draft : Issue 44 (#54)

* feat : add ubuntu 22.04 name in distro

* fix : allow Chrome's system dependence installation

how: a more cleaver compact_sysreqs function is used

* chore: update news , bump version

* fix : unit test

Author: VincentGuyader

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dockerfiler
 Title: Easy Dockerfile Creation from R
-Version: 0.2.1
+Version: 0.2.1.9001
 Authors@R: c(
     person("Colin", "Fay", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0001-7343-1846")),

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(Dockerfile)
+export(compact_sysreqs)
 export(dock_from_desc)
 export(dock_from_renv)
 export(docker_ignore_add)

NEWS.md

@@ -4,6 +4,10 @@
 
 - feat: Added `dock_from_renv()`, to create a Dockerfile from a renv.lock file (@JosiahParry, @statnmap)
 
+- fix: the dedicated `compact_sysreqs` function allow to deal with 'complex' sysreqs, such as chromimum installation
+
+- feat: add jammy ubuntu distro in available distro
+
 # dockerfiler 0.1.4
 
 * new version of `dock_from_desc()`

R/compact_sysreqs.R

@@ -0,0 +1,62 @@
+#' Compact Sysreqs
+#'
+#' @param pkg_installs pkg_sysreqs as vector, `pak::pkg_system_requirements` output
+#' @param update_cmd command used to update packages, "apt-get update -y" by default
+#' @param install_cmd command used to install packages, "apt-get install -y" by default
+#' @param clean_cmd command used to clean package folder, "rm -rf /var/lib/apt/lists/*" by default
+#'
+#' @return vector of compacted command to run to install sysreqs
+#' @export
+#'
+#' @examples
+#' pkg_installs <- list("apt-get install -y htop", "apt-get install -y top")
+#' compact_sysreqs(pkg_installs)
+
+compact_sysreqs <- function(pkg_installs,
+                            update_cmd = "apt-get update -y",
+                            install_cmd = "apt-get install -y",
+                            clean_cmd ="rm -rf /var/lib/apt/lists/*"){
+
+  # on va extraire tout ce qui commence par pkg_installs
+  pkg_ <-  pkg_installs[lapply(pkg_installs,length)!=0]
+  apt <-  grepl(pattern = paste0("^",install_cmd),x = pkg_)
+
+  with_apt <- pkg_[apt]
+  without_apt <- pkg_[!apt]
+  # we choose to not compact unusals sysreqs
+  without_apt_out <- unlist(without_apt)
+
+if ( length(without_apt_out) > 0 && isTRUE( all(without_apt_out != "")) ){
+  without_apt_out[1] <- paste(update_cmd,     "&&", without_apt_out[1] )
+  without_apt_out[length(without_apt_out)] <- paste( without_apt_out[length(without_apt_out)],"&&",clean_cmd)
+} else {
+  without_apt_out <- NULL
+}
+
+
+  compact <- paste(
+    unique(unlist(strsplit(gsub(
+      with_apt,
+      pattern = install_cmd,
+      replacement = ""
+    ),split = " "))),
+    collapse = " "
+  )
+  if (compact != "") {
+    apt_out <- paste(
+      update_cmd,
+      "&&",
+      install_cmd,
+      compact,
+      "&&",
+      clean_cmd
+    )
+  }else { apt_out <-NULL}
+
+ out<- unlist(c(apt_out,without_apt_out))
+
+
+
+
+  out
+}

R/dock_from_renv.R

@@ -93,6 +93,10 @@ dock_from_renv <- function(
     focal = list(
       os = "ubuntu",
       os_release = "20.04"
+    ),
+    jammy = list(
+      os = "ubuntu",
+      os_release = "22.04"
     )
   )
 
@@ -102,7 +106,8 @@ dock_from_renv <- function(
     centos8 = "yum install -y",
     xenial = "apt-get install -y",
     bionic = "apt-get install -y",
-    focal = "apt-get install -y"
+    focal = "apt-get install -y",
+    jammy = "apt-get install -y"
   )
 
   update_cmd <- switch(
@@ -111,7 +116,8 @@ dock_from_renv <- function(
     centos8 = "yum update -y",
     xenial = "apt-get update -y",
     bionic = "apt-get update -y",
-    focal = "apt-get update -y"
+    focal = "apt-get update -y",
+    jammy = "apt-get update -y"
   )
 
   clean_cmd <- switch(
@@ -120,7 +126,8 @@ dock_from_renv <- function(
     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/*"
+    focal = "rm -rf /var/lib/apt/lists/*",
+    jammy = "rm -rf /var/lib/apt/lists/*"
   )
 
   pkgs <- names(lock$data()$Packages)
@@ -136,7 +143,7 @@ dock_from_renv <- function(
 
     message(
       sprintf(
-        "Fetching system dependencies for %s package records.",
+        "Fetching system dependencies for %s package(s) records.",
         length(pkgs)
       )
     )
@@ -162,9 +169,13 @@ dock_from_renv <- function(
       .e = ~ character(0)
     )
 
