added copy export, to fix #171

DESCRIPTION

@@ -70,6 +70,7 @@ Imports:
     versions
 Suggests:
     BiocGenerics,
+    units (>= 0.7.0),
     codetools,
     covr,
     coxrobust,
@@ -97,7 +98,7 @@ Remotes:
     github::r-hub/sysreqs
 Encoding: UTF-8
 LazyData: TRUE
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Collate:
     'Class-Instruction.R'
     'Class-Add.R'

NAMESPACE

@@ -7,6 +7,7 @@ export(CMD_Render)
 export(CMD_Rscript)
 export(Cmd)
 export(Comment)
+export(Copy)
 export(Entrypoint)
 export(Expose)
 export(Label)

R/Class-Cmd.R

@@ -5,7 +5,7 @@
 #'
 #' See official documentation at \url{https://docs.docker.com/engine/reference/builder/#cmd}.
 #'
-#' @slot exec exectuable, character
+#' @slot exec executable, character
 #' @slot params parameters, character (vector)
 #' @slot form the form to use for output (exec or shell)
 #'

R/Class-Copy.R

@@ -13,6 +13,7 @@
 #' @family instruction classes
 #' @examples
 #' #no example yet
+#' Copy("here", "/here")
 setClass("Copy",
          slots = list(src = "character", dest = "character"),
          contains = "Instruction")
@@ -26,6 +27,7 @@ setClass("Copy",
 #' @param addTrailingSlashes (boolean) add trailing slashes to the given paths if the source is an existing directory
 #'
 #' @return the object
+#' @export
 #' @importFrom fs dir_exists
 #' @importFrom stringr str_detect
 Copy <- function(src, dest, addTrailingSlashes = TRUE) {

R/dockerfile.R

@@ -39,6 +39,7 @@
 #' @param soft (boolean) Whether to include soft dependencies when system dependencies are installed, default is no.
 #' @param offline (boolean) Whether to use an online database to detect system dependencies or use local package information (slower!), default is no.
 #' @param copy whether and how a workspace should be copied; allowed values: "script", "script_dir" (paths relative to file, so only works for file-base \code{from} inputs, which (can be nested) within current working directory), a list of file paths relative to the current working directory to be copied into the payload directory, or \code{NULL} to disable copying of files
+#' @param instructions an ordered list of instructions in the Dockerfile
 #' @param container_workdir the working directory in the container, defaults to \code{/payload/} and must end with \code{/}. Can be skipped with value \code{NULL}.
 #' @param cmd The CMD statement that should be executed by default when running a parameter. Use \code{CMD_Rscript(path)} in order to reference an R script to be executed on startup, \code{CMD_Render(path)} to render an R Markdown document, or \code{Cmd(command)} for any command. If \code{character} is provided it is passed wrapped in a \code{Cmd(command)}.
 #' @param entrypoint the ENTRYPOINT statement for the Dockerfile
@@ -73,6 +74,7 @@ dockerfile <- function(from = utils::sessionInfo(),
                        soft = FALSE,
                        offline = FALSE,
                        copy = NULL,
+                       instructions = list(),
                        # nolint start
                        container_workdir = "/payload/",
                        # nolint end
@@ -141,7 +143,7 @@ dockerfile <- function(from = utils::sessionInfo(),
 
     # base dockerfile
     the_dockerfile <- methods::new("Dockerfile",
-                                instructions = list(),
+                                instructions = instructions,
                                 maintainer = maintainer,
                                 image = image,
                                 entrypoint = entrypoint,

R/utility-functions.R

@@ -147,6 +147,8 @@ getImageForVersion <- function(r_version, nearest = TRUE) {
     if (nearest) {
       # get numeric versions with all parts (maj.min.minor), i.e. two dots
       numeric_tags <- tags[which(grepl("\\d.\\d.\\d", tags))]
+      # issue is cuda/ubuntu
+      numeric_tags <- numeric_tags[!grepl("[[:alpha:]]", numeric_tags)]
       closest <- as.character(closestMatch(r_version, numeric_tags))
       image <- From(.rocker_images[["versioned"]], tag = closest)
 
@@ -423,6 +425,12 @@ clean_session <- function(expr = c(),
 
   futile.logger::flog.debug("Creating an R session with the following expressions:\n%s", toString(expr))
 
+  if (is.call(expr)) {
+    # so functions such as
+    # containerit::clean_session(expr = quote(library("BiocGenerics")))
+    # still work
+    expr = c(expr)
+  }
   the_info <- callr::r_vanilla(function(expressions) {
     for (e in expressions) {
       eval(e)

tests/testthat/package_markdown/units/2016-09-29-plot_units.Rmd

@@ -45,7 +45,7 @@ Here is an example using `mtcars`. First, we specify the imperial units to those
 
 ```{r}
 library(units)
-gallon = make_unit("gallon")
+gallon = as_units("gallon")
 consumption = mtcars$mpg * with(ud_units, mi/gallon)
 displacement = mtcars$disp * ud_units[["in"]]^3
 ```

vignettes/bioconductor.Rmd

@@ -36,7 +36,7 @@ df <- dockerfile(from = info)
 A shortcut to this is provided with the function `containerit::clean_session(..)`:
 
 ```{r bioc_dockerfile_clean_session, results='hide'}
-containerit::clean_session(expr = quote(library("BiocGenerics")))
+containerit::clean_session(expr = c(quote(library("BiocGenerics"))))
 ```