refactor extraction functions and fix most tests

also expose them as part of regular functions
remove some never-going-to-do tests
expect more warnings

.Rbuildignore

@@ -7,3 +7,4 @@
 ^README-.*\.png$
 ^CONDUCT\.md$
 .lintr
+docs

.gitignore

@@ -35,3 +35,5 @@ tests/testthat/Rplots\.pdf
 vignettes/sessionInfo\.Rdata
 
 sessionInfo\.Rdata
+
+tests/testthat/v.*\.yaml

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: containerit
 Type: Package
 Title: Package R in Docker Containers
-Version: 0.5.0.9001
+Version: 0.5.0.9002
 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]
@@ -50,7 +50,8 @@ Suggests:
     proj4,
     fortunes,
     remotes,
-    ggplot2
+    ggplot2,
+    lattice
 RoxygenNote: 6.1.0
 Collate:
     'Class-Instruction.R'
@@ -82,7 +83,6 @@ Collate:
     'dockerfile.R'
     'package-installation-bespoke.R'
     'package-installation-methods.R'
-    'sessionInfo-localbuild-methods.R'
     'utility-functions.R'
 Remotes: github::r-hub/sysreqs,
     github::richfitz/stevedore

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(docker_build,Dockerfile)
+S3method(docker_build,character)
 export("addInstruction<-")
 export(Add)
 export(Arg)
@@ -29,10 +31,12 @@ export(clean_session)
 export(containerit_write_config)
 export(docker_build)
 export(dockerfile)
+export(empty_session)
+export(extract_session_file)
+export(extract_session_image)
 export(getGitHubRef)
 export(getImageForVersion)
 export(getRVersionTag)
-export(getSessionInfoFromRdata)
 export(get_installed_packages)
 export(parseFrom)
 exportClasses(Add)
@@ -69,4 +73,13 @@ importFrom(methods,slot)
 importFrom(semver,parse_version)
 importFrom(stevedore,docker_available)
 importFrom(stevedore,docker_client)
+importFrom(stringr,regex)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_extract)
+importFrom(stringr,str_length)
+importFrom(stringr,str_sub)
+importFrom(utils,capture.output)
+importFrom(utils,install.packages)
+importFrom(utils,installed.packages)
+importFrom(utils,read.csv)
 importFrom(utils,sessionInfo)

R/Class-Comment.R

@@ -25,7 +25,7 @@ setClass("Comment",
 #' @examples
 #' # A simple label that occupies one line:
 #' comment <- Comment(text = "this is important to note")
-#' the_dockerfile <- dockerfile(clean_session())
+#' the_dockerfile <- dockerfile(empty_session())
 #' addInstruction(the_dockerfile) <- comment
 #' print(the_dockerfile)
 #'

R/Class-Label.R

@@ -39,7 +39,7 @@ setClass("Label",
 #' )
 #' #label with fixed namespace for all keys
 #' label3 <- Label("name"="A name", "description" = "A description", label_ns = "my.label.ns.")
-#' the_dockerfile <- dockerfile(clean_session())
+#' the_dockerfile <- dockerfile(empty_session())
 #' addInstruction(the_dockerfile) <- list(label1, label2, label3)
 #' cat(format(the_dockerfile),sep = "\n")
 #'
@@ -64,11 +64,12 @@ Label <-
 #' @return A label with key 'R.session-info' and the deparsed session information in one line
 #' @export
 #' @family label
+#' @importFrom utils capture.output
 #'
 #' @examples
-#' session <- clean_session()
-#' the_dockerfile <- dockerfile(session)
-#' addInstruction(the_dockerfile) <- Label_SessionInfo(session)
+#' the_session <- empty_session()
+#' the_dockerfile <- dockerfile(the_session)
+#' addInstruction(the_dockerfile) <- Label_SessionInfo(the_session)
 Label_SessionInfo <-
   function(session = sessionInfo(),
            as_json = FALSE) {

R/LabelSchemaFactory.R

@@ -19,7 +19,7 @@
 #' @family label
 #'
 #' @examples
-#' the_dockerfile <- dockerfile(clean_session())
+#' the_dockerfile <- dockerfile(empty_session())
 #' factory <- LabelSchemaFactory()
 #' label <- factory(name = "ImageName",
 #'   description = "Description of the image",

R/baseimages.R

@@ -10,6 +10,7 @@
 #' @return A \code{data.frame} with installed packages and their version of the image
 #' @export
 #' @importFrom stevedore docker_client docker_available
+#' @importFrom utils read.csv
 get_installed_packages <- function(image) {
   stopifnot(stevedore::docker_available())
 