-    pkg_installs <- unique(unlist(pkg_sysreqs))
 
-    if (length(pkg_installs) == 0) {
+
+
+
+    pkg_installs <- unique(pkg_sysreqs)
+
+    if (length(unlist(pkg_installs)) == 0) {
       cat_bullet(
         "No sysreqs required",
         bullet = "info",
@@ -179,36 +190,31 @@ dock_from_renv <- function(
 
   # extra_sysreqs
 
+
+
+
   if (length(extra_sysreqs) > 0) {
     extra <- paste(
       install_cmd,
       extra_sysreqs
     )
-    pkg_installs <- c(pkg_installs, extra)
+    pkg_installs <- unique(c(pkg_installs, extra))
   }
 
+
+
+
+
   # compact
   if (!expand) {
     # we compact sysreqs
-
-    compact <- paste(
-      gsub(
-        pkg_installs,
-        pattern = install_cmd,
-        replacement = ""
-      ),
-      collapse = " "
+    pkg_installs <- compact_sysreqs(
+      pkg_installs,
+      update_cmd = update_cmd,
+      install_cmd = install_cmd,
+      clean_cmd = clean_cmd
     )
-    if (compact != "") {
-      pkg_installs <- paste(
-        update_cmd,
-        "&&",
-        install_cmd,
-        compact,
-        "&&",
-        clean_cmd
-      )
-    }
+
   } else {
     dock$RUN(update_cmd)
   }

man/compact_sysreqs.Rd

@@ -0,0 +1,57 @@
+test_that("compact_sysreqs works", {
+  pkg_installs <-
+    list("apt-get install -y htop", "apt-get install -y top")
+  expect_equal(
+    compact_sysreqs(pkg_installs),
+    "apt-get update -y && apt-get install -y  htop top && rm -rf /var/lib/apt/lists/*"
+  )
+})
+test_that("empty compact_sysreqs works", {
+  pkg_installs <-
+    list("")
+  expect_equal(
+    compact_sysreqs(pkg_installs),
+    NULL
+  )
+
+  pkg_installs <-
+NULL
+  expect_equal(
+    compact_sysreqs(pkg_installs),
+    NULL
+  )
+
+
+
+
+})
+
+test_that("compact_sysreqs works with chromote", {
+  pkg_installs  <- list(character(0), character(0), character(0), character(0),
+                        character(0), "apt-get install -y make", character(0), c("[ $(which google-chrome) ] || apt-get install -y gnupg curl",
+                                                                                 "[ $(which google-chrome) ] || curl -fsSL -o /tmp/google-chrome.deb https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb",
+                                                                                 "[ $(which google-chrome) ] || DEBIAN_FRONTEND='noninteractive' apt-get install -y /tmp/google-chrome.deb",
+                                                                                 "apt-get install -y make libssl-dev libcurl4-openssl-dev"
+                        ), character(0), character(0), character(0), character(0),
+                        character(0), "apt-get install -y libcurl4-openssl-dev libssl-dev",
+                        character(0), character(0), character(0), character(0), "apt-get install -y make",
+                        character(0), "apt-get install -y make zlib1g-dev", character(0),
+                        character(0), "apt-get install -y make zlib1g-dev", character(0),
+                        character(0), character(0), character(0), character(0), character(0),
+                        character(0), character(0), character(0), character(0), character(0),
+                        "apt-get install -y git", character(0), character(0), "apt-get install -y make",
+                        "apt-get install -y make zlib1g-dev", character(0), "apt-get install -y make libssl-dev",
+                        character(0), character(0), character(0))
+
+
+
+  expect_equal(
+    compact_sysreqs(pkg_installs),
+    c("apt-get update -y && apt-get install -y  make libcurl4-openssl-dev libssl-dev zlib1g-dev git && rm -rf /var/lib/apt/lists/*",
+      "apt-get update -y && [ $(which google-chrome) ] || apt-get install -y gnupg curl",
+      "[ $(which google-chrome) ] || curl -fsSL -o /tmp/google-chrome.deb https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb",
+      "[ $(which google-chrome) ] || DEBIAN_FRONTEND='noninteractive' apt-get install -y /tmp/google-chrome.deb",
+      "apt-get install -y make libssl-dev libcurl4-openssl-dev && rm -rf /var/lib/apt/lists/*"
+    )
+  )
+})