pass CRAN documentation checks

DESCRIPTION

@@ -2,13 +2,15 @@ Package: harbor
 Title: Control docker containers from R
 Version: 0.0.1
 Authors@R: "Winston Chang <winston@stdout.org> [aut, cre]"
-Description: Control docker containers from R
+Description: Control docker containers from R, for local of cloud based instances.
 Depends:
     R (>= 3.0)
 Imports:
-    jsonlite (>= 0.9.12)
+    jsonlite (>= 0.9.12),
+    analogsea (>= 0.4.0),
+    googleComputeEngineR
 License: GPL-2
 LazyData: true
-Suggests:
-    analogsea
-Remotes: cloudyr/googleComputeEngineR
+Remotes:
+    cloudyr/googleComputeEngineR
+RoxygenNote: 5.0.1

NAMESPACE

@@ -1,9 +1,10 @@
-# Generated by roxygen2 (4.0.2): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method(as.container,character)
 S3method(as.container,container)
 S3method(as.container,list)
 S3method(docker_cmd,droplet)
+S3method(docker_cmd,gce_instance)
 S3method(docker_cmd,localhost)
 S3method(print,container)
 S3method(print,localhost)
@@ -18,3 +19,6 @@ export(docker_inspect)
 export(docker_pull)
 export(docker_run)
 export(localhost)
+importFrom(googleComputeEngineR,gce_ssh)
+importFrom(stats,setNames)
+importFrom(utils,capture.output)

R/boot2docker.R

@@ -1,5 +1,7 @@
-# If we're on Mac and Windows, we're using boot2docker, and we need to run the
-# equivalent of `$(boot2docker shellinit)`.
+#' If we're on Mac and Windows, we're using boot2docker, and we need to run the
+#' equivalent of `$(boot2docker shellinit)`.
+#' @importFrom stats setNames
+#' @keywords internal
 boot2docker_shellinit <- function() {
   if (!(Sys.info()["sysname"] %in% c("Darwin", "Windows")))
     return()
@@ -15,7 +17,7 @@ boot2docker_shellinit <- function() {
   if (length(envvars) != 0) {
     envvars <- sub("^ +export +", "", envvars)
     envvars <- strsplit(envvars, "=")
-    envvars <- setNames(pluck(envvars, 2), pluck(envvars, 1))
+    envvars <- stats::setNames(pluck(envvars, 2), pluck(envvars, 1))
     do.call(Sys.setenv, envvars)
   }
 }

R/container.R

@@ -1,5 +1,8 @@
 #' Coerce an object into a container object.
 #'
+#' @param x An object to coerce
+#' @param host A docker host
+#'
 #' A container object represents a Docker container on a host.
 #' @export
 as.container <- function(x, host = localhost) UseMethod("as.container")
@@ -35,6 +38,7 @@ as.container.container <- function(x, host = localhost) {
 }
 
 #' @export
+#' @importFrom utils capture.output
 print.container <- function(x, ...) {
   cat("<container>")
   cat(
@@ -44,7 +48,7 @@ print.container <- function(x, ...) {
     "\n  Command: ", x$cmd,
     "\n  Host:  ",
     indent(
-      paste(capture.output(print(x$host)), collapse = "\n"),
+      paste(utils::capture.output(print(x$host)), collapse = "\n"),
       indent = 2
     )
   )
@@ -57,6 +61,8 @@ print.container <- function(x, ...) {
 #' This does not use reference semantics, so if you want to store the updated
 #' information, you need to save the result.
 #'
+#' @param container A container object
+#'
 #' @examples
 #' \dontrun{
 #' con <- container_update_info(con)
@@ -69,6 +75,8 @@ container_update_info <- function(container) {
 
 #' Report whether a container is currently running.
 #'
+#' @inheritParams container_update_info
+#'
 #' @examples
 #' \dontrun{
 #' container_running(con)
@@ -82,6 +90,7 @@ container_running <- function(container) {
 
 #' Delete a container.
 #'
+#' @inheritParams container_update_info
 #' @param force Force removal of a running container.
 #' @examples
 #' \dontrun{
@@ -96,8 +105,9 @@ container_rm <- function(container, force = FALSE) {
 
 #' Retrieve logs for a container.
 #'
+#' @inheritParams container_update_info
 #' @param follow Follow log output as it is happening.
-#' @param timestamp Show timestamps.
+#' @param timestamps Show timestamps.
 #' @examples
 #' \dontrun{
 #' container_rm(con)

R/containers.R

@@ -1,4 +1,5 @@
 #' Get list of all containers on a host.
+#' @inheritParams docker_cmd
 #' @export
 containers <- function(host = localhost, ...) {
   ids <- docker_cmd(host, "ps", "-qa", capture_text = TRUE, ...)