R/dockerfile.R

@@ -54,6 +54,8 @@
 #' @export
 #'
 #' @import futile.logger
+#' @importFrom utils capture.output
+#' @importFrom stringr str_detect regex str_extract str_length str_sub
 #'
 #' @examples
 #' dockerfile <- dockerfile()
@@ -220,7 +222,7 @@ dockerfile <- function(from = utils::sessionInfo(),
     if (isTRUE(save_image)) {
       futile.logger::flog.debug("Saving image to file %s with %s and adding COPY instruction using environment %s",
                                 .filename, toString(ls(envir = envir)),
-                                capture.output(envir))
+                                utils::capture.output(envir))
       save(list = ls(envir = envir), file = .filename, envir = envir)
       addInstruction(.dockerfile) <- Copy(src = .filename, dest = .filename)
     } else if (is.list(save_image)) {
@@ -376,7 +378,7 @@ dockerfileFromSession.session_info <- function(session,
   pkgs_gh <- packages_df[stringr::str_detect(string = packages_df$source, stringr::regex("GitHub", ignore_case = TRUE)),]
   if (nrow(pkgs_gh) > 0) {
     for (pkg in pkgs_gh$name) {
-      currentPkg <- subset(pkgs_gh, name == pkg)
+      currentPkg <- subset(pkgs_gh, pkgs_gh$name == pkg)
       versionString <- stringr::str_extract(string = currentPkg$source, pattern = "(?<=\\()(.*)(?=\\))")
       packages_df[packages_df$name == pkg,c("version")] <- versionString
     }
@@ -423,18 +425,22 @@ dockerfileFromFile <- function(file,
     rel_path <- .makeRelative(file, context)
 
     # execute script / markdowns or read Rdata file to obtain sessioninfo
-    if (stringr::str_detect(file, ".R$")) {
+    if (stringr::str_detect(string = file,
+                            pattern = stringr::regex(".R$", ignore_case = TRUE))) {
       futile.logger::flog.info("Processing R script file '%s' locally.", rel_path)
-      sessionInfo <- containerit:::obtain_localSessionInfo(file = file,
-                                             echo = !silent,
-                                             predetect = predetect)
-    } else if (stringr::str_detect(file, ".Rmd$")) {
+      sessionInfo <- clean_session(file = file,
+                                   echo = !silent,
+                                   predetect = predetect)
+    } else if (stringr::str_detect(string = file,
+                                   pattern = stringr::regex(".rmd$", ignore_case = TRUE))) {
       futile.logger::flog.info("Processing Rmd file '%s' locally using rmarkdown::render(...)", rel_path)
-      sessionInfo <- containerit:::obtain_localSessionInfo(rmd_file = file,
-                                             echo = !silent,
-                                             predetect = predetect)
-    } else if (stringr::str_detect(file, ".Rdata$")) {
-      sessionInfo <- getSessionInfoFromRdata(file)
+      sessionInfo <- clean_session(rmd_file = file,
+                                   echo = !silent,
+                                   predetect = predetect)
+    } else if (stringr::str_detect(string = file,
+                                   pattern = stringr::regex(".rdata$", ignore_case = TRUE))) {
+      futile.logger::flog.info("Extracting session object from RData file %s", rel_path)
+      sessionInfo <- extract_session_file(file)
     } else{
       futile.logger::flog.info("The supplied file %s has no known extension. containerit will handle it as an R script for packaging.", rel_path)
     }
@@ -519,13 +525,15 @@ dockerfileFromWorkspace <- function(path,
                    pattern = "\\.R$",
                    full.names = TRUE,
                    include.dirs = FALSE,
-                   recursive = TRUE)
+                   recursive = TRUE,
+                   ignore.case = TRUE)
 
     .md_Files <- dir(path = path,
                      pattern = "\\.Rmd$", #|\\.Rnw$",
                      full.names = TRUE,
                      include.dirs = FALSE,
-                     recursive = TRUE)
+                     recursive = TRUE,
+                     ignore.case = TRUE)
     futile.logger::flog.debug("Found %s scripts and %s documents", length(.rFiles), length(.md_Files))
 
     if (length(.rFiles) > 0 && length(.md_Files) > 0) {

R/package-installation-bespoke.R

@@ -28,11 +28,6 @@
                              lib,
                              version,
                              .package_config))
-        no_apt <<- append(add_apt,
-                          .get_lib_pkgs_names(
-                            lib = lib,
-                            platform = .debian_platform,
-                            config = .package_config))
         add_inst <<- append(add_inst,
                             .get_lib_install_instructions(
                               lib = lib,