TinyTex installing additional packages which are already present in Docker image

[Biagio74]

I am building a Docker image from the rocker/verse:4.04 image and I am installing other packages with tlmgr. I am expecting that the extra installs are installed at build. But once I try to use knitr to knit my Rmd document to PDF then the my Docker logs shows extra LaTeX installs which should be already present.

Here is my Dockerfile:

FROM rocker/verse:4.0.4

LABEL  author.email="email@domain.com"
LABEL  author.name="Balazs Kisfali"

RUN apt-get update -qq && apt-get install -y \
  git-core \
  libssl-dev \
  libcurl4-gnutls-dev

# Install Python
RUN apt-get install -y python3 python3-pip
# Copy first just the reqs to leverage Docker cache
COPY ./requirements.txt ./requirements.txt
# Install dependencies
RUN pip3 install -r requirements.txt

RUN R -e "install.packages(c('plumber', 'rmarkdown', 'purrr', 'fs', 'reticulate','knitr', 'googleCloudStorageR'))"

# install some packages
RUN tlmgr init-usertree
RUN tlmgr update --self --all && \
  tlmgr install fancyhdr cleveref multirow listings \
  xcolor grffile titling amsmath kvsetkeys etoolbox \
  pdftexcmds infwarerr geometry fancyvrb framed booktabs \
  mdwtools epstopdf-pkg kvoptions ltxcmds auxhook bigintcalc \
  bitset etexcmds gettitlestring hycolor hyperref intcalc kvdefinekeys \
  letltxmacro pdfescape refcount rerunfilecheck stringenc uniquecounter \
  zapfding

ENV APP_HOME /app
WORKDIR $APP_HOME

COPY . ./

ENV PORT=5012
EXPOSE $PORT

CMD ["Rscript", "Main.R"]

For instance this package is installing: kvoptions even if it was installed at build time of the container image. But beside this there are another 15 packages at least which were already installed. This makes my plumber API very slow at the first request where I kick-off a PDF conversion. Takes about 4 minutes, then the next one obviously few seconds as there are no missing packages anymore. But once I deploy the container to Cloud Run in GCP it happens all the time, I guess due to the fact the new workers are spin up.

How can I restrict my installation to avoid installing missing packages? How can I know exactly which packages I need if I have the following in my .Rmd file:

output: 
  pdf_document:
    pandoc_args: ["--extract-media", "."]
    fig_caption: true
    toc: yes
    number_sections: true
    extra_dependencies:
      inputenc: ["utf8"]
      fancyhdr: null
      cleveref: null
      multirow: null
      listings: null
      # cmbright: null # this caused a lots of problem and the packages was
      # not installed in anyway
      fontenc: ["T1"]
      array: null
      xcolor: null
      grffile: null # recognise multidots in image files

and something more in the header-includes:

header-includes:
  - \usepackage{titling}
  - \usepackage{graphicx}
  - \pretitle{\begin{center}
    \includegraphics[width=2in,height=2in]{shapemaker_logo_long.png}\LARGE\\}
  - \setlength\headheight{33pt}
  - \posttitle{\end{center}}
  - \usepackage{fancyhdr}
  - \pagestyle{fancy}
  - \fancyfoot{} # ridd of the default page number
  - \fancyhead{} # ridd of the default head
  - \fancyfoot[R]{| Page \thepage}
  - \fancyfoot[L]{© 2021. Shapemaker AS.}
  - \fancyhead[L,C]{}
  - \fancyhead[L]{Test site \\ Second  }
  - \fancyhead[C]{007 \\  line  }
  - \fancyhead[R]{\includegraphics[height=0.8cm]{shapemaker_logo_long.png}}

Since RStudio installs smartly all missing packages when I knit my doc, I don't know which packages were installed exactly.