Merge pull request #128 from nuest/master

Use stevedore
o2r-project · Aug 15, 2018 · 51d7b26 · 51d7b26
2 parents d0ca269 + c96e3a5
commit 51d7b26
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diff --git a/.gitignore b/.gitignore
@@ -2,7 +2,7 @@
 .Rhistory
 .Rapp.history
 # Session Data files
-.RData
+.Rdata
 # Example code in package build process
 *-Ex.R
 # Output files from R CMD build
@@ -32,8 +32,6 @@ tests/testthat/package_markdown/units/*\.html
 
 tests/testthat/Rplots\.pdf
 
-tests/testthat/package_markdown/spacetime/main\.html
-
 vignettes/sessionInfo\.Rdata
 
 sessionInfo\.Rdata
diff --git a/.travis.yml b/.travis.yml
@@ -4,6 +4,8 @@
 # For a potential alternative configuration see https://github.com/metacran/r-builder
 
 language: r
+services:
+  - docker
 
 r:
   - release
@@ -28,48 +30,5 @@ before_install:
   # activate liblwgeom by:
   - sudo ldconfig
   - Rscript -e 'update.packages(ask = FALSE)' # https://github.com/travis-ci/travis-ci/issues/6850
-  - Rscript -e 'install.packages("devtools"); devtools::install_deps(dependencies = TRUE)'
-  #- Rscript -e 'devtools::install_dev_deps()'
 
 warnings_are_errors: true
-
-services:
-  - docker
-
-r_packages:
-  - rgdal
-  - roxygen2
-  - covr
-  #- lintr
-  - testthat
-  - codetools
-  - sp
-  - gstat
-  - proj4
-  - devtools
-  - units
-  - sf
-  - fortunes
-  - lwgeom
-  # needed for rendering spacetime/main.Rmd
-  - plm
-  - spacetime
-  - mapdata
-  - lattice
-  - RColorBrewer
-  - xts
-  - maptools
-  - maps
-  - diveMove
-  - trip
-  - adehabitatLT
-  - cshapes
-
-after_failure:
-  - Rscript -e 'library(methods)' -e 'devtools::test()'
-
-#after_success:
-#  - Rscript -e 'covr::codecov()'
-#  - Rscript -e 'lintr::lint_package()'
-#  - echo $TRAVIS_R_VERSION
-#  - echo $TRAVIS_OS_NAME
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: containerit
 Type: Package
 Title: Package R in Docker Containers
-Version: 0.4.0
+Version: 0.5.0.9000
 Authors@R: c(person("Daniel", "Nuest", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-2392-6140")),
     person("Matthias", "Hinz", role = c("aut"), email = "[email protected]", comment = c(ORCID = "0000-0001-6837-9406")))
 Author: Daniel Nuest [aut, cre], Matthias Hinz [aut]
@@ -19,11 +19,13 @@ Imports:
     devtools,
     semver,
     automagic,
-    sessioninfo
+    sessioninfo,
+    stevedore,
+    versions
 VignetteBuilder: knitr
 Description: Package R sessions, scripts, workspaces and vignettes together with
     all dependencies to execute them in Docker containers. This package is supported
-    by the project Opening Reproducible Research (http://o2r.info).
+    by the project Opening Reproducible Research (https://o2r.info).
 License: GPL-3 + file LICENSE
 URL: https://github.com/o2r/containerit/
 BugReports: https://github.com/o2r/containerit/issues
@@ -38,7 +40,6 @@ Suggests:
     rgdal,
     maptools,
     magrittr,
-    harbor,
     lintr,
     sp,
     gstat,
@@ -49,7 +50,7 @@ Suggests:
     fortunes,
     remotes,
     ggplot2
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
 Collate:
     'Class-Instruction.R'
     'Class-Add.R'
@@ -83,4 +84,4 @@ Collate:
     'sessionInfo-localbuild-methods.R'
     'utility-functions.R'
 Remotes: github::r-hub/sysreqs,
-    github::wch/harbor
+    github::richfitz/stevedore
diff --git a/NAMESPACE b/NAMESPACE
@@ -28,7 +28,6 @@ export(Workdir)
 export(clean_session)
 export(containerit_write_config)
 export(docker_build)
-export(docker_inspect)
 export(dockerfile)
 export(getGitHubRef)
 export(getImageForVersion)
@@ -64,10 +63,10 @@ exportMethods(print)
 exportMethods(toString)
 exportMethods(write)
 import(futile.logger)
-importFrom(harbor,docker_cmd)
-importFrom(harbor,localhost)
 importFrom(methods,"slot<-")
 importFrom(methods,new)
 importFrom(methods,slot)
 importFrom(semver,parse_version)
+importFrom(stevedore,docker_available)
+importFrom(stevedore,docker_client)
 importFrom(utils,sessionInfo)
diff --git a/R/Class-Add.R b/R/Class-Add.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Add-instruction class yet to be implemented
 #' @include Class-Instruction.R

