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I am trying to create a working docker image (based on Shiny) which includes a BioConductor package. The packages are installed during the build phase, but they do not persist. I have tried installing it using 4 different methods ; none works.
Dockerfile :
FROM rocker/shiny:4.0.5
RUN apt-get update && apt-get install -y \
libcurl4-gnutls-dev \
libssl-dev
# A repo from Rpackagemanager
RUN install2.r --repos=https://packagemanager.rstudio.com/all/2022-08-18+Y3JhbiwyOjQ1MjYyMTU7RkU2MERFREE \
shinycssloaders \
... \
BiocManager
RUN install2.r --repos=https://packagemanager.rstudio.com/all/2022-08-18+Y3JhbiwyOjQ1MjYyMTU7RkU2MERFREE \
littler
# Four different ways to install clusterProfiler
RUN install2.r -r http://bioconductor.org/packages/3.12/bioc --deps TRUE \
clusterProfile
RUN /usr/local/lib/R/site-library/littler/examples/installBioc.r clusterProfiler
RUN R -e 'BiocManager::install("clusterProfiler", version="3.12")'
RUN R -e 'install.packages("clusterProfiler", repos=BiocManager::repositories())'
COPY ./*.R ./
CMD ["R", "-e" , "shiny::runApp(port=8080, host='0.0.0.0')"]
None of the four ways I tried works.
There are probably some docker experts on here that might have better ideas but my initial thought is you might have to have a host specific library set up for persistence. Some helpful links might be the Bioconductor docker which shows our Dockerfile for Bioconductor and the Bioconductor help page that shows how to customize this base docker file with packages or additional system dependencies.
Please show both the full build command
docker build ...and the way you assessed / checked that the package was not installed. There is not much magic going on actually, the shown commands should all be fine.I simply use
docker build -t withmistake .and run it withdocker run --rm withmistakeand I get the error
Error in library(clusterProfiler) : there is no package called ‘clusterProfilerWhen I use
FROM bioconductor/bioconductor_docker:RELEASE_3_12instead ofFROM rocker/shiny:4.0.5no such error is thrown, and I even manage do deploy it on fly.io ( however, the image size is about 3GB larger in such a case ).I prefer a small image size, and (though I don't really know) I think that the Shiny base image would be better for a Shiny app.
Could you provide the error message that you get, so that we can diagnose the problem better?
A strategy that I've used recently was to include the required packages in an Rscript and call that in the Dockerfile
RUN Rscript rpkgs.RWorking example: https://github.com/casbap/ncRNA/tree/main/docker
The error message is simply
Error in library(clusterProfiler) : there is no package called ‘clusterProfiler‘