How to create a dockerfile reliably?

[udurraniAtPresage]

I am on version 0.4.1 of golem. Whenever I do golem::add_dockerfile_with_renv(document = FALSE, lockfile = "renv.lock"), it does not generate a dockerfile, instead it creates a temporary README with commands to run in terminal. But there is no dockerfile.

So, I run golem::add_dockerfile(), and it does this:

> golem::add_dockerfile()
• golem::add_dockerfile() is not recommended anymore.
Please use golem::add_dockerfile_with_renv() instead.
✔ Setting active project to 'C:/Users/presage/Documents/GitHub/myProject'
ℹ Please wait while we compute system requirements...
• Unable to query the sysreqs.
• Possible explanation: no internet connection or sysreqs.r-hub.io is unavailable.
• Unable to query the sysreqs.
• Possible explanation: no internet connection or sysreqs.r-hub.io is unavailable.
• Unable to query the sysreqs.
• Possible explanation: no internet connection or sysreqs.r-hub.io is unavailable.
• Unable to query the sysreqs.
• Possible explanation: no internet connection or sysreqs.r-hub.io is unavailable.
• Unable to query the sysreqs.
• Possible explanation: no internet connection or sysreqs.r-hub.io is unavailable.
✔ Done
• .dockerignore already present, skipping its creation.
✔ Dockerfile created at Dockerfile

The generated dockerfile is:

FROM rocker/verse:4.3.2
RUN apt-get update && apt-get install -y   && rm -rf /var/lib/apt/lists/*
RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site
RUN R -e 'install.packages("remotes")'
RUN Rscript -e 'remotes::install_version("rlang",upgrade="never", version = "1.1.3")'
RUN Rscript -e 'remotes::install_version("bslib",upgrade="never", version = "0.7.0")'
RUN Rscript -e 'remotes::install_version("glue",upgrade="never", version = "1.7.0")'
RUN Rscript -e 'remotes::install_version("htmltools",upgrade="never", version = "0.5.8")'
RUN Rscript -e 'remotes::install_version("jsonlite",upgrade="never", version = "1.8.8")'
RUN Rscript -e 'remotes::install_version("tibble",upgrade="never", version = "3.2.1")'
RUN Rscript -e 'remotes::install_version("stringr",upgrade="never", version = "1.5.1")'
RUN Rscript -e 'remotes::install_version("tidyr",upgrade="never", version = "1.3.1")'
RUN Rscript -e 'remotes::install_version("purrr",upgrade="never", version = "1.0.2")'
RUN Rscript -e 'remotes::install_version("dplyr",upgrade="never", version = "1.1.4")'
RUN Rscript -e 'remotes::install_version("shiny",upgrade="never", version = "1.8.0")'
RUN Rscript -e 'remotes::install_version("config",upgrade="never", version = "0.3.2")'
RUN Rscript -e 'remotes::install_version("ggplot2",upgrade="never", version = "3.4.4")'
RUN Rscript -e 'remotes::install_version("waiter",upgrade="never", version = "0.2.5")'
RUN Rscript -e 'remotes::install_version("uuid",upgrade="never", version = "1.1-1")'
RUN Rscript -e 'remotes::install_version("testthat",upgrade="never", version = "3.2.1")'
RUN Rscript -e 'remotes::install_version("spelling",upgrade="never", version = "2.2.1")'
RUN Rscript -e 'remotes::install_version("shinyWidgets",upgrade="never", version = "0.8.1")'
RUN Rscript -e 'remotes::install_version("shinyjs",upgrade="never", version = "2.1.0")'
RUN Rscript -e 'remotes::install_version("sever",upgrade="never", version = "0.0.7")'
RUN Rscript -e 'remotes::install_version("readxl",upgrade="never", version = "1.4.3")'
RUN Rscript -e 'remotes::install_version("readr",upgrade="never", version = "2.1.5")'
RUN Rscript -e 'remotes::install_version("reactable",upgrade="never", version = "0.4.4")'
RUN Rscript -e 'remotes::install_version("lubridate",upgrade="never", version = "1.9.3")'
RUN Rscript -e 'remotes::install_version("httr2",upgrade="never", version = "1.0.0")'
RUN Rscript -e 'remotes::install_version("httr",upgrade="never", version = "1.4.7")'
RUN Rscript -e 'remotes::install_version("golem",upgrade="never", version = "0.4.1")'
RUN Rscript -e 'remotes::install_version("ggtext",upgrade="never", version = "0.1.2")'
RUN Rscript -e 'remotes::install_version("ggrepel",upgrade="never", version = "0.9.4")'
RUN Rscript -e 'remotes::install_version("echarts4r",upgrade="never", version = "0.4.5")'
RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.29")'
RUN Rscript -e 'remotes::install_version("bsicons",upgrade="never", version = "0.1.1")'
RUN Rscript -e 'remotes::install_github("MangoTheCat/shinytoastr@4cf139c7841dad3e35f6d00aacdfac41a260dc42")'
RUN Rscript -e 'remotes::install_github("stefanwilhelm/ShinyRatingInput@0dc69c9766453f3cd38cbb89b08fe421b829e9b0")'
RUN Rscript -e 'remotes::install_github("dreamRs/shufflecards@7874f3dddcd29b073451018c5b4d494349808e19")'
RUN Rscript -e 'remotes::install_github("kennedymwavu/frbs@ee10778ec626d36b9f79d7fee0a38e7b76f55ae3")'
RUN mkdir /build_zone
ADD . /build_zone
WORKDIR /build_zone
RUN R -e 'remotes::install_local(upgrade="never")'
RUN rm -rf /build_zone
EXPOSE 80
COPY .Renviron .Renviron
CMD R -e "options('shiny.port'=80,shiny.host='0.0.0.0');library(myProject);myProject::run_app()"

