ThinkR-open · VincentGuyader · Jul 19, 2024 · Jul 1, 2024 · Jul 1, 2024 · Jul 1, 2024
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dockerfiler
 Title: Easy Dockerfile Creation from R
-Version: 0.2.2.9003
+Version: 0.2.3
 Authors@R: c(
     person("Colin", "Fay", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0001-7343-1846")),
@@ -25,12 +25,11 @@ Imports:
     glue (>= 1.4.2),
     jsonlite (>= 1.7.2),
     memoise,
-    pak (>= 0.2.0),
+    pak (>= 0.6.0),
     pkgbuild (>= 1.2.0),
     purrr,
     R6 (>= 2.5.0),
     remotes (>= 2.2.0),
-    renv,
     usethis (>= 2.0.1),
     utils
 Suggests:

diff --git a/NEWS.md b/NEWS.md
@@ -1,11 +1,14 @@
-# 0.2.2.xxxx
+# dockerfile 0.2.3
 
 - 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,
+- Set the minimum version of the {pak} package to 0.6.0. 
+- Parameterize the `sysreqs_platform` used to find system dependencies in pkg_sysreqs (only debian/ubuntu based images are supported)
 
-# dockerfile 0.2.2
+
+# dockerfiler 0.2.2
 
 - fix : create a `use_pak` parameters in `dock_from_renv` to set `renv.config.pak.enabled = FALSE` instead of `renv.config.pak.enabled = TRUE` to avoid issues with {pak} during `renv::restore()`
 
@@ -22,7 +25,7 @@
 - feat: Added `renv_version` parameter to `dock_from_renv` to be able to fix the renv version to use during `renv::restore()` (@campbead)
 
 
-# dockerfile 0.2.0 
+# dockerfiler 0.2.0 
 
 - fix: graceful failing in case no internet
 

diff --git a/R/dock_from_renv.R b/R/dock_from_renv.R
@@ -31,6 +31,7 @@ pkg_sysreqs_mem <- memoise::memoise(
 #'     dependencies,
 #'   - `FALSE`: do not install any dependencies. (You might end up with a
 #'     non-working package, and/or the installation might fail.)
+#' @param sysreqs_platform System requirements platform.`ubuntu` by default. If `NULL`, then the  current platform is used. Can be : "ubuntu-22.04" if needed to fit with the `FROM` Operating System. Only debian or ubuntu based images are supported
 #' @importFrom utils getFromNamespace
 #' @return A R6 object of class `Dockerfile`.
 #' @details
@@ -67,6 +68,7 @@ dock_from_renv <- function(
   use_pak = FALSE,
   user = NULL,
   dependencies = NA,
+  sysreqs_platform = "ubuntu",
   renv_version
 ) {
   try(dockerfiler::renv$initialize(),silent=TRUE)
@@ -100,12 +102,7 @@ dock_from_renv <- function(
           )
 
 
-  # ici il faut connaire l'image utilisé par l'image.
-
-
-  # distro_args <- list(sysreqs_platform = "ubuntu-22.04")
-
-  distro_args <- list(sysreqs_platform = "ubuntu")
+  distro_args <- list(sysreqs_platform = sysreqs_platform)
 
   install_cmd <- "apt-get install -y"
   update_cmd <-"apt-get update -y"

diff --git a/README.md b/README.md
@@ -18,16 +18,16 @@ You’re reading the doc about version :
 
 ``` r
 desc::desc_get_version()
-#> [1] '0.2.2'
+#> [1] '0.2.3'
 ```
 
