I have an R plumber server, that i want to run using a docker container, and i have this configuration so far in my dockerfile
FROM rocker/r-ver:3.5.0
#update OS and install linux libraries needed to run plumber
RUN apt-get update -qq && apt-get install -y \
libssl-dev \
libcurl4-gnutls-dev
#load in dependencies from 00_Libraries.R file
RUN R -e "install.packages('plumber')"
#Copy all files from current directory
COPY / /
#Expose port :80 for traffic
EXPOSE 80
#when the container starts, start the runscript.R script
ENTRYPOINT ["Rscript", "runscript.R"]
in my runscript.R file, i have my server configuration like this:
pr <- plumber::plumb("/home/kristoffer/Desktop/plumber-api/rfiles/plumber.R")$run(port=8000)
whenever i try to run the docker image, i get this error:
File does not exist: /home/kristoffer/Desktop/plumber-api/rfiles/plumber.R
Execution halted
i have ensured, that all the necessary files are located in the right directory.
EDIT:
i included an image of all the files i have in my directory, to ensure, that the dockerfile is in the same directory as my other files
you are copying everything under / change your copy command to:
COPY . .
and make sure that Dockerfile is in the same directory.
beside this :
plumber::plumb("/home/kristoffer/Desktop/plumber-api/rfiles/plumber.R")
will also not work since the path is not in your container change it to :
plumber::plumb("plumber.R")
if this file is in the same directory
Related
Bottom line: output from container is not appearing in mounted local directory
I have read the documentation for bind mounts and on another project had success with this.
My docker file:
FROM ubuntu:18.04
RUN apt-get update && apt-get install -yq build-essential autoconf libnetcdf-dev libxml2-dev libproj-dev valgrind wget unzip git nano
# pulls ADBM from github and unzips in folder ADMBcode
RUN mkdir /ADMBcode
RUN wget https://github.com/admb-project/admb/releases/download/admb-12.2/admb-12.2-linux.zip
RUN mv admb-12.2-linux.zip /ADMBcode
RUN unzip ADMBcode/admb-12.2-linux.zip -d /ADMBcode
# pulls hydra repo from github into folder HYDRA
RUN mkdir /HYDRA
RUN git clone https://github.com/NOAA-EDAB/hydra_sim.git /HYDRA
# compiles and runs model
WORKDIR /HYDRA
RUN /ADMBcode/admb-12.2/admb hydra_sim.tpl
RUN ./hydra_sim
# create dir for output and move output
#RUN mkdir -p /HYDRA/output/diagnostics
#RUN mkdir /HYDRA/output/indices
# moves output to folder to be mounted
RUN mv *.out /HYDRA/output/diagnostics
RUN mv *.txt /HYDRA/output/indices
I build the image
podman build -t hydra .
and run the container using the following :
podman run --rm --name hydra --mount "type=bind,src=/path_on_local_machine/test,dst=/HYDRA/output" hydra
I have test folder on my local machine but the output is not mounted.
I have entered the container
podman run -it hydra
and checked that the output is there
I have done this before for another model and everything behaved. Not sure why this is not.
Any ideas what i am doing wrong?
Thanks
However
I have a code of 200 lines in R for shiny app which works perfect when I run from RStudio , while I have to Dockerize the app but when I run docker version of the app , I only see Hello-World app on localhost but not the actual code. I see inside container there are some extra files which docker always copies which is the problem, Can someone help me out ?
this is 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("library(shiny)","shinydashboard","xlsx", "V8"))"
# copy the app to the image
COPY app /srv/shiny-server/
# make all app files readable (solves issue when dev in Windows, but building in Ubuntu)
RUN chmod -R 755 /srv/shiny-server/
EXPOSE 3838
CMD ["/usr/bin/shiny-server.sh"]
Thanks
Thanks
You could copy additional files / folders individually, e.g.:
COPY modules /srv/shiny-server/modules
COPY R /srv/shiny-server/R
COPY *.R /srv/shiny-server/
COPY www /srv/shiny-server/www
Not sure, but are you copying your shiny-server.sh file over? I usually run my dockerized Shiny Apps with:
CMD ["Rscript", "-e", "shiny::runApp('/srv/shiny-server/', host='0.0.0.0', port=3838)"]
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 built a Docker Image for an R Shiny App and ran the corresponding container with Docker Toolbox on Windows 10 Home. When trying to open the App with my web browser, only the index is shown. I don't know why the app isn't executed.
