurl4-openssl-dev libv8-3.14-dev -y &&\
mkdir -p /var/lib/shiny-server/bookmarks/shiny
# Download and install library
RUN R -e "install.packages(c('shinydashboard', 'shinyjs', 'V8'))"
# copy the app to the image COPY shinyapps /srv/shiny-server/
COPY "reports" "/srv/shiny-server/sample-apps/reports/"
# make all app files readable (solves issue when dev in Windows, but building in Ubuntu)
RUN chmod -R 755 /srv/shiny-server/
RUN sed -i -e 's/\blisten 3838\b/listen 80/g' /path/to/shiny-server.conf
EXPOSE 80
CMD ["/usr/bin/shiny-server.sh"]
(I know multiple layers can be inefficient if not compacted, over to you if you want to combine the sed line with the previous RUN command. You might want to combine more of those RUN lines, if that's a concern.)
I am trying to run a shiny application on an open port on my server. I usually run docker images using command docker run -p 4000:3838 tag_name, assuming that docker container has exposed port, and shiny app is running at this port.
This all works completely fine for any shiny application that is using http. But I need https.
So the Dockerfile I use consists of:
FROM rocker/r-ver:4.0.1
# System libs:
RUN apt-get update
RUN apt-get install -y libcurl4-openssl-dev
RUN apt-get install -y libssl-dev
RUN apt-get install -y zlib1g-dev
RUN apt-get install -y libxml2-dev
# R packages installed
RUN R -e "install.packages('remotes')"
RUN R -e "remotes::install_version('searchConsoleR')"
RUN R -e "remotes::install_version('googleAuthR')"
# [...] more R libraries are installed
# Copy application files to a dir
RUN mkdir /root/app
COPY . /root/app
# Expose and set run command from dir above
EXPOSE 3838
CMD ["R", "-e", "shiny::runApp('/root/app', port = 3838, host = '0.0.0.0')"]
Then I execute docker build -t tag_name . and docker run -p 4000:3838 tag_name.
The page is available at http://server.host:4000
However, since I am using Google Login, I need to use https. But when I visit server's https://server.host:4000 I see an error of page not existing.
Can someone please help?
I have a Docker container running a shiny app (Dockerfile here).
Shiny server logs are output to stdout and application logs are written to /var/log/shiny-server. I'm deploying this container to AWS Fargate and logging applications only display stdout which makes debugging an application when deployed challenging. I'd like to write the application logs to stdout.
I've tried a number of potential solutions:
I've tried the solution provided here, but have had no luck.. I added the exec xtail /var/log/shiny-server/ to my shiny-server.sh as the last line in the file. App logs are not written to stdout
I noticed that writing application logs to stdout is now the default behavior in rocker/shiny, but as I'm using rocker/verse:3.6.2 (upgraded from 3.6.0 today) along with RUN export ADD=shiny, I don't think this is standard behavior for the rocker/verse:3.6.2 container with Shiny add-on. As a result, I don't get the default behavior out of the box.
This issue on github suggests an alternative method of forcing application logging to stdout by way of an environment variable SHINY_LOG_STDERR=1 set at runtime but I'm not Linux-savvy enough to know where that env variable needs to be set to be effective. I found this documentation from Shiny Server v1.5.13 which gave suggestions in which file to set the environment variable depending on Linux distro; however, the output from my container when I run cat /etc/os-release is:
which doesn't really line up with any of the distributions in the Shiny Server documentation, thus making the documentation unhelpful.
I tried adding adding the environment variable from the github issue above in the docker run command, i.e.,
docker run --rm -e SHINY_LOG_STDERR=1 -p 3838:3838 [my image]
as well as
docker run --rm -e APPLICATION_LOGS_TO_STDOUT=true -p 3838:3838 [my image]
and am still not getting the logs to stdout.
I must be missing something here. Can someone help me identify how to successfully get application logs to stdout successfully?
