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I am rendering an Rmarkdown pdf in docker. In the markdown file I have two packages, lavaan and semPlot that are called with the library() function. I am using the following Dockerfile:

FROM rocker/r-ver:4.2.2

RUN Rscript -e "install.packages('lavaan')"

RUN Rscript -e "install.packages('semPlot')"

RUN apt-get update \
  && apt-get install -y --no-install-recommends \
    wget \ 
    graphviz \ 
    texlive-latex-extra \ 
    lmodern \ 
    perl && \ 
    /rocker_scripts/install_pandoc.sh && \
    install2.r rmarkdown

ENV RSTUDIO_PANDOC=/usr/lib/rstudio/bin/pandoc

COPY . /home/user
WORKDIR /home/user/

RUN Rscript -e "rmarkdown::render('Paper.Rmd')"

When I run docker build . -t analysis, lavaan loads properly however I get the error:

=> ERROR [7/7] RUN Rscript -e "rmarkdown::render('Paper.Rmd')"            3.9s 
------                                                                          
 > [7/7] RUN Rscript -e "rmarkdown::render('Paper.Rmd')":                       
#10 2.470                                                                       
#10 2.470                                                                       
#10 2.470 processing file: Paper.Rmd                                            
  |..........................................          |  80% (unnamed-chunk-1)Quitting from lines 18-28 (Paper.Rmd) 
#10 3.781 Error in library(semPlot) : there is no package called 'semPlot'
#10 3.781 Calls: <Anonymous> ... withVisible -> eval_with_user_handlers -> eval -> eval -> library
                                                                                                            
#10 3.784 Execution halted
------
executor failed running [/bin/sh -c Rscript -e "rmarkdown::render('Paper.Rmd')"]: exit code: 1

I have tried solutions from: Can't install R package in docker image (added a repos argument) and semPlot package dependency issues (added installs to the Dockerfile)

Any help is appreciated, please let me know if additional information is needed. I am on a Mac with Linux.

Laura Jamison
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  • Are you sure you don't get an error earlier in the build? I would expect those `install.packages` commands to be after the `apt-get update` command. – MrFlick Apr 06 '23 at 19:02
  • Changing the order does not fix it, if I take out `semPlot()` from the Dockerfile and .Rmd then everything runs perfectly – Laura Jamison Apr 07 '23 at 15:48

0 Answers0