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‎DESCRIPTION‎

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@@ -11,13 +11,13 @@ Description: The goal of checkpoint is to solve the problem of package
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updates that came later and may have altered your results. In this way,
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anyone using checkpoint's checkpoint() can ensure the reproducibility of
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your scripts or projects at any time. To create the snapshot archives, once
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a day (at midnight UTC) we refresh the Austria CRAN mirror, on the "Managed
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a day (at midnight UTC) Revolution Analytics refreshes the Austria CRAN mirror, on the "Managed
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R Archived Network" server (http://mran.revolutionanalytics.com/).
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Immediately after completion of the rsync mirror process, we take a
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Immediately after completion of the rsync mirror process, the process takes a
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snapshot, thus creating the archive. Snapshot archives exist starting from
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2014-09-17.
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Version: 0.3.9
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Date: 2015-03-17
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Version: 0.3.10
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Date: 2015-04-27
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Author: Revolution Analytics
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Maintainer: Andrie de Vries <[email protected]>
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Copyright: Revolution Analytics

‎NAMESPACE‎

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# Generated by roxygen2 (4.0.2): do not edit by hand
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# Generated by roxygen2 (4.1.0): do not edit by hand
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export(checkpoint)
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export(setSnapshot)
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importFrom(utils,install.packages)

‎R/checkpoint.R‎

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@@ -46,7 +46,7 @@ checkpoint <- function(snapshotDate, project = getwd(), R.version, scanForPackag
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checkpointLocation = "~/",
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verbose=TRUE,
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use.knitr = system.file(package="knitr") != "") {
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if(!missing("R.version") && !is.null(R.version)){
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if(!correctR(as.character(R.version))){
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message <- sprintf("Specified R.version %s does not match current R (%s)",
@@ -57,41 +57,39 @@ checkpoint <- function(snapshotDate, project = getwd(), R.version, scanForPackag
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stop(message)
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}
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}
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checkpointLocation = authorizeFileSystemUse(checkpointLocation)
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fixRstudioBug()
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if(!createFolders(snapshotDate = snapshotDate, checkpointLocation = checkpointLocation))
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stop("Unable to create checkpoint folders at checkpointLocation = \"", checkpointLocation, "\"")
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snapshoturl <- getSnapshotUrl(snapshotDate=snapshotDate)
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compiler.path <- system.file(package = "compiler", lib.loc = .Library[1])
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# set repos
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setMranMirror(snapshotUrl = snapshoturl)
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libPath <- checkpointPath(snapshotDate, type = "lib", checkpointLocation = checkpointLocation)
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installMissingBasePackages(checkpointLocation = checkpointLocation)
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# Set lib path
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setLibPaths(checkpointLocation = checkpointLocation, libPath = libPath)
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# Scan for packages used
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exclude.packages = c("checkpoint", # this very package
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c("base", "compiler", "datasets", "graphics", "grDevices", "grid",
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"methods", "parallel", "splines", "stats", "stats4", "tcltk",
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"tools", "utils")) # all base priority packages, not on CRAN or MRAN
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packages.installed <- unname(installed.packages()[, "Package"])
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if(isTRUE(scanForPackages)){
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mssg(verbose, "Scanning for packages used in this project")
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pkgs <- projectScanPackages(project, use.knitr = use.knitr)
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packages.detected <- pkgs[["pkgs"]]
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mssg(verbose, "- Discovered ", length(packages.detected), " packages")
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if(length(pkgs[["error"]]) > 0){
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files.not.parsed <- pkgs[["error"]]
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mssg(verbose, "Unable to parse ", length(pkgs[["error"]]), " files:")
@@ -103,18 +101,20 @@ checkpoint <- function(snapshotDate, project = getwd(), R.version, scanForPackag
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packages.detected <- character(0)
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files.not.parsed <- character(0)
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}
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packages.to.install <- setdiff(packages.detected, c(packages.installed, exclude.packages))
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# detach checkpointed pkgs already loaded
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packages.in.search <- findInSearchPath(packages.to.install)
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detachFromSearchPath(packages.in.search)
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# check if packages are available in snapshot
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if(length(packages.to.install) > 0) {
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# set repos
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setMranMirror(snapshotUrl = snapshoturl)
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not.available <- !packages.to.install %in% available.packages()[, "Package"]
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if(sum(not.available > 0)){
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mssg(verbose, "Packages not available in repository and won't be installed:")
@@ -124,9 +124,9 @@ checkpoint <- function(snapshotDate, project = getwd(), R.version, scanForPackag
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} else {
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not.available <- character(0)
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}
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# install missing packages
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if(length(packages.to.install) > 0) {
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mssg(verbose, "Installing packages used in this project ")
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for(pkg in packages.to.install){
@@ -144,15 +144,15 @@ checkpoint <- function(snapshotDate, project = getwd(), R.version, scanForPackag
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} else {
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if(isTRUE(scanForPackages)) mssg(verbose, "No packages found to install")
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}
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# Reload detached packages
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if(length(packages.in.search > 0)){
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lapply(packages.in.search, library, character.only = TRUE, quietly = TRUE)
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}
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mssg(verbose, "checkpoint process complete")
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mssg(verbose, "---")
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z <- list(
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files_not_scanned = files.not.parsed,
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pkgs_found = packages.detected,
@@ -161,30 +161,40 @@ checkpoint <- function(snapshotDate, project = getwd(), R.version, scanForPackag
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)
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invisible(z)}
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# ------------------------------------------------------------------------
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setMranMirror <- function(snapshotDate, snapshotUrl = checkpoint:::getSnapShotUrl(snapshotDate)){
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options(repos = snapshotUrl)}
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setLibPaths <- function(checkpointLocation, libPath){
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assign(".lib.loc", c(libPath, checkpointBasePkgs(checkpointLocation)), envir = environment(.libPaths))}
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assign(".lib.loc", c(libPath, checkpointBasePkgs(checkpointLocation)), envir = environment(.libPaths))}
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mranUrl <- function()"http://mran.revolutionanalytics.com/snapshot/"
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getSnapshotUrl <- function(snapshotDate, url = mranUrl()){
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mran.root = url(url)
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snapshot.url = paste(gsub("/$", "", url), snapshotDate, sep = "/")
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on.exit(close(mran.root))
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tryCatch(
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suppressWarnings(readLines(mran.root)),
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error =
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function(e) {
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stop(sprintf("Unable to reach MRAN: %s", e$message))})
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snapshot.url = paste(gsub("/$", "", url), snapshotDate, sep = "/")
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warning(sprintf("Unable to reach MRAN: %s", e$message))
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return(snapshot.url)
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}
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)
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con = url(snapshot.url)
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on.exit(close(con), add = TRUE)
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tryCatch(
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suppressWarnings(readLines(con)),
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error =
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function(e) {
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stop("Unable to find snapshot on MRAN")})
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warning("Unable to find snapshot on MRAN")
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return(snapshot.url)
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}
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)
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snapshot.url}
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‎R/checkpoint_paths.R‎