You can add the line ENV SHINY_LOG_STDERR=1 to your Dockerfile (at least, this works with rocker/shiny, not sure about rocker/verse), such as with your Dockerfile:
FROM rocker/verse:3.6.2
## Add shiny capabilities to container
RUN export ADD=shiny && bash /etc/cont-init.d/add
## Install curl and xtail
RUN apt-get update && apt-get install -y \
curl \
xtail
## Add pip3 and other Python packages
RUN sudo apt-get update -y && apt-get install -y python3-pip
RUN pip3 install boto3
## Add R packages
RUN R -e "install.packages(c('shiny', 'tidyverse', 'tidyselect', 'knitr', 'rmarkdown', 'jsonlite', 'odbc', 'dbplyr', 'RMySQL', 'DBI', 'pander', 'sciplot', 'lubridate', 'zoo', 'stringr', 'stringi', 'openxlsx', 'promises', 'future', 'scales', 'ggplot2', 'zip', 'Cairo', 'tinytex', 'reticulate'), repos = 'https://cran.rstudio.com/')"
## Update and install
RUN tlmgr update --self --all
RUN tlmgr install ms
RUN tlmgr install beamer
RUN tlmgr install pgf
#Copy app dir and theme dirs to their respective locations
COPY iarr /srv/shiny-server/iarr
COPY iarr/reports/interim_annual_report/theme/SwCustom /opt/TinyTeX/texmf-dist/tex/latex/beamer/
#Force texlive to find my custom beamer theme
RUN texhash
EXPOSE 3838
## Add shiny-server information
COPY shiny-server.sh /usr/bin/shiny-server.sh
COPY shiny-customized.config /etc/shiny-server/shiny-server.conf
## Add dos2unix to eliminate Win-style line-endings and run
RUN apt-get update -y && apt-get install -y dos2unix
RUN dos2unix /usr/bin/shiny-server.sh && apt-get --purge remove -y dos2unix && rm -rf /var/lib/apt/lists/*
# Enable Logging from stdout
ENV SHINY_LOG_STDERR=1
RUN ["chmod", "+x", "/usr/bin/shiny-server.sh"]
CMD ["/usr/bin/shiny-server.sh"]
I'm trying to put my shiny app in docker container. My shiny app works totally fine on my local computer. But after dockerize my shiny app, I always have error message on my localhost like The application failed to start. The application exited during initialization..
I have no idea why that happens. I'm new to docker. How can I find the error logs when I run the docker image? I need the log to know what goes wrong.
Here is my dockfile:
# 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
# TODO: add further package if you need!
RUN R -e "install.packages(c( 'tidyverse', 'ggplot2','shiny','shinydashboard', 'DT', 'plotly', 'RColorBrewer'), repos='http://cran.rstudio.com/')"
# 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"]
I built image and ran like below:
docker build -t myshinyapp .
docker run -p 80:80 myshinyapp
Usually the logs for any (live or dead) container can be found by just using:
docker logs full-container-name
or
docker logs CONTAINERID
(replacing the actual ID of your container)
As first said, this usually works as well even for stopped (not still removed) containers, which you can list with:
docker container ls -a
or just
docker ps -a
However, sometimes you won't even have a log, since the container was never created at all (which I think, by experience, fits more to your case)
And it can be happening simply because the docker engine is unable to allocate all of the resources that your service definition is requiring to have available.
The application failed to start. The application exited during initialization
is usually reflect of your docker engine being unable to get the required resources.
And the most common case for that, is just as simple as your host ports:
If you have another service (being dockerized or not) using (for example) that port that you want to use for your service (in your case, port 80) then Docker would just be unable to start your container.
So... in short... the easiest fix for that situation (and your first try whenever you face this kind of issues) is just to bind any other port from your host (say: 8080), to that 80 port that your service will be listening to internally (inside your container):
docker run -p 8080:80 myshinyapp
The same principle applies to unallocatable volumes (e.g.: trying to bind a volume as read-only that doesn't actually exist in the host)
As an aside comment/trick:
Since you're not setting a name for your container, you will need to use the container id instead when looking for its logs.