diff --git a/R/Class-All.R b/R/Class-All.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Class union for slots taking either numeric or character input
 #'

diff --git a/R/Class-Arg.R b/R/Class-Arg.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Arg-instruction class yet to be implemented
 #' @include Class-Instruction.R

diff --git a/R/Class-Cmd.R b/R/Class-Cmd.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' An S4 class to represent a CMD instruction
 #' @include Class-Instruction.R

diff --git a/R/Class-Comment.R b/R/Class-Comment.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Instructionclass representing a comment
 #'
@@ -25,9 +25,9 @@ setClass("Comment",
 #' @examples
 #' # A simple label that occupies one line:
 #' comment <- Comment(text = "this is important to note")
-#' df <- dockerfile(clean_session())
-#' addInstruction(df) <- comment
-#' print(df)
+#' the_dockerfile <- dockerfile(clean_session())
+#' addInstruction(the_dockerfile) <- comment
+#' print(the_dockerfile)
 #'
 Comment <- function(text) {
   methods::new("Comment", text = text)

diff --git a/R/Class-Copy.R b/R/Class-Copy.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' S4 Class representing a COPY-instruction
 #'

diff --git a/R/Class-Dockerfile.R b/R/Class-Dockerfile.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' An S4 class to represent a Dockerfile
 #'

diff --git a/R/Class-Entrypoint.R b/R/Class-Entrypoint.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Entrypoint class yet to be implemented
 #' @include Class-Instruction.R

diff --git a/R/Class-Env.R b/R/Class-Env.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Env class yet to be implemented
 #' @include Class-Instruction.R

diff --git a/R/Class-Expose.R b/R/Class-Expose.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' S4 Class representing an EXPOSE-instruction
 #'

diff --git a/R/Class-From.R b/R/Class-From.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 setClass("Tag", contains = "character")
 setClass("Digest", contains = "character")

diff --git a/R/Class-Healthcheck.R b/R/Class-Healthcheck.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Healthcheck-instruction class yet to be implemented
 #' @include Class-Instruction.R

diff --git a/R/Class-Instruction.R b/R/Class-Instruction.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' The Docker Instruction - Class
 #'

diff --git a/R/Class-Label.R b/R/Class-Label.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Instruction class representing a LABEL
 #'
@@ -39,9 +39,9 @@ setClass("Label",
 #' )
 #' #label with fixed namespace for all keys
 #' label3 <- Label("name"="A name", "description" = "A description", label_ns = "my.label.ns.")
-#' df <- dockerfile(clean_session())
-#' addInstruction(df) <- list(label1, label2, label3)
-#' cat(format(df),sep = "\n")
+#' the_dockerfile <- dockerfile(clean_session())
+#' addInstruction(the_dockerfile) <- list(label1, label2, label3)
+#' cat(format(the_dockerfile),sep = "\n")
 #'
 Label <-
   function(...,
@@ -67,8 +67,8 @@ Label <-
 #'
 #' @examples
 #' session <- clean_session()
-#' df <- dockerfile(session)
-#' addInstruction(df) <- Label_SessionInfo(session)
+#' the_dockerfile <- dockerfile(session)
+#' addInstruction(the_dockerfile) <- Label_SessionInfo(session)
 Label_SessionInfo <-
   function(session = sessionInfo(),
            as_json = FALSE) {

diff --git a/R/Class-Maintainer.R b/R/Class-Maintainer.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' An S4 class to represent a Dockerfile's maintainer
 #' @include Class-Instruction.R