 The check results are:
 
 ``` r
 devtools::check(quiet = TRUE)
 #> ℹ Loading dockerfiler
-#> ── R CMD check results ────────────────────────────────── dockerfiler 0.2.2 ────
-#> Duration: 1m 0.6s
+#> ── R CMD check results ────────────────────────────────── dockerfiler 0.2.3 ────
+#> Duration: 1m 31.3s
 #> 
 #> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 ```

diff --git a/dev/flat_dock_from_renv.Rmd b/dev/flat_dock_from_renv.Rmd
@@ -75,6 +75,7 @@ pkg_sysreqs_mem <- memoise::memoise(
 #'     dependencies,
 #'   - `FALSE`: do not install any dependencies. (You might end up with a
 #'     non-working package, and/or the installation might fail.)
+#' @param sysreqs_platform System requirements platform.`ubuntu` by default. If `NULL`, then the  current platform is used. Can be : "ubuntu-22.04" if needed to fit with the `FROM` Operating System. Only debian or ubuntu based images are supported
 #' @importFrom utils getFromNamespace
 #' @return A R6 object of class `Dockerfile`.
 #' @details
@@ -106,6 +107,7 @@ dock_from_renv <- function(
   use_pak = FALSE,
   user = NULL,
   dependencies = NA,
+  sysreqs_platform = "ubuntu",
   renv_version
 ) {
   try(dockerfiler::renv$initialize(),silent=TRUE)
@@ -139,12 +141,7 @@ dock_from_renv <- function(
           )
 
 
-  # ici il faut connaire l'image utilisé par l'image.
-
-
-  # distro_args <- list(sysreqs_platform = "ubuntu-22.04")
-
-  distro_args <- list(sysreqs_platform = "ubuntu")
+  distro_args <- list(sysreqs_platform = sysreqs_platform)
 
   install_cmd <- "apt-get install -y"
   update_cmd <-"apt-get update -y"
@@ -330,10 +327,12 @@ writeLines(renv_file, file.path(dir_build, "renv.lock"))
 
 # dock_from_renv ----
 test_that("dock_from_renv works", {
+
+
   # testthat::skip_on_cran()
   # skip_if_not(interactive())
   # Create Dockerfile
-
+  skip_if(is_rdevel, "skip on R-devel")
   out <- dock_from_renv(
     lockfile = the_lockfile,
     FROM = "rocker/verse",
@@ -346,8 +345,7 @@ test_that("dock_from_renv works", {
     out,
     "R6"
   )
-  #python3 is not a direct dependencies from custom_packages
-  expect_false(  any(grepl("python3",out$Dockerfile)))
+
 
   # read Dockerfile
   out$write(
@@ -373,7 +371,10 @@ test_that("dock_from_renv works", {
     1
   )
 
-
+  skip_if(is_rdevel, "Skip R-devel")
+  #python3 is not a direct dependencies from custom_packages
+  expect_false(  any(grepl("python3",out$Dockerfile)))
+
   # System dependencies are different when build in interactive environment?
   # yes.  strange.
   skip_if_not(interactive())
@@ -409,7 +410,7 @@ test_that("dock_from_renv works with full dependencies", {
   # testthat::skip_on_cran()
   # skip_if_not(interactive())
   # Create Dockerfile
-
+skip_if(is_rdevel, "skip on R-devel")
   out <- dock_from_renv(
     dependencies = TRUE,
     lockfile = the_lockfile,
@@ -423,6 +424,7 @@ test_that("dock_from_renv works with full dependencies", {
     out,
     "R6"
   )
+  skip_if(is_rdevel, "Skip R-devel")
   #python3 is  a un-direct dependencies from custom_packages
   expect_true(  any(grepl("python3",out$Dockerfile)))
 })
@@ -468,6 +470,8 @@ test_that("gen_base_image works", {
 
 
 test_that("dock_from_renv works with specific renv", {
+
+  skip_if(is_rdevel, "skip on R-devel")
   # testthat::skip_on_cran()
 the_lockfile1.0.0 <- system.file("renv_with_1.0.0.lock",package = "dockerfiler")
 

diff --git a/man/dock_from_renv.Rd b/man/dock_from_renv.Rd
diff --git a/tests/testthat/setup_cache_dir.R b/tests/testthat/setup_cache_dir.R
@@ -1,3 +1,6 @@
 R_USER_CACHE_DIR<-tempfile()