But instead of typing (or copy-pasting) the full container id (usually something like: 1283c66babea or even larger) you can just type in a few first digits instead, and it will still work as expected:
docker logs 1283c6 or docker logs 1283 or even docker logs 128
(of course... as long as you don't have any other 128***** container)
I am trying to launch a shiny app using ShinyProxy - something I have done many times before. However, this app is not correctly using any of the CSS or JS files that is required to make it run.
When I run the app manually with docker run -p 3838:3838 my_app everything works perfectly fine. However, when pointing ShinyProxy to the my_app image, the resulting app fails to load any CSS or JS files.
Dockerfile
FROM openanalytics/r-base
MAINTAINER Daniel Beachnau "DannyBeachnau#gmail.com"
# Dependencies outside of R
RUN apt-get update && apt-get install -y \
sudo \
gdebi-core \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev \
libxt-dev \
xtail \
wget \
libpq-dev \
libmariadb-client-lgpl-dev \
# Might be needed for the archivist R-Library
dbus \
systemd \
# needed for odbc
unixodbc-dev
RUN apt-get install apt-transport-https curl -y
RUN curl http://packages.microsoft.com/keys/microsoft.asc | apt-key add -
RUN curl https://packages.microsoft.com/config/ubuntu/16.04/prod.list > /etc/apt/sources.list.d/mssql-release.list
RUN apt-get update
RUN ACCEPT_EULA=Y apt-get install msodbcsql17 -y
# Download R-Packages
# tidyverse
RUN R -e "install.packages('tidyr')"
RUN R -e "install.packages('dplyr')"
RUN R -e "install.packages('readr')"
# Shiny Packages
RUN R -e "install.packages('shiny')"
RUN R -e "install.packages('shinycssloaders')"
RUN R -e "install.packages('shinydashboard')"
RUN R -e "install.packages('shinyWidgets')"
RUN R -e "install.packages('DT')"
RUN R -e "install.packages('shinyjs')"
RUN R -e "install.packages('flexdashboard')"
# Database Packages
RUN R -e "install.packages('odbc')"
RUN R -e "install.packages('RMySQL')"
# Other
RUN R -e "install.packages('devtools')"
RUN R -e "install.packages('lubridate')"
RUN R -e "install.packages('reshape2')"
RUN R -e "install.packages('grid')"
RUN R -e "install.packages('lemon')"
RUN R -e "install.packages('scales')"
RUN R -e "install.packages('ggthemes')"
RUN R -e "install.packages('ggplot2')"
RUN R -e "devtools::install_bitbucket(repo = 'my_repo/my_package', auth_user = 'my_username', password = 'my_password')"
# copy the app to the image
COPY . /root
# run the script to update the app data
WORKDIR /root
RUN Rscript app_data_update.R
WORKDIR /root/app
COPY Rprofile.site /usr/lib/R/etc/
EXPOSE 3838
CMD ["R", "-e", "shiny::runApp('/root/app', host='0.0.0.0', port=3838)"]
application.yml
shiny:
proxy:
title: ShinyProxy Server
logo-url: /images/logo-image.png
landing-page: /
heartbeat-rate: 10000
heartbeat-timeout: 60000
container-wait-time: 60000
port: 8080
authentication: ldap
# Docker configuration
docker:
cert-path: /home/none
url: http://localhost:2375
port-range-start: 20000
support:
container-log-path: ./container-logs
mail-to-address: DannyBeachnau#gmail.co,
- name: my_apps_name
display-name: Shiny App
docker-image: dbeachnau/my_app
groups: [Shiny Users Management]
logo-url: /images/logo-image.png
container-volumes: ["/path/to/app:/root/app"]
logging:
file:
shinyproxy.log
Here is how app looks in shiny proxy.
problem
Here is hoe my app looks when running manually.
desired
The console in chrome's inspect tool is replete with errors such as
GET https://myshinyserver.com/container_name/font-awesome-5.3.1/css/all.min.css net::ERR_ABORTED 404 (Not Found)
I do have other apps running on ShinyProxy which display properly, but I cannot solve the difference between how those apps are configured to how this app is configured. Let me know if additional details are required for diagnosing the issue. All feedback is appreciated - thank you.
