dockerfile-method

Create a Dockerfile based on either a sessionInfo, a workspace or a file.

dockerfile(from = utils::sessionInfo(),
  image = getImageForVersion(getRVersionTag(from)),
  maintainer = Sys.info()[["user"]], save_image = FALSE,
  envir = .GlobalEnv, env = list(generator = paste("containerit",
  utils::packageVersion("containerit"))), soft = FALSE,
  offline = FALSE, copy = NULL, container_workdir = "/payload/",
  cmd = "R", entrypoint = NULL, add_self = FALSE, silent = FALSE,
  predetect = TRUE, versioned_libs = FALSE,
  versioned_packages = FALSE, filter_baseimage_pkgs = FALSE)

Arguments

from	The source of the information to construct the Dockerfile. Can be a `sessionInfo` object, a path to a file within the working direcotry, a `DESCRIPTION` file, or the path to a workspace). If `NULL` then no automatic derivation of dependencies happens. If a `DESCRIPTION` file, then the minimum R version (e.g. "R (3.3.0)") is used for the image version and all "Imports" are explicitly installed.
image	(From-object or character) Specifes the image that shall be used for the Docker container (`FROM` instruction). By default, the image selection is based on the given session. Alternatively, use `getImageForVersion(..)` to get an existing image for a manually defined version of R, matching the version with tags from the base image rocker/r-ver (see details about the rocker/r-ver at 'https://hub.docker.com/r/rocker/r-ver/'). Or provide a correct image name yourself.
maintainer	Specify the maintainer of the Dockerfile. See documentation at 'https://docs.docker.com/engine/reference/builder/#maintainer'. Defaults to `Sys.info()[["user"]]`. Can be removed with `NULL`.
save_image	When TRUE, it calls save.image in the current working directory and copys the resulting `.RData` file to the container's working directory. The created file in the local working director will not be deleted. Alternatively, you can pass a list of objects to be saved, which may also include arguments to be passed down to `save`, e.g. `save_image = list("object1", "object2")`. You can configure the name of the file the objects are saved to by adding a file name to the list of arguments, e.g. `save_image = list("objectA", save_image_filename = "mydata.RData")`, in which case the file path must be in UNIX notation. Note that you may not use `save_image_filename` for other objects in your session! `save` will be called with `envir`.
envir	The environment for `save_image`.
env	optionally specify environment variables to be included in the image. See documentation: 'https://docs.docker.com/engine/reference/builder/#env
soft	(boolean) Whether to include soft dependencies when system dependencies are installed, default is no.
offline	(boolean) Whether to use an online database to detect system dependencies or use local package information (slower!), default is no.
copy	whether and how a workspace should be copied - values: "script", "script_dir" or a list of relative file paths to be copied, or `NA` ot disable copying of files
container_workdir	the working directory in the container, defaults to `/payload/` and must end with `/`. Can be skipped with value `NULL`.
cmd	The CMD statement that should be executed by default when running a parameter. Use `CMD_Rscript(path)` in order to reference an R script to be executed on startup, `CMD_Render(path)` to render an R Markdown document, or `Cmd(command)` for any command. If `character` is provided it is passed wrapped in a `Cmd(command)`.
entrypoint	the ENTRYPOINT statement for the Dockerfile
add_self	Whether to add the package containerit itself if loaded/attached to the session
silent	Whether or not to print information during execution
predetect	Extract the required libraries based on `library` calls using the package `automagic` before running a script/document
versioned_libs	[EXPERIMENTAL] Whether it shall be attempted to match versions of linked external libraries
versioned_packages	Whether it shall be attempted to match versions of R packages
filter_baseimage_pkgs	Do not add packages from CRAN that are already installed in the base image. This does not apply to non-CRAN dependencies, e.g. packages install from GitHub.

Value

An object of class Dockerfile

Based on `sessionInfo`

Use the current sessionInfo) to create a Dockerfile.

Based on a workspace/directory

Given an existing path to a directory, the method tries to automatically find the main R file within that directory. Files are searched recursively. The following types are supported:

regular R script files, identified by file names ending in .R
weaved documents, identified by file names ending in R Markdown (.Rmd)

After identifying the main file, the process continues as described in the section file. If both types are found, documents are given priority over scripts. If multiple files are found, the first file as returned by dir will be used.