The log shows me this:
*** warning - no files are being watched ***
[2019-08-12T15:34:42.688] [INFO] shiny-server - Shiny Server v1.5.12.1 (Node.js v10.15.3)
[2019-08-12T15:34:42.704] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
[2019-08-12T15:34:43.100] [INFO] shiny-server - Starting listener on http://[::]:3838
I already specified the app host-to-container path by executing the following command which refers to a docker hub image:
docker run --rm -p 3838:3838 -v /C/Docker/App/:/srv/shinyserver/ -v /C/Docker/shinylog:/var/log/shiny-server/ didsh123/ps_app:heatmap
My Docker File looks like the following:
# get shiny serves plus tidyverse packages image
FROM rocker/shiny-verse:latest
# 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
##Install R packages that are required--> were already succesfull
RUN R -e "install.packages(c('shinydashboard','shiny', 'plotly', 'dplyr', 'magrittr'))"
#Heatmap related packages
RUN R -e "install.packages('gpclib', type='source')"
RUN R -e "install.packages('rgeos', type='source')"
RUN R -e "install.packages('rgdal', type='source')"
# copy app to image
COPY ./App /srv/shiny-server/App
# add .conf file to image/container to preserve log file
COPY ./shiny-server.conf /etc/shiny-server/shiny-server.conf
##When run image and create a container, this container will listen on port 3838
EXPOSE 3838
###Avoiding running as root --> run container as user instead
# allow permission
RUN sudo chown -R shiny:shiny /srv/shiny-server
# execute in the following as user --> imortant to give permission before that step
USER shiny
##run app
CMD ["/usr/bin/shiny-server.sh"]
So when I address the docker ip and the assessed port in the browser, the app should run there, but only the index is displayed. I use the following line:
http://192.168.99.100:3838/App/
I'm glad for every hint or advice. I'm new to Docker, so I'm also happy for detailed explanations.
To use shiny with docker, I suggest you use the golem package. golem provides a framework for builing shiny apps. If you have an app developed according to their framework, the function golem::add_dockerfile() can be used to create dockerfiles automatically.
If you are not interested in a framework, You can still have a look at the source for add_dockerfile() to see how they manage the deployment. Their strategy is to use shiny::runApp() with the port argument. Therefore, shiny-server is not necessary in this case.
The Dockerfile in golem looks roughly like this
FROM rocker/tidyverse:3.6.1
RUN R -e 'install.packages("shiny")'
COPY app.R /app.R
EXPOSE 3838
CMD R -e 'shiny::runApp("app.R", port = 3838, host = "0.0.0.0")'
This will make the app available on port 3838. Of course, you will have to install any other R packages and system dependencies.
Additional tips
To increase reproducibility, I would suggest you use remotes::install_version() instead of install.packages().
If you are going to deploy several applications with similar dependencies (for example shinydashboard), it makes sense to write your own base image that can be used in place of rocker/tidyverse:3.6.1. This way, your builds will be much quicker.
Minimal Reproducible Example
Create an empty directory (can be called anything you want)
Inside it, create two things:
i. A file called Dockerfile
ii. An empty directory called app
Place your shiny app inside the directory called app.
Your shiny app can be a single app.R file, or, for older shiny apps, ui.R and server.R. Either way is fine (see here for more on that).
If unsure about any of the above, just copy the files found here.
Place this in Dockerfile
FROM rocker/shiny:latest
COPY ./app/* /srv/shiny-server/
CMD ["/usr/bin/shiny-server"]
In the terminal, cd to the root of the empty directory you created in step 1, and build the image with
docker build -t shinyimage .
Run the container with
docker run -p 3838:3838 shinyimage
Finally, visit this url to see your shiny app: http://localhost:3838/
Here's a copy of all of the above in case anything's unclear.
Check the logs for any useful information? And exec into the container to verify if the App content is copied to the correct location.
Because the way /App content is copied looks incorrect
The content of /App is copied into the image to /srv/shiny-server/App during the build phase and you are trying to override /srv/shiny-server content using -v option when running the container.
Looks like during runtime the App data copied is being overwritten.
Try without -v /C/Docker/App/:/srv/shinyserver/ or use -v /C/Docker/App/:/srv/shinyserver/App/
docker run --rm -p 3838:3838 -v /C/Docker/shinylog:/var/log/shiny-server/ didsh123/ps_app:heatmap
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)