Hi everyone, I just need some help. I'm sure someone already had the same problem.

I've got a shiny app which uses phyloseq, but somehow when I create the image and want to start the image I always get the same error

    Error in library(): ! there is no package called 'phyloseq' Backtrace: 1. base::library(phyloseq) Execution halted

I really don't know where the problem is, first I thought there's a version problem with R and Bioconductor so I changed the R version to 3.4.2. However this didn't work, at the same time I also tried to take the BiocManager version 3.18 which should be compatible with with the R version I've got. Also no results.

After some hours spent, I now desperately search for some help, and hope that someone could help.

Below you'll see the Dockerfile I've got.

If someone know the problem or could help here I'd be very thankful.

FROM rocker/shiny:4.3.2


RUN wget https://quarto.org/download/latest/quarto-linux-amd64.deb && \
    dpkg -i quarto-linux-amd64.deb && \
    rm quarto-linux-amd64.deb


RUN R -e "install.packages('tinytex'); tinytex::install_tinytex()"


RUN apt-get update && apt-get install -y \
  libcurl4-openssl-dev \
  libssl-dev \
  libxml2-dev \
  libxt6 \
  libxrender1 \
  libfontconfig1 \
  libharfbuzz-dev \
  libfribidi-dev \
  zlib1g-dev \
  git


# Install CRAN packages
RUN R -e "install.packages(c( \
  'shiny', 'bslib', 'bsicons', 'tidyverse', 'DT', 'plotly', 'readxl', 'tools', \
  'knitr', 'kableExtra', 'base64enc', 'ggrepel', 'pheatmap', 'viridis', 'gridExtra', \
  'quarto' \
))"


# Install Bioconductor and required packages
RUN R -e "install.packages('BiocManager')"
RUN R -e "BiocManager::install(version = '3.18')"
RUN R -e "BiocManager::install('phyloseq', dependencies = TRUE, ask = FALSE)"
RUN R -e "BiocManager::install('DESeq2', dependencies = TRUE, ask = FALSE)"
RUN R -e "BiocManager::install('apeglm', dependencies = TRUE, ask = FALSE)"
RUN R -e "BiocManager::install('vegan', dependencies = TRUE, ask = FALSE)"


COPY src/ /srv/shiny-server/
COPY data/ /srv/shiny-server/data/
RUN chown -R shiny:shiny /srv/shiny-server

USER shiny

EXPOSE 3838 

CMD ["/usr/bin/shiny-server"]