 dir.create(R_USER_CACHE_DIR)
 Sys.setenv("R_USER_CACHE_DIR"=R_USER_CACHE_DIR)
+r_version <- R.Version()$version.string
+is_rdevel <- grepl("unstable", r_version)
+# is_debian <- grepl("debian", tolower(Sys.info()['release']))
diff --git a/tests/testthat/test-dock_from_desc.R b/tests/testthat/test-dock_from_desc.R
@@ -37,6 +37,9 @@ withr::with_dir(
   descdir,
   {
     test_that("dock_from_desc works", {
+
+      skip_if(is_rdevel, "skip on R-devel")
+
       my_dock <- dock_from_desc(file.path(".", "DESCRIPTION__"))
 
       expect_s3_class(my_dock, "R6")
@@ -57,12 +60,8 @@ withr::with_dir(
           tpf
         )
       )
-      expect_true(
-        grepl(
-          "apt-get update && apt-get install",
-          tpf
-        )
-      )
+
+
       expect_true(
         grepl(
           "mkdir /build_zone",
@@ -92,6 +91,26 @@ withr::with_dir(
       # Only if package I guess
       # expect_true(file.exists(file.path(descdir, ".Rbuildignore")))
       expect_true(file.exists(file.path(descdir, ".dockerignore")))
+
+
+
+
+
+
+
+
+
+      skip_if(is_rdevel, "Skippé sous R-devel")
+
+      expect_true(
+        grepl(
+          "apt-get update && apt-get install",
+          tpf
+        )
+      )
+
+
+
     })
   }
 )
diff --git a/tests/testthat/test-dock_from_renv.R b/tests/testthat/test-dock_from_renv.R
@@ -36,10 +36,12 @@ writeLines(renv_file, file.path(dir_build, "renv.lock"))
 
 # dock_from_renv ----
 test_that("dock_from_renv works", {
+
+
   # testthat::skip_on_cran()
   # skip_if_not(interactive())
   # Create Dockerfile
-
+  skip_if(is_rdevel, "skip on R-devel")
   out <- dock_from_renv(
     lockfile = the_lockfile,
     FROM = "rocker/verse",
@@ -52,8 +54,7 @@ test_that("dock_from_renv works", {
     out,
     "R6"
   )
-  #python3 is not a direct dependencies from custom_packages
-  expect_false(  any(grepl("python3",out$Dockerfile)))
+
 
   # read Dockerfile
   out$write(
@@ -79,7 +80,10 @@ test_that("dock_from_renv works", {
     1
   )
 
-
+  skip_if(is_rdevel, "Skip R-devel")
+  #python3 is not a direct dependencies from custom_packages
+  expect_false(  any(grepl("python3",out$Dockerfile)))
+
   # System dependencies are different when build in interactive environment?
   # yes.  strange.
   skip_if_not(interactive())
@@ -115,7 +119,7 @@ test_that("dock_from_renv works with full dependencies", {
   # testthat::skip_on_cran()
   # skip_if_not(interactive())
   # Create Dockerfile
-
+skip_if(is_rdevel, "skip on R-devel")
   out <- dock_from_renv(
     dependencies = TRUE,
     lockfile = the_lockfile,
@@ -129,6 +133,7 @@ test_that("dock_from_renv works with full dependencies", {
     out,
     "R6"
   )
+  skip_if(is_rdevel, "Skip R-devel")
   #python3 is  a un-direct dependencies from custom_packages
   expect_true(  any(grepl("python3",out$Dockerfile)))
 })
@@ -174,6 +179,8 @@ test_that("gen_base_image works", {
 
 
 test_that("dock_from_renv works with specific renv", {
+
+  skip_if(is_rdevel, "skip on R-devel")
   # testthat::skip_on_cran()
 the_lockfile1.0.0 <- system.file("renv_with_1.0.0.lock",package = "dockerfiler")
 

diff --git a/tests/testthat/test-dockerbuild.R b/tests/testthat/test-dockerbuild.R
@@ -1,5 +1,6 @@
 n_temp <- tempdir()
 file.copy("renv.lock", n_temp)
+skip_if(is_rdevel, "skip on R-devel")
 withr::with_dir(
   n_temp,
   {

diff --git a/tests/testthat/test-get_sysreqs.R b/tests/testthat/test-get_sysreqs.R
@@ -1,5 +1,6 @@
 test_that("get_sysreqs works", {
   skip_on_cran()
+  skip_if(is_rdevel, "Skip R-devel")
   res <- get_sysreqs(
     c("mongolite"),
     quiet = TRUE