diff --git a/R/Class-Onbuild.R b/R/Class-Onbuild.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Onbuild-instruction class yet to be implemented
 #' @include Class-Instruction.R

diff --git a/R/Class-Run.R b/R/Class-Run.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' An S4 class to represent a RUN instruction in shell form
 #' @include Class-Instruction.R
@@ -79,7 +79,7 @@ setClass("Run",
 #' Create objects representing a RUN instruction
 #'
 #' @param exec character argument naming the executable
-#' @param params parameter arguments
+#' @param params parameter arguments, of class character
 #' @family Run instruction
 #' @return An S4 object of class Run
 #' @export

diff --git a/R/Class-Shell.R b/R/Class-Shell.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Shell-instruction class yet to be implemented
 #' @include Class-Instruction.R

diff --git a/R/Class-Stopsignal.R b/R/Class-Stopsignal.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Stopsignal-instruction class yet to be implemented
 #' @include Class-Instruction.R

diff --git a/R/Class-Volume.R b/R/Class-Volume.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Volume class yet to be implemented
 #' @include Class-Instruction.R

diff --git a/R/Class-Workdir.R b/R/Class-Workdir.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' S4 Class representing a WORKDIR instruction
 #' @include Class-Instruction.R

diff --git a/R/LabelSchemaFactory.R b/R/LabelSchemaFactory.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Create Build-time labels according to Label Schema Convention
 #'
@@ -19,14 +19,14 @@
 #' @family label
 #'
 #' @examples
-#' df <- dockerfile(clean_session())
+#' the_dockerfile <- dockerfile(clean_session())
 #' factory <- LabelSchemaFactory()
 #' label <- factory(name = "ImageName",
 #'   description = "Description of the image",
 #'   build_date = Sys.time()
 #'  )
-#' addInstruction(df) <- label
-#' cat(format(df))
+#' addInstruction(the_dockerfile) <- label
+#' cat(format(the_dockerfile))
 #'
 #'
 LabelSchemaFactory <- function() {

diff --git a/R/baseimages.R b/R/baseimages.R
@@ -1,22 +1,28 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' Detect packages in a Docker image
 #'
 #' Extracts all installed packages from a Docker image by running it.
-#' The method is based on \code{harbor::docker_cmd}.
+#' The method is based on \code{stevedore}.
 #'
-#' @param host A host object (see harbor-package)
 #' @param image Name of the new image to be run
 #'
 #' @return A \code{data.frame} with installed packages and their version of the image
 #' @export
-#@importFrom harbor localhost docker_cmd
-get_installed_packages <- function(host = harbor::localhost, image) {
-  args = c("--rm", image, "Rscript", "-e", "write.csv(as.data.frame(installed.packages())[,c(\"Version\")])")
-  futile.logger::flog.info("EXEC: docker run %s", paste(args, collapse = " "))
+#' @importFrom stevedore docker_client docker_available
+get_installed_packages <- function(image) {
+  stopifnot(stevedore::docker_available())
 
-  output <- harbor::docker_cmd(host = harbor::localhost, cmd = "run", args = args, capture_text = TRUE)
-  pkgs <- read.csv(text = output)
+  cmd = c("Rscript", "-e", "write.csv(x = as.data.frame(installed.packages())[,c(\"Version\")])")
+  futile.logger::flog.info("Running command %s in %s", paste(cmd, collapse = " "), image)
+
+  .client <- stevedore::docker_client()
+  .container <- .client$container$run(image = image,
+                                      cmd = cmd,
+                                      rm = TRUE,
+                                      name = "containerit_get_installed_packages")
+
+  pkgs <- read.csv(text = .container$logs)
   names(pkgs) <- c("pkg", "version")
   attributes(pkgs)$image <- image
   return(pkgs)

diff --git a/R/containerit-config.R b/R/containerit-config.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 # You can use the following code to manually inspect and manipulate the configuration file.
 if (FALSE) {

diff --git a/R/containerit.R b/R/containerit.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 #' containerit: A package for packaging R objects and their dependencies in software containers
 #'

diff --git a/R/defaults.R b/R/defaults.R
@@ -1,4 +1,4 @@
-# Copyright 2017 Opening Reproducible Research (http://o2r.info)
+# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 .rocker_images <- c(
   versioned = "rocker/r-ver",