`{dockerfiler}`

Easy Dockerfile Creation from R.

Installation

You can install dockerfiler from GitHub with:

# install.packages("remotes")
remotes::install_github("ThinkR-open/dockerfiler")

Or from CRAN with :

install.packages("dockerfiler")

Basic worflow

By default, Dockerfiles are created with FROM "rocker/r-base".

You can set another FROM in new()

library(dockerfiler)
# Create a dockerfile template
my_dock <- Dockerfile$new()
my_dock$MAINTAINER("Colin FAY", "[email protected]")

Wrap your raw R Code inside the r() function to turn it into a bash command with R -e.

my_dock$RUN(r(install.packages("attempt", repo = "http://cran.irsn.fr/")))

Classical Docker stuffs:

my_dock$RUN("mkdir /usr/scripts")
my_dock$RUN("cd /usr/scripts")
my_dock$COPY("plumberfile.R", "/usr/scripts/plumber.R")
my_dock$COPY("torun.R", "/usr/scripts/torun.R")
my_dock$EXPOSE(8000)
my_dock$CMD("Rscript /usr/scripts/torun.R ")

See your Dockerfile :

my_dock
#> FROM rocker/r-base
#> MAINTAINER Colin FAY <[email protected]>
#> RUN R -e 'install.packages("attempt", repo = "http://cran.irsn.fr/")'
#> RUN mkdir /usr/scripts
#> RUN cd /usr/scripts
#> COPY plumberfile.R /usr/scripts/plumber.R
#> COPY torun.R /usr/scripts/torun.R
#> EXPOSE 8000
#> CMD Rscript /usr/scripts/torun.R

If you’ve made a mistake in your script, you can switch lines with the switch_cmd method. This function takes as arguments the positions of the two cmd you want to switch :

# Switch line 8 and 7
my_dock$switch_cmd(8, 7)
my_dock
#> FROM rocker/r-base
#> MAINTAINER Colin FAY <[email protected]>
#> RUN R -e 'install.packages("attempt", repo = "http://cran.irsn.fr/")'
#> RUN mkdir /usr/scripts
#> RUN cd /usr/scripts
#> COPY plumberfile.R /usr/scripts/plumber.R
#> EXPOSE 8000
#> COPY torun.R /usr/scripts/torun.R
#> CMD Rscript /usr/scripts/torun.R

You can also remove a cmd with remove_cmd:

my_dock$remove_cmd(8)
my_dock
#> FROM rocker/r-base
#> MAINTAINER Colin FAY <[email protected]>
#> RUN R -e 'install.packages("attempt", repo = "http://cran.irsn.fr/")'
#> RUN mkdir /usr/scripts
#> RUN cd /usr/scripts
#> COPY plumberfile.R /usr/scripts/plumber.R
#> EXPOSE 8000
#> CMD Rscript /usr/scripts/torun.R

This also works with a vector:

my_dock$remove_cmd(5:7)
my_dock
#> FROM rocker/r-base
#> MAINTAINER Colin FAY <[email protected]>
#> RUN R -e 'install.packages("attempt", repo = "http://cran.irsn.fr/")'
#> RUN mkdir /usr/scripts
#> CMD Rscript /usr/scripts/torun.R

add_after add a command after a given line.

my_dock$add_after(
  cmd = "RUN R -e 'remotes::install_cran(\"rlang\")'", 
  after = 3
)

Save your Dockerfile:

my_dock$write()

Create a Dockerfile from a DESCRIPTION

You can use a DESCRIPTION file to create a Dockerfile that installs the dependencies and the package.

my_dock <- dock_from_desc("DESCRIPTION")
#> ℹ Please wait while we compute system requirements...
#> ✓ Done
my_dock
#> FROM rocker/r-ver:4.1.2
#> RUN apt-get update && apt-get install -y  git-core libcurl4-openssl-dev libgit2-dev libicu-dev libssl-dev make pandoc pandoc-citeproc && rm -rf /var/lib/apt/lists/*
#> RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" >> /usr/local/lib/R/etc/Rprofile.site
#> RUN R -e 'install.packages("remotes")'
#> RUN Rscript -e 'remotes::install_version("glue",upgrade="never", version = "1.6.1")'
#> RUN Rscript -e 'remotes::install_version("cli",upgrade="never", version = "3.1.1")'
#> RUN Rscript -e 'remotes::install_version("R6",upgrade="never", version = "2.5.1")'
#> RUN Rscript -e 'remotes::install_version("desc",upgrade="never", version = "1.4.0")'
#> RUN Rscript -e 'remotes::install_version("fs",upgrade="never", version = "1.5.2")'
#> RUN Rscript -e 'remotes::install_version("jsonlite",upgrade="never", version = "1.7.3")'
#> RUN Rscript -e 'remotes::install_version("knitr",upgrade="never", version = "1.37")'
#> RUN Rscript -e 'remotes::install_version("testthat",upgrade="never", version = "3.1.2")'
#> RUN Rscript -e 'remotes::install_version("rmarkdown",upgrade="never", version = "2.11")'
#> RUN Rscript -e 'remotes::install_version("usethis",upgrade="never", version = "2.1.5")'
#> RUN Rscript -e 'remotes::install_version("renv",upgrade="never", version = "0.15.2")'
#> RUN Rscript -e 'remotes::install_version("remotes",upgrade="never", version = "2.4.2")'
#> RUN Rscript -e 'remotes::install_version("pkgbuild",upgrade="never", version = "1.3.1")'
#> RUN Rscript -e 'remotes::install_version("pak",upgrade="never", version = "0.2.0")'
#> RUN Rscript -e 'remotes::install_version("attempt",upgrade="never", version = "0.3.1")'
#> RUN mkdir /build_zone
#> ADD . /build_zone
#> WORKDIR /build_zone
#> RUN R -e 'remotes::install_local(upgrade="never")'
#> RUN rm -rf /build_zone

