remove the distro parameter (#73)

* remove the distro parameter

* add dependencies parameter

* update doc

Author: VincentGuyader

NEWS.md

@@ -3,6 +3,7 @@
 - remove sysreqs.r-hub.io to use {pak} instead for system requirement detection
 - move from `pak::pkg_system_requirements` to `pak::pkg_sysreqs()` thanks to @B0ydT 
 - `dock_from_renv` allow to specify user to use in Dockerfile
+- the `dependencies` parameter in `dock_from_renv` if set to `TRUE` will install required dependencies plus optional and development dependencies. defaut is `NA` only required (hard) dependencies,
 
 # dockerfile 0.2.2
 

R/dock_from_renv.R

@@ -1,14 +1,5 @@
 # WARNING - Generated by {fusen} from dev/flat_dock_from_renv.Rmd: do not edit by hand
 
-# ignoring opensuse for the time being
-available_distros <- c(
-  "xenial",
-  "bionic",
-  "focal",
-  "centos7",
-  "centos8"
-)
-
 #' @importFrom memoise memoise
 pkg_sysreqs_mem <- memoise::memoise(
     pak::pkg_sysreqs
@@ -20,7 +11,7 @@ pkg_sysreqs_mem <- memoise::memoise(
 #' @param lockfile Path to an `renv.lock` file to use as an input..
 #' @param FROM Docker image to start FROM Default is FROM rocker/r-base
 #' @param AS The AS of the Dockerfile. Default it `NULL`.
-#' @param distro One of "focal", "bionic", "xenial", "centos7",or "centos8". See available distributions     at https://hub.docker.com/r/rstudio/r-base/.
+#' @param distro - deprecated - only debian/ubuntu based images are supported
 #' @param sysreqs boolean. If `TRUE`, the Dockerfile will contain sysreq installation.
 #' @param expand boolean. If `TRUE` each system requirement will have its own `RUN` line.
 #' @param repos character. The URL(s) of the repositories to use for `options("repos")`.
@@ -33,6 +24,13 @@ pkg_sysreqs_mem <- memoise::memoise(
 #'   If you set it to `NULL`, the latest available version of renv will be used.
 #' @param use_pak boolean. If `TRUE` use pak to deal with dependencies  during `renv::restore()`. FALSE by default
 #' @param user Name of the user to specify in the Dockerfile with the USER instruction. Default is `NULL`, in which case the user from the FROM image is used.
+#' @param dependencies What kinds of dependencies to install. Most commonly
+#'   one of the following values:
+#'   - `NA`: only required (hard) dependencies,
+#'   - `TRUE`: required dependencies plus optional and development
+#'     dependencies,
+#'   - `FALSE`: do not install any dependencies. (You might end up with a
+#'     non-working package, and/or the installation might fail.)
 #' @importFrom utils getFromNamespace
 #' @return A R6 object of class `Dockerfile`.
 #' @details
@@ -59,7 +57,7 @@ pkg_sysreqs_mem <- memoise::memoise(
 #' }
 dock_from_renv <- function(
   lockfile = "renv.lock",
-  distro = "focal",
+  distro = NULL,
   FROM = "rocker/r-base",
   AS = NULL,
   sysreqs = TRUE,
@@ -68,9 +66,9 @@ dock_from_renv <- function(
   extra_sysreqs = NULL,
   use_pak = FALSE,
   user = NULL,
+  dependencies = NA,
   renv_version
 ) {
-  distro <- match.arg(distro, available_distros)
   try(dockerfiler::renv$initialize(),silent=TRUE)
   lock <- dockerfiler::renv$lockfile_read(file = lockfile) # using vendored renv
   # https://rstudio.github.io/renv/reference/vendor.html?q=vendor#null
@@ -79,7 +77,6 @@ dock_from_renv <- function(
   R_major_minor <- lock$R$Version
   dock <- Dockerfile$new(
     FROM = gen_base_image(
-      distro = distro,
       r_version = R_major_minor,
       FROM = FROM
     ),
@@ -101,58 +98,18 @@ dock_from_renv <- function(
   message("renv version = ", 
           ifelse(!is.null(renv_version),renv_version,"the must up to date in the repos")
           )
+  
+  
+  # ici il faut connaire l'image utilisé par l'image.
+  
 
-  distro_args <- switch(
-    distro,
-    centos7 = list(
-      sysreqs_platform = "centos-7"
-    ),
-    centos8 = list(
-      sysreqs_platform = "centos-8"
-    ),
-    xenial = list(
-      sysreqs_platform = "ubuntu-16.04"
-    ),
-    bionic = list(
-      sysreqs_platform = "ubuntu-18.04"
-    ),
-    focal = list(
-      sysreqs_platform = "ubuntu-20.04"
-    ),
-    jammy = list(
-      sysreqs_platform = "ubuntu-2.04"
-    )
-  )
-
-  install_cmd <- switch(
-    distro,
-    centos7 = "yum install -y",
-    centos8 = "yum install -y",
-    xenial = "apt-get install -y",
-    bionic = "apt-get install -y",
-    focal = "apt-get install -y",
-    jammy = "apt-get install -y"
-  )
-
-  update_cmd <- switch(
-    distro,
-    centos7 = "yum update -y",
-    centos8 = "yum update -y",
-    xenial = "apt-get update -y",
-    bionic = "apt-get update -y",
-    focal = "apt-get update -y",
-    jammy = "apt-get update -y"
-  )
+  # distro_args <- list(sysreqs_platform = "ubuntu-22.04")
+  
+  distro_args <- list(sysreqs_platform = "ubuntu")
 
-  clean_cmd <- switch(
-    distro,
-    centos7 = "yum clean all && rm -rf /var/cache/yum",
-    centos8 = "yum clean all && rm -rf /var/cache/yum",
-    xenial = "rm -rf /var/lib/apt/lists/*",
-    bionic = "rm -rf /var/lib/apt/lists/*",
-    focal = "rm -rf /var/lib/apt/lists/*",
-    jammy = "rm -rf /var/lib/apt/lists/*"
-  )
+  install_cmd <- "apt-get install -y"
+  update_cmd <-"apt-get update -y"
+  clean_cmd <- "rm -rf /var/lib/apt/lists/*"
 
   pkgs <- names(lock$Packages)
 
@@ -176,7 +133,8 @@ dock_from_renv <- function(
       pkgs,
       FUN = function(x) {
         c(
-          list(pkg = x),
+          list(pkg = x,
+               dependencies = dependencies),
           distro_args
         )
       }

R/gen_base_image.R

@@ -7,15 +7,15 @@
 #' @keywords internal
 #' @noRd
 gen_base_image <- function(
-  distro = "bionic",
+  distro = NULL,
   r_version = "4.0",
   FROM = "rstudio/r-base"
 ) {
-  distro <- match.arg(distro, available_distros)
 
-  if (FROM == "rstudio/r-base") {
-    glue::glue("{FROM}:{r_version}-{distro}")
-  } else {
+if (!is.null(distro)){
+  warning("the `distro` parameter is not used anymore, only debian/ubuntu based images are supported")
+}
+
     glue::glue("{FROM}:{r_version}")
-  }
+
 }