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@@ -8,7 +8,7 @@ checkpointPath <- function(snapshotDate, checkpointLocation,
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if(type == "base") return(
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normalizePath(
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file.path(rootPath, paste0("R-", getRversion())),
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winslash = "/", mustWork = FALSE)
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winslash = "/", mustWork = FALSE)
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)
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snapshotPath <- file.path(rootPath, snapshotDate)
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libPath <- file.path(snapshotPath, "lib", R.version$platform, base::getRversion())
@@ -45,9 +45,14 @@ authorizeFileSystemUse =
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else {
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if(interactive()) {
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answer = readline(paste("Can I create directory", checkpointRoot, "for internal checkpoint use?(y/n)\n"))
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if(answer != "y")
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if(tolower(answer) != "y")
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stop("Cannot proceed without access to checkpoint directory")}
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else {
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warning("Will have to use a temporary directory for internal use. All information will be lost at the end of session")
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checkpointLocation = tempdir()}}
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checkpointLocation}
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stop(paste(
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"The .checkpoint folder does not exist. Please try again after creating the folder at",
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normalizePath(checkpointRoot)
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))
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}
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}
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checkpointLocation
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}

‎R/setSnapshot.R‎

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#' Set default CRAN repository to MRAN snapshot date.
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#'
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#' @inheritParams checkpoint
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#'
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#' @export
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#' @example /inst/examples/example_setSnapshot.R
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#'
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setSnapshot <- function(snapshotDate){
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if (missing(snapshotDate) || is.null(snapshotDate)) return(getOption("repos"))
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repoDate <- paste0("http://mran.revolutionanalytics.com/snapshot/", snapshotDate)
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response <- tryCatch(
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suppressWarnings(readLines(repoDate)),
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error = function(e)e
14+
)
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if(inherits(response, "error")) stop(paste0("Invalid snapshot date."))
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options(repos = c(CRAN = repoDate))
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message(paste("Using CRAN mirror at", repoDate))
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}

‎inst/examples/example_setSnapshot.R‎

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# Empty date field returns current repo
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oldRepos <- getOption("repos")
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setSnapshot()
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# Valid snapshot date
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setSnapshot("2014-11-16")
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# Invalid snapshot date (in future), returns error
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\dontrun{
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setSnapshot("2100-01-01")
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}
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options(repos = oldRepos)

‎man/checkpoint-package.Rd‎

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% Generated by roxygen2 (4.0.2): do not edit by hand
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% Generated by roxygen2 (4.1.0): do not edit by hand
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% Please edit documentation in R/checkpoint-package.R
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\docType{package}
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\name{checkpoint-package}
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\alias{checkpoint-package}

‎man/checkpoint.Rd‎

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% Generated by roxygen2 (4.0.2): do not edit by hand
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% Generated by roxygen2 (4.1.0): do not edit by hand
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% Please edit documentation in R/checkpoint.R
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\name{checkpoint}
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\alias{checkpoint}
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\title{Configures R session to use packages as they existed on CRAN at time of snapshot.}

‎man/setSnapshot.Rd‎

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% Generated by roxygen2 (4.1.0): do not edit by hand
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% Please edit documentation in R/setSnapshot.R
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\name{setSnapshot}
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\alias{setSnapshot}
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\title{Set default CRAN repository to MRAN snapshot date.}
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\usage{
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setSnapshot(snapshotDate)
8+
}
9+
\arguments{
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\item{snapshotDate}{Date of snapshot to use in \code{YYYY-MM-DD} format,e.g. \code{"2014-09-17"}. Specify a date on or after \code{"2014-09-17"}. MRAN takes one snapshot per day.}
11+
}
12+
\description{
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Set default CRAN repository to MRAN snapshot date.
14+
}
15+
\examples{
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# Empty date field returns current repo
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18+
oldRepos <- getOption("repos")
19+
setSnapshot()
20+
21+
# Valid snapshot date
22+
setSnapshot("2014-11-16")
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24+
# Invalid snapshot date (in future), returns error
25+
\dontrun{
26+
setSnapshot("2100-01-01")
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}
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options(repos = oldRepos)
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}
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‎tests/testthat/test-0-snapshots.R‎

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test_that("snapshot functions return correct results", {
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skip_on_cran()
5-
expect_error(
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expect_warning(
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getSnapshotUrl("1972-01-01"))
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dd <- "2014-09-08"

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