R/docker.R

@@ -10,6 +10,8 @@
 #'   This is useful for chaining functions. If \code{TRUE}, capture the text
 #'   output from both stdout and stderr, and return that. Note that \code{TRUE}
 #'   may not be available on all types of hosts.
+#' @param ... Other arguments passed to the SSH command for the host
+#'
 #' @examples
 #' \dontrun{
 #' docker_cmd(localhost, "ps", "-a")
@@ -23,6 +25,8 @@ docker_cmd <- function(host, cmd = NULL, args = NULL, docker_opts = NULL,
 
 #' Pull a docker image onto a host.
 #'
+#' @inheritParams docker_cmd
+#' @param image The docker image to pull e.g. \code{rocker/rstudio}
 #' @examples
 #' \dontrun{
 #' docker_pull(localhost, "debian:testing")
@@ -37,6 +41,7 @@ docker_pull <- function(host = localhost, image, ...) {
 
 #' Run a command in a new container on a host.
 #'
+#' @inheritParams docker_cmd
 #' @param host An object representing the host where the container will be run.
 #' @param image The name or ID of a docker image.
 #' @param cmd A command to run in the container.
@@ -92,6 +97,8 @@ docker_run <- function(host = localhost, image = NULL, cmd = NULL,
 
 #' Inspect one or more containers, given name(s) or ID(s).
 #'
+#' @inheritParams docker_cmd
+#' @param names Names of the containers
 #' @return A list of lists, where each sublist represents one container. This is
 #'   the output of `docker inspect` translated directly from raw JSON to an R
 #'   object.

R/googleComputeEngine.R

@@ -1,4 +1,5 @@
 #' @export
+#' @importFrom googleComputeEngineR gce_ssh
 docker_cmd.gce_instance <- function(host, cmd = NULL, args = NULL,
                                     docker_opts = NULL, capture_text = FALSE, ...) {
   cmd_string <- paste(c("docker", cmd, docker_opts, args), collapse = " ")

README.md

@@ -8,7 +8,7 @@ It presently works with:
 
 * The local computer that R is running on (`localhost`)
 * Remote virtual machines running on Digital Ocean, with the [analogsea](https://github.com/sckott/analogsea) package.
-
+* Remote virtual machines running on Google Compute Engine, with the [googleComputeEngineR](https://github.com/cloudyr/googleComputeEngineR) package.
 
 ## Installation
 
@@ -17,6 +17,9 @@ devtools::install_github("wch/harbor")
 
 # Optional
 devtools::install_github("sckott/analogsea")
+
+# Optional
+devtools::install_github("cloudyr/googleComputeEngineR")
 ```
 
 
@@ -54,6 +57,8 @@ The same commands can be used with docker images on a remote host, using the ana
 
 Note: you may need to configure ssh host keys on Digital Ocean for the following to work.
 
+## DigitalOcean
+
 ```R
 library(analogsea)
 
@@ -84,3 +89,38 @@ con
 # Destroy the virtual machine from Digital Ocean
 droplet_delete(dhost)
 ```
+
+## Google Compute Engine
+
+```R
+library(googleComputeEngineR)
+
+# Create a virtual machine on Digital Ocean
+ghost <- gce_vm_create("demo", 
+                       image_project = "google-containers",
+                       image_family = "gci-stable")
+
+# Create and run a container in the virtual machine.
+# This might take a while.
+con <- docker_run(ghost, "debian", "echo foo")
+#> Unable to find image 'debian' locally
+#> debian:latest: The image you are pulling has been verified
+#> Status: Downloaded newer image for debian:latest
+#> foo
+
+con
+#> <container>
+#>   ID:       5aa987cef673 
+#>   Name:     harbor_8pfvgi 
+#>   Image:    busybox 
+#>   Command:  echo foo 
+#>   Host:     <droplet>dhost (2941098)
+#>     IP:     107.170.247.231
+#>     Status: active
+#>     Region: San Francisco 1
+#>     Image:  Docker 1.3.0 on Ubuntu 14.04
+#>     Size:   512mb ($0.00744 / hr)
+
+# Destroy the virtual machine from Google Compute Engine
+gce_vm_delete(ghost)
+```

harbor.Rproj

@@ -18,4 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace,vignette