added copy export, to fix #171

.Rbuildignore

@@ -14,3 +14,5 @@ docs
 ^paper\.bib$
 ^paper\.md$
 ^codemeta\.json$
+^CONTRIBUTING\.md$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,62 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: rcmdcheck
+
+      - uses: docker-practice/actions-setup-docker@master
+
+      - run: docker version
+
+      - uses: r-lib/actions/check-r-package@v1
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

DESCRIPTION

@@ -70,6 +70,7 @@ Imports:
     versions
 Suggests:
     BiocGenerics,
+    units (>= 0.7.0),
     codetools,
     covr,
     coxrobust,
@@ -90,14 +91,15 @@ Suggests:
     sessioninfo,
     sf,
     sp,
-    testthat
+    testthat,
+    httr
 VignetteBuilder: 
     knitr
 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

@@ -3,11 +3,15 @@
 S3method(docker_build,Dockerfile)
 S3method(docker_build,character)
 export("addInstruction<-")
+export(Arg)
 export(CMD_Render)
+export(CMD_Rexpr)
 export(CMD_Rscript)
 export(Cmd)
 export(Comment)
+export(Copy)
 export(Entrypoint)
+export(Env)
 export(Expose)
 export(Label)
 export(LabelSchemaFactory)
@@ -16,6 +20,7 @@ export(Label_SessionInfo)
 export(Run)
 export(Run_shell)
 export(Shell)
+export(Workdir)
 export(clean_session)
 export(docker_build)
 export(dockerfile)

R/Class-Arg.R

@@ -8,23 +8,41 @@
 #' @return object
 #' @family instruction classes
 #' @examples
-#' #no example yet
-setClass("Arg", contains = "Instruction")
+#' x = Arg("myarg")
+#' print(x)
+setClass(
+  "Arg",
+  slots = list(argument = "character"),
+  contains = "Instruction",
+  validity = function(object) {
+    if (length(object@argument) == 1) TRUE else "argument must be length 1"
+  }
+  )
 
-#' Arg constructor yet to be implemented
+#' create objects of class Arg
 #'
-#' @param ... fields yet to be implemented
 #'
-#' @return the object
-#' @examples
-#' #no example yet
-Arg <- function(...) {
-  stop("Constructor not yet implemented for this class.")
+#' @param argument the argument name
+#' @export
+#' @return Arg-object
+Arg <- function(argument) {
+  return(new("Arg", argument = argument))
 }
 
+setMethod(
+  "docker_key",
+  signature = signature(obj = "Arg"),
+  definition =
+    function(obj) {
+      return("ARG")
+    }
+)
+
+
 setMethod("docker_arguments",
           signature(obj = "Arg"),
           function(obj) {
-            stop("The generic function docker_arguments is not implemented for class ",
-                 class(obj))
+            argument <- methods::slot(obj, "argument")
+            return(argument)
           })
+

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)
 #'
@@ -143,6 +143,28 @@ CMD_Rscript <-
     Cmd("R", params = params)
   }
 
+#' Create CMD instruction for running an R expression
+#'
+#' Schema: R [--options] [file] [args]
+#'
+#' @export
+#' @rdname CMD_Rexpr
+#' @param expr character vector of expressions to run
+#' @inheritParams CMD_Rscript
+#' @return A CMD instruction
+CMD_Rexpr <-
+  function(expr,
+           options = character(0),
+           args = character(0),
+           vanilla = TRUE) {
+    if (vanilla)
+      options <- append(options, "--vanilla")
+    params <- rep("-e", length = length(expressions))
+    params <- c(t(cbind(params, expressions)))
+    params <- append(options, params)
+    params <- append(params, args)
+    Cmd("R", params = params)
+  }
 
 
 #' Create CMD instruction for rendering a markdown file

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/Class-Dockerfile.R

@@ -1,5 +1,9 @@
 # Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
+# The Entrypoint is optional in a Dockerfile
+setClassUnion("NullOrCmd",
+              members = c("Cmd", "NULL"))
+
 #' An S4 class to represent a Dockerfile
 #'
 #' @include Class-Maintainer.R
@@ -15,23 +19,36 @@
 #' @slot instructions an ordered list of instructions in the Dockerfile (list of character)
 #' @slot entrypoint the entrypoint instruction applied to the container
 #' @slot cmd the default cmd instruction applied to the container
+#' @slot syntax the syntax given for the header of the container
 #'
 #' @details The entrypoint and cmd are provided outside of instructions, as only one of them takes effect.
 #' If Cmd or Entrypoint instructions are provided as part of the regular instructions, they appear in the Dockerfile but have no effect.
 #'
 #' @return an object of class \code{Dockerfile}
 #' @export
 Dockerfile <- setClass("Dockerfile",
-                    slots = list(image = "From",
-                                 maintainer = "NullOrLabelOrMaintainer",
-                                 instructions = "list",
-                                 entrypoint = "NullOrEntrypoint",
-                                 cmd = "Cmd")
+                       slots = list(
+                         image = "From",
+                         maintainer = "NullOrLabelOrMaintainer",
+                         instructions = "list",
+                         entrypoint = "NullOrEntrypoint",
+                         cmd = "NullOrCmd",
+                         syntax = "NullOrCharacter")
 )
 