my_dock$CMD(r(library(dockerfiler)))

my_dock$add_after(
  cmd = "RUN R -e 'remotes::install_cran(\"rlang\")'", 
  after = 3
)
my_dock
#> FROM rocker/r-ver:4.1.2
#> RUN apt-get update && apt-get install -y  git-core libcurl4-openssl-dev libgit2-dev libicu-dev libssl-dev make pandoc pandoc-citeproc && rm -rf /var/lib/apt/lists/*
#> RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" >> /usr/local/lib/R/etc/Rprofile.site
#> RUN R -e 'remotes::install_cran("rlang")'
#> RUN R -e 'install.packages("remotes")'
#> RUN Rscript -e 'remotes::install_version("glue",upgrade="never", version = "1.6.1")'
#> RUN Rscript -e 'remotes::install_version("cli",upgrade="never", version = "3.1.1")'
#> RUN Rscript -e 'remotes::install_version("R6",upgrade="never", version = "2.5.1")'
#> RUN Rscript -e 'remotes::install_version("desc",upgrade="never", version = "1.4.0")'
#> RUN Rscript -e 'remotes::install_version("fs",upgrade="never", version = "1.5.2")'
#> RUN Rscript -e 'remotes::install_version("jsonlite",upgrade="never", version = "1.7.3")'
#> RUN Rscript -e 'remotes::install_version("knitr",upgrade="never", version = "1.37")'
#> RUN Rscript -e 'remotes::install_version("testthat",upgrade="never", version = "3.1.2")'
#> RUN Rscript -e 'remotes::install_version("rmarkdown",upgrade="never", version = "2.11")'
#> RUN Rscript -e 'remotes::install_version("usethis",upgrade="never", version = "2.1.5")'
#> RUN Rscript -e 'remotes::install_version("renv",upgrade="never", version = "0.15.2")'
#> RUN Rscript -e 'remotes::install_version("remotes",upgrade="never", version = "2.4.2")'
#> RUN Rscript -e 'remotes::install_version("pkgbuild",upgrade="never", version = "1.3.1")'
#> RUN Rscript -e 'remotes::install_version("pak",upgrade="never", version = "0.2.0")'
#> RUN Rscript -e 'remotes::install_version("attempt",upgrade="never", version = "0.3.1")'
#> RUN mkdir /build_zone
#> ADD . /build_zone
#> WORKDIR /build_zone
#> RUN R -e 'remotes::install_local(upgrade="never")'
#> RUN rm -rf /build_zone
#> CMD R -e 'library(dockerfiler)'

Create a Dockerfile from renv.lock

Create renv.lock

dir_build <- tempfile(pattern = "renv")
dir.create(dir_build)

# Create a lockfile
the_lockfile <- file.path(dir_build, "renv.lock")
custom_packages <- c(
  # attachment::att_from_description(),
  "renv",
  "cli", "glue", "golem",
  "shiny", "stats", "utils",
  "testthat",
  "knitr"
)
renv::snapshot(
  packages = custom_packages,
  lockfile = the_lockfile,
  prompt = FALSE)

Build Dockerfile

my_dock <- dock_from_renv(lockfile = the_lockfile,
                   distro = "focal",
                   FROM = "rocker/verse"
    )
#> ℹ Please wait while we compute system requirements...
#> Fetching system dependencies for 81 package records.
#> Warning: `lang()` is deprecated as of rlang 0.2.0.
#> Please use `call2()` instead.
#> This warning is displayed once per session.
#> ✓ Done
my_dock
#> FROM rocker/verse:4.1
#> RUN apt-get update -y && apt-get install -y  make  libcurl4-openssl-dev  libssl-dev  git  libgit2-dev  libicu-dev  libxml2-dev  zlib1g-dev  pandoc && rm -rf /var/lib/apt/lists/*
#> RUN echo "options(renv.config.pak.enabled = TRUE, repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" >> /usr/local/lib/R/etc/Rprofile.site
#> RUN R -e 'install.packages(c("renv","remotes"))'
#> COPY renv.lock renv.lock
#> RUN R -e 'renv::restore()'

Contact

Questions and feedbacks welcome!

You want to contribute ? Open a PR :) If you encounter a bug or want to suggest an enhancement, please open an issue.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Name		Name	Last commit message	Last commit date
Latest commit History 54 Commits
.github		.github
R		R
data-raw		data-raw
dev		dev
inst		inst
man		man
tests		tests
vignettes		vignettes
.Rbuildignore		.Rbuildignore
.gitattributes		.gitattributes
.gitignore		.gitignore
CODE_OF_CONDUCT.md		CODE_OF_CONDUCT.md
DESCRIPTION		DESCRIPTION
LICENSE		LICENSE
LICENSE.md		LICENSE.md
NAMESPACE		NAMESPACE
NEWS.md		NEWS.md
README.Rmd		README.Rmd
README.md		README.md
codecov.yml		codecov.yml
dockerfiler.Rproj		dockerfiler.Rproj

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{dockerfiler}

Installation

Basic worflow

Create a Dockerfile from a DESCRIPTION

Create a Dockerfile from renv.lock

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