This works.

[VincentGuyader]

hi,
thanks for your message.

do you have more details about the fails with golem::add_dockerfile_with_renv ?

can you try with golem::add_dockerfile_with_renv(output_dir = "deploy")

by defaut it create a temp folder using output_dir = fs::path(tempdir(), "deploy") is it empty in your case ?

Regards

[VincentGuyader]

there is an issue with sysreqs.

dockerfiler::get_sysreqs(c("renv","dplyr","gert"))
#> * Unable to query the sysreqs.
#> * Possible explanation: no internet connection or sysreqs.r-hub.io is unavailable.
#> [1] ""

you can use : golem::add_dockerfile(sysreqs = FALSE)

and check the potential missing system requirements to add in the Dockerfile

[udurraniAtPresage]

Thanks. I will try with both of your suggestions.

[VincentGuyader]

can you try with thsi version of {dockerfiler} 2.2.9000

remotes::install-github("thinkr-open/dockerfiler@remove_sysreqsio")

[VincentGuyader]

[udurraniAtPresage]

Hi @VincentGuyader,
Thanks for your help in understanding and using the golem options for generating docker files. I can successfully do:

golem::add_dockerfile_with_renv(lockfile = "renv.lock", output_dir = "deploy")

This creates a deploy folder with multiple files. However, the golem::add_dockerfile(), which I know is not recommended anymore, generates a single Dockerfile. On Google Cloud Run, I can easily generate a service that looks for this Dockerfile in the main branch of my GitHub repo, and deploys the app. Every time there is a push to main, the app deployment is revised so I can easily update the app.

But with the former option that generates multiple files in the deploy folder, I can't just share the Dockerfile as it depends on the base image. Is there a way to generate a single Dockerfile in the root of the shiny app directory with golem::add_dockerfile_with_renv? It would then be possible for me to deploy to Google Cloud Run.

[VincentGuyader]

I see the issue clearly :)

One strategy would be to group everything into a single Dockerfile manually, like this:

FROM rocker/verse:4.4.2
RUN apt-get update -y && apt-get install -y make zlib1g-dev git && rm -rf /var/lib/apt/lists/*
RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
RUN echo "options(renv.config.pak.enabled = FALSE, repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site
RUN R -e 'install.packages("remotes")'
RUN R -e 'remotes::install_version("renv", version = "1.0.3")'
COPY renv.lock.prod renv.lock
RUN R -e 'options(renv.config.pak.enabled = FALSE); renv::restore()'
COPY mygolem_*.tar.gz /app.tar.gz
RUN R -e 'remotes::install_local("/app.tar.gz", upgrade="never")'
RUN rm /app.tar.gz
EXPOSE 80
USER rstudio
CMD R -e "options('shiny.port'=80, shiny.host='0.0.0.0'); library(mygolem); mygolem::run_app()"

Alternatively, you could use Docker's multi-stage build like this...

FROM rocker/verse:4.4.2 AS builder
RUN apt-get update -y && apt-get install -y make zlib1g-dev git && rm -rf /var/lib/apt/lists/*
RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
RUN echo "options(renv.config.pak.enabled = FALSE, repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site
RUN R -e 'install.packages("remotes")'
RUN R -e 'remotes::install_version("renv", version = "1.0.3")'
COPY renv.lock.prod renv.lock
RUN R -e 'renv::restore()'

FROM builder
COPY renv.lock.prod renv.lock
RUN R -e 'options(renv.config.pak.enabled = FALSE); renv::restore()'
COPY mygolem_*.tar.gz /app.tar.gz
RUN R -e 'remotes::install_local("/app.tar.gz", upgrade="never")'
RUN rm /app.tar.gz
EXPOSE 80
USER rstudio
CMD R -e "options('shiny.port'=80, shiny.host='0.0.0.0'); library(mygolem); mygolem::run_app()"

(As I'm writing this, I realize that the multi-stage approach looks promising... If it allows me to rerun only the second stage while benefiting from the builder's cache, I need to investigate further. If that's the case, it might become the new way to do things.)

[VincentGuyader]

with docker build --build-arg FINAL_BUILD=2 -t mygolem:latest . you can rerun the sedond part , using the cache from builder.. nice feat. I will implement this soon

[udurraniAtPresage]

Cool! That'd be a great option. Thanks.