 toString.Dockerfile <- function(x, ...) {
   #initialize dockerfile with from
   output <- c()
+  syntax <- methods::slot(x, "syntax")
+  if (!is.null(syntax)) {
+    syntax = trimws(syntax)
+    syntax = sub("^#*", "", syntax)
+    syntax = trimws(syntax)
+    syntax = sub("syntax=", "", syntax)
+    syntax = trimws(syntax)
+    syntax = paste0("# syntax=", syntax)
+    output <- append(output, syntax)
+  }
   from <- toString(methods::slot(x, "image"))
   output <- append(output, from)
   maintainer <- methods::slot(x, "maintainer")

R/Class-Env.R

@@ -1,30 +1,62 @@
 # Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
-#' Env class yet to be implemented
+#' Env-instruction class
 #' @include Class-Instruction.R
 #'
 #' See official documentation at \url{https://docs.docker.com/engine/reference/builder/#env}.
 #'
-#' @return the object
+#' @return object
 #' @family instruction classes
 #' @examples
-#' #no example yet
-setClass("Env", contains = "Instruction")
+#' x = Env("myarg", "default value")
+#' print(x)
+#' x = Env("myarg")
+#' print(x)
+setClass(
+  "Env",
+  slots = list(argument = "character",
+               value = "NullOrCharacter"),
+  contains = "Instruction",
+  validity = function(object) {
+    if (length(object@argument) == 1 && length(object@value) <= 1) {
+      TRUE
+      } else {
+        "argument must be length 1 and value must be max length 1"
+      }
+  }
+)
 
-#' Constructor for Env yet to be implemented
+#' create objects of class Env
 #'
-#' @param ... fields yet to be implemented
 #'
-#' @return the object
-#' @examples
-#' #no example yet
-Env <- function(...) {
-  stop("Constructor not yet implemented for this class.")
+#' @param argument the argument name
+#' @param value the value to be set to the argument
+#' @export
+#' @return Env-object
+Env <- function(argument, value = NULL) {
+  return(new("Env", argument = argument, value = value))
 }
 
+
+setMethod(
+  "docker_key",
+  signature = signature(obj = "Env"),
+  definition =
+    function(obj) {
+      return("ENV")
+    }
+)
+
 setMethod("docker_arguments",
           signature(obj = "Env"),
           function(obj) {
-            stop("The generic function docker_arguments is not implemented for class ",
-                 class(obj))
+            argument <- methods::slot(obj, "argument")
+            value <- methods::slot(obj, "value")
+            if (is.null(value)) {
+              value = ""
+            } else {
+              value = paste0('"', value, '"')
+            }
+            return(paste0(argument, "=", value))
           })
+

R/Class-Instruction.R

@@ -1,5 +1,8 @@
 # Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
+# put this here because used in many others
+setClassUnion("NullOrCharacter", c("NULL", "character"))
+
 #' The Docker Instruction - Class
 #'
 #' See official documentation at \url{https://docs.docker.com/engine/reference/builder/#format}.

R/Class-Label.R

@@ -74,7 +74,8 @@ Label_SessionInfo <-
   function(session = sessionInfo(),
            as_json = FALSE) {
     if (as_json) {
-      session_string <- rjson::toJSON(session)
+      # session_string <- rjson::toJSON(session)
+      session_string <- jsonlite::toJSON(session)
     } else{
       session_string <- utils::capture.output(session)
       session_string <- paste(session_string, collapse = "\n")

R/Class-Workdir.R

@@ -16,9 +16,10 @@ setClass("Workdir",
 #' @param path The path of the working directory
 #'
 #' @return the object
+#' @export
 #'
 #' @examples
-#' instruction <- containerit:::Workdir("~/myDir/subdir/")
+#' instruction <- containerit::Workdir("~/myDir/subdir/")
 #' toString(instruction)
 Workdir <- function(path) {
   methods::new("Workdir",

R/LabelSchemaFactory.R

@@ -83,7 +83,8 @@ LabelSchemaFactory <- function() {
   }
   formals(factory) <- namesArgs
 
-  futile.logger::flog.info("According to Label Schema Convention %s you can use the following arguments for constructing metadata labels:",
-                           schema_version, paste(names, collapse = ", "))
+  futile.logger::flog.info(
+    "According to Label Schema Convention %s you can use the following arguments for constructing metadata labels: %s",
+    schema_version, paste(names, collapse = ", "))
   return(factory)
 }