Based on a file

Given an executable R script or document, create a Dockerfile to execute this file. This executes the whole file to obtain a complete sessionInfo object, see section "Based on sessionInfo", and copies required files and documents into the container.

Examples

dockerfile <- dockerfile()
#> INFO [2019-08-20 16:43:57] Going online? TRUE  ... to retrieve system dependencies (sysreq-api)
#> INFO [2019-08-20 16:43:57] Trying to determine system requirements for the package(s) 'assertthat,automagic,backports,BiocManager,callr,cli,codetools,commonmark,crayon,curl,debugme,desc,devtools,digest,evaluate,fansi,formatR,fs,futile.logger,futile.options,glue,highlight,htmltools,httpuv,httr,jsonlite,knitr,lambda.r,later,magrittr,MASS,memoise,mime,miniUI,pillar,pkgbuild,pkgconfig,pkgdown,pkgload,prettyunits,processx,promises,ps,purrr,R6,Rcpp,rematch2,remotes,rjson,rlang,rmarkdown,roxygen2,rprojroot,rstudioapi,semver,sessioninfo,shiny,shinyFiles,stevedore,stringi,stringr,sysreqs,testthat,tibble,usethis,versions,whisker,withr,xfun,xml2,xtable,yaml' from sysreqs online DB
#> INFO [2019-08-20 16:44:01] Adding CRAN packages: assertthat, automagic, backports, BiocManager, callr, cli, codetools, commonmark, crayon, curl, debugme, desc, devtools, digest, evaluate, fansi, formatR, fs, futile.logger, futile.options, glue, highlight, htmltools, httpuv, httr, jsonlite, knitr, lambda.r, later, magrittr, MASS, memoise, mime, miniUI, pillar, pkgbuild, pkgconfig, pkgdown, pkgload, prettyunits, processx, promises, ps, purrr, R6, Rcpp, rematch2, remotes, rjson, rlang, rmarkdown, roxygen2, rprojroot, rstudioapi, semver, sessioninfo, shiny, shinyFiles, stevedore, stringi, stringr, testthat, tibble, usethis, versions, whisker, withr, xfun, xml2, xtable, yaml
#> INFO [2019-08-20 16:44:01] Adding GitHub packages: r-hub/sysreqs@3860f2b512a9c3bd3db6791c2ff467a1158f4048
#> INFO [2019-08-20 16:44:01] Created Dockerfile-Object based on sessionInfo
print(dockerfile)
#> FROM rocker/r-ver:3.6.1
#> LABEL maintainer="daniel"
#> RUN export DEBIAN_FRONTEND=noninteractive; apt-get -y update \
#>   && apt-get install -y git-core \
#> 	libcurl4-openssl-dev \
#> 	libssl-dev \
#> 	libxml2-dev \
#> 	make \
#> 	pandoc \
#> 	pandoc-citeproc
#> RUN ["install2.r", "assertthat", "automagic", "backports", "BiocManager", "callr", "cli", "codetools", "commonmark", "crayon", "curl", "debugme", "desc", "devtools", "digest", "evaluate", "fansi", "formatR", "fs", "futile.logger", "futile.options", "glue", "highlight", "htmltools", "httpuv", "httr", "jsonlite", "knitr", "lambda.r", "later", "magrittr", "MASS", "memoise", "mime", "miniUI", "pillar", "pkgbuild", "pkgconfig", "pkgdown", "pkgload", "prettyunits", "processx", "promises", "ps", "purrr", "R6", "Rcpp", "rematch2", "remotes", "rjson", "rlang", "rmarkdown", "roxygen2", "rprojroot", "rstudioapi", "semver", "sessioninfo", "shiny", "shinyFiles", "stevedore", "stringi", "stringr", "testthat", "tibble", "usethis", "versions", "whisker", "withr", "xfun", "xml2", "xtable", "yaml"]
#> RUN ["installGithub.r", "r-hub/sysreqs@3860f2b512a9c3bd3db6791c2ff467a1158f4048"]
#> WORKDIR /payload/
#> CMD ["R"]