Deploy shinyapp in Docker Error in shinyAppDir(x)

Question

I have the following dockfile

# 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 \
    coinor-libcbc-dev coinor-libclp-dev libglpk-dev


## update system libraries
RUN apt-get update && \
    apt-get upgrade -y && \
    apt-get clean

# copy necessary files
## app folder
COPY ./app ./app

# Docker inheritance
FROM bioconductor/bioconductor_docker:RELEASE_3_12

RUN apt-get update
    RUN R -e 'BiocManager::install(ask = F)' && R -e 'BiocManager::install(c("rtracklayer", \
    "GenomicAlignments", "Biostrings", "SummarizedExperiment", "Rsamtools", ask = F))'


# install renv & restore packages
RUN Rscript -e 'install.packages("renv")'
RUN Rscript -e 'install.packages("devtools")'
RUN Rscript -e 'install.packages("shiny")'
RUN Rscript -e 'install.packages("shinyBS")'
RUN Rscript -e 'install.packages("ggvis")'
RUN Rscript -e 'install.packages("shinydashboardPlus")'
RUN Rscript -e 'install.packages("shinycssloaders")'
RUN Rscript -e 'install.packages("shinyWidgets")'
RUN Rscript -e 'install.packages("plotly")'
RUN Rscript -e 'install.packages("RSQLite")'
RUN Rscript -e 'install.packages("forecast", dependencies = TRUE)'
RUN Rscript -e 'install.packages("tsutils")'
RUN Rscript -e 'install.packages("readxl")'
RUN Rscript -e 'install.packages("tidyverse")'
RUN Rscript -e 'install.packages("knitr")'
RUN Rscript -e 'install.packages("knitcitations")'
RUN Rscript -e 'install.packages("nycflights13")'
RUN Rscript -e 'install.packages("Matrix")'
RUN Rscript -e 'install.packages("plotly")'
RUN Rscript -e 'install.packages("igraph")'
RUN Rscript -e 'install.packages("ggthemes")'
RUN Rscript -e 'install.packages("evaluate")'
RUN Rscript -e 'install.packages("psych")'
RUN Rscript -e 'install.packages("kableExtra")'
RUN Rscript -e 'install.packages("ggjoy")'
RUN Rscript -e 'install.packages("gtools")'
RUN Rscript -e 'install.packages("gridExtra")'
RUN Rscript -e 'install.packages("cowplot")'
RUN Rscript -e 'install.packages("ggrepel")'
RUN Rscript -e 'install.packages("data.table")'
RUN Rscript -e 'install.packages("stringr")'
RUN Rscript -e 'install.packages("rmarkdown")'

RUN Rscript -e 'install.packages("shinyjqui")'
#RUN Rscript -e 'install.packages("BiocManager")'
#RUN R -e 'BiocManager::install("rtracklayer")'
#RUN R -e 'BiocManager::install("GenomicAlignments")'
#RUN R -e 'BiocManager::install("Biostrings")'
#RUN R -e 'BiocManager::install("SummarizedExperiment")'
#RUN R -e 'BiocManager::install("Rsamtools")'
RUN Rscript -e 'install.packages("V8")'
RUN Rscript -e 'devtools::install_github("ThomasSiegmund/D3TableFilter")'
RUN Rscript -e 'devtools::install_github("leonawicz/apputils")'
RUN Rscript -e 'devtools::install_github("Marlin-Na/trewjb")'

RUN Rscript -e 'devtools::install_github("dirkschumacher/ompr")'
RUN Rscript -e 'devtools::install_github("dirkschumacher/ompr.roi")'

RUN Rscript -e 'install.packages("ROI.plugin.glpk")'

RUN Rscript -e 'install.packages("shinydashboard")'
RUN Rscript -e 'install.packages("dplyr")'
RUN Rscript -e 'install.packages("dashboardthemes")'
RUN Rscript -e 'install.packages("shinyjs")'
RUN Rscript -e 'install.packages("magrittr")'
RUN Rscript -e 'install.packages("DT")'
RUN Rscript -e 'install.packages("rhandsontable")'
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)"]

When I try to upload without Bioconductor packages the app running But when I am trying to upload as the dockfile is I receive the following error.

Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help shiny::runApp('/app', host = '0.0.0.0', port = 3838) Error in shinyAppDir(x) : No Shiny application exists at the path "/app" Calls: ... as.shiny.appobj -> as.shiny.appobj.character -> shinyAppDir Execution halted

I visit some solution but I do not understand them....please I need your help

Chai · Accepted Answer · 2021-01-20 17:17:22Z

1

Check out the docs on multistage builds You have a COPY statement, and right after that a FROM statement. After that last statement you no longer have access to whatever was in there in previous stage. You can copy files from one stage to the next if needed with --from=stagename where you named the stage with FROM somerepo/someimage as stagename. In this case it means that everything you do in the first stage is never used or available again. Normally this is used something like

FROM baseimage as build
RUN install some dependencies
COPY some sourcefiles
RUN install stuff eg mvn install

FROM runImage as run
COPY --from=build somepath/executable
CMD ["do", "something"]

This way you keep the final image small, removing everything you need at build time, but not at runtime. In your case you have to rethink this a bit and see what you need at which stage.

I do not know the specifics of your app but the way you have it set up now is that you start with a base image, then install debian suff, then system stuff and then start all over with a "empty" new baseimage. You probably want to use just one image and go from there, with just one FROM instruction. Then if you want to optimize it for production you can always consider the multistage build if that is worth it in your case.

answered Jan 20, 2021 at 17:17

Chai

2,0363 gold badges24 silver badges35 bronze badges

Sign up to request clarification or add additional context in comments.

3 Comments

Adam Over a year ago

Thank you very much for your answer. But is a difficult concept. So I need 2 dockerfiles ( as the suggested article described) one is going to deeply the app and the other is going to deploy the bioconductor packages?

Adam Over a year ago

Based on your answer I try to move and to post the block of Bioconductor before deploying the app. The app needs a library from Bioconductor. Everything seems to run....maybe it was that the solution? Changing the blocks in dockerfile?

Chai Over a year ago

Yes exactly, as I suggested, keep everything in one stage, and if needed later you can optimize to get a smaller final image.

Collectives™ on Stack Overflow

Deploy shinyapp in Docker Error in shinyAppDir(x)

1 Answer 1

3 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

3 Comments

Your Answer

Sign up or log in

Post as a guest

Related