You're probably seeing this with Shiny v1.3.0, and not with earlier versions. If so, it's probably because of a misconfiguration in your NGINX proxy directives. I've written up the details here, but I'll also post the salient details here.
proxy_set_header Connection "upgrade";
This directive causes NGINX to add a Connection: upgrade header to every HTTP request, when it's only supposed to be used for WebSockets.
This line is recommended by NGINX Inc. themselves, however, those recommendations are intended for proxying of traffic that is exclusively WebSockets, whereas Shiny traffic is a combination of normal HTTP requests and WebSockets. Older versions of shiny/httpuv didn't mind this situation, but the new versions are stricter.
A correct configuration looks something like this:
http {
map $http_upgrade $connection_upgrade {
default upgrade;
'' close;
}
server {
listen 80;
location / {
proxy_pass http://localhost:3838;
proxy_redirect / $scheme://$http_host/;
proxy_http_version 1.1;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection $connection_upgrade;
proxy_read_timeout 20d;
proxy_buffering off;
}
}
}
See the articles linked in the RStudio Community post for other examples.
You will have to install the requested font at the top of your Dockerfile. You can add it to your list "Dependencies outside of R":
sudo apt-get install fonts-font-awesome
I have solved my problem, although, this still may not count as a sufficient answer or explanation, because I cannot account for why this solution makes a difference. I decided to rewrite the Dockerfile using a different base image which now works. Nothing else in my code changed - just the Dockerfile. The working docker file is as follows:
FROM rocker/shiny-verse
# based on debian 9
MAINTAINER Daniel Beachnau "DannyBeachnau#gmail.com"
# Dependencies outside of R
RUN apt-get update && apt-get install -y \
gnupg2 \
apt-utils \
sudo \
gdebi-core \
libxt-dev \
xtail \
wget
# Install ODBC driver from microsoft
RUN apt-get install apt-transport-https curl -y
RUN curl http://packages.microsoft.com/keys/microsoft.asc | apt-key add -
RUN curl https://packages.microsoft.com/config/debian/9/prod.list > /etc/apt/sources.list.d/mssql-release.list
RUN apt-get update
RUN ACCEPT_EULA=Y apt-get install msodbcsql17 -y
# Download R-Packages
# Shiny Packages
RUN R -e "install.packages('shinycssloaders')"
RUN R -e "install.packages('shinydashboard')"
RUN R -e "install.packages('shinyWidgets')"
RUN R -e "install.packages('DT')"
RUN R -e "install.packages('shinyjs')"
RUN R -e "install.packages('flexdashboard')"
# Database Packages
RUN R -e "install.packages('odbc')"
RUN R -e "install.packages('RMySQL')"
# Other
RUN R -e "install.packages('lubridate')"
RUN R -e "install.packages('reshape2')"
RUN R -e "install.packages('scales')"
RUN R -e "install.packages('ggthemes')"
RUN R -e "install.packages('ggplot2')"
RUN R -e "devtools::install_bitbucket(repo = 'my_repo', auth_user = 'my_username', password = 'my_password')"
# copy the app to the image
COPY . /root
# run the script to update the app data
WORKDIR /root
RUN Rscript app_data_update.R
WORKDIR /root/app
COPY Rprofile.site /usr/lib/R/etc/
EXPOSE 3838
CMD ["R", "-e", "shiny::runApp('/root/app', host='0.0.0.0', port=3838)"]
If anyone has insight to why this behavior is observed I would love to hear it because I am baffled to say the least.
why this solution makes a difference
It seems to be an issue with the Shiny version, changing the base image has very probably fixed that.
See Shiny apps not rendering after updated to v1.3.0