Unable to install Cluster Profiler through Docker File

Question

[Srinka]

Can anyone please suggest ways to solve the error?

I tried running a Docker image where I installed the dependencies of RNA Seq analysis using R.

This is the error I am getting when I try to run the Docker image:

Thank you in advance.

This is the code I used

FROM rocker/r-base

WORKDIR /app

COPY . /app

RUN apt-get update && apt-get install -y \
    libxml2-dev \
    libcurl4-openssl-dev \
    libssl-dev RUN R -e "install.packages(c('shiny', 'shinydashboard', 'shinyjs', 'DT', 'ggplot2', 'gplots'))"

RUN R -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')" 

RUN R -e "BiocManager::install(c('Rsubread', 'DESeq2', 'SummarizedExperiment', 'edgeR', 'org.Hs.eg.db', 'EnhancedVolcano', 'org.Mm.eg.db', 'limma', 'enrichplot', 'pathview', 'pheatmap', 'clusterProfiler'))"

CMD ["R", "-e", "shiny::runApp('app.R', host = '0.0.0.0', port = 3838)"]

[ATpoint]

Please understand that this question is not reproducible as it lacks any detail how and which container you start and how you installed this package (if at all). Please show the Dockerfile at least. People here cannot see your screen so you have to give enough minimal information to reproduce the problem as this is the basis for debugging. No screenshots please, just paste the plain text and use the 10101 button or standard markdown for highlighting.

[Srinka]

Thank you for letting me know. I have updated my query.

[Meisam]

does this answer your question?

Answer 1

[ATpoint]

My recommendation is to run an interactive session via:

docker run -it rocker/r-base:latest bash

and then run the installation commands to see the full logs. It seems an error pops up somewhere but we do not know which. What you can also do is to use bioconductor/bioconductor_docker:RELEASE_3_17 as base image as this comes with all dependencies for any bioconductor package already installed so installation is almost certain to work.

[Srinka]

Thank you so much for your reply. bioconductor/bioconductor_docker:RELEASE_3_17 as the base image worked.