Merge branch 'dev'

Author: andrie

.gitignore

@@ -3,3 +3,4 @@
 .Rproj.user
 checkpoint.Rproj
 .RData
+inst/doc

DESCRIPTION

@@ -16,8 +16,8 @@ Description: The goal of checkpoint is to solve the problem of package
     Immediately after completion of the rsync mirror process, we take a
     snapshot, thus creating the archive. Snapshot archives exist starting from
     2014-09-17.
-Version: 0.3.3
-Date: 2014-10-01
+Version: 0.3.4
+Date: 2015-01-14
 Author: Revolution Analytics
 Maintainer: Andrie de Vries <[email protected]>
 Copyright: Revolution Analytics
@@ -30,3 +30,4 @@ Imports:
     knitr
 Suggests:
     testthat(>= 0.9)
+VignetteBuilder: knitr

R/checkpoint.R

@@ -40,16 +40,20 @@ checkpoint <- function(snapshotDate, project = getwd(), verbose=TRUE) {
   snapshoturl <- getSnapshotUrl(snapshotDate=snapshotDate)
 
 
-  compiler.path= system.file(package = "compiler")
+  compiler.path <- system.file(package = "compiler", lib.loc = .Library[1])
   # set repos
   setMranMirror(snapshotUrl = snapshoturl)
 
   # Set lib path
   setLibPaths(snapshotDate)
 
-  if(.Platform$OS.type != "windows")
+  if(.Platform$OS.type == "windows"){
+    dir.create(file.path(.libPaths(), "compiler"), showWarnings = FALSE)
+    file.copy(to = .libPaths(), from = compiler.path, recursive = TRUE)
+  } else {
     install.packages(repos = NULL, pkgs = compiler.path, type = "source")
-
+  }
+  
   mssg(verbose, "Scanning for loaded pkgs")
 
   # Scan for packages used
@@ -58,30 +62,28 @@ checkpoint <- function(snapshotDate, project = getwd(), verbose=TRUE) {
                        c("base", "compiler", "datasets", "graphics", "grDevices", "grid",
                          "methods", "parallel", "splines", "stats", "stats4", "tcltk",
                          "tools", "utils"))  # all base priority packages, not on CRAN or MRAN
-  packages.to.install = setdiff(projectScanPackages(project), exclude.packages)
+  packages.to.install <- setdiff(projectScanPackages(project), exclude.packages)
 
+  # detach checkpointed pkgs already loaded
+  
+  packages.in.search <- findInSearchPath(packages.to.install)
+  detachFromSearchPath(packages.in.search)
+  
   # install missing packages
 
   if(length(packages.to.install) > 0) {
     mssg(verbose, "Installing packages used in this project ")
-    utils::install.packages(pkgs = packages.to.install, verbose=FALSE, quiet=TRUE)
+    utils::install.packages(pkgs = packages.to.install, verbose = FALSE, quiet = TRUE)
   } else {
     mssg(verbose, "No packages found to install")
   }
 
-  # detach and reload checkpointed pkgs already loaded
-  search.path = search()
-  lapply(
-    unlist(
-      lapply(
-        packages.to.install,
-        grep,
-        x = search.path)),
-    function(x) {
-      detach(x, unload = TRUE, force = TRUE)
-      library(search.path[x], character.only = TRUE)})
-
-  NULL}
+  # Reload detached packages
+  if(length(packages.in.search > 0)){
+    lapply(packages.in.search, library, character.only = TRUE, quietly = TRUE)
+  }
+  
+  invisible(NULL)}
 
 setMranMirror <- function(snapshotDate, snapshotUrl = checkpoint:::getSnapShotUrl(snapshotDate)){
   options(repos = snapshotUrl)}

R/detach.R

@@ -0,0 +1,36 @@
+# Given a character vector with package names, construct regular expression that matches search()
+makeSearchString <- function(pkg, search = TRUE) {
+  regex <- "package:%s"
+  if(search) regex <- paste0(regex, "$")
+  paste(sprintf(regex, pkg), collapse="|")
+}
+
+makeDetachString <- function(pkg) makeSearchString(pkg, search = FALSE)
+
+# Determine if package is in search()
+findInSearchPath <- function(pkg){
+  s <- search()
+  z <- unlist(
+    regmatches(s, gregexpr(makeSearchString(pkg), s))
+  )
+  setdiff(gsub("package:", "", z), "")
+}
+
+# Detach package from search()
+detachFromSearchPath <- function(p){
+  max.n <- 1 + length(p) # Prevent endless loop as a failsafe
+  n <- 0
+  repeat {
+    d <- findInSearchPath(p)
+    if(length(d) == 0) break # Stop if all packages unloaded
+    for(to.detach in d){
+      try({
+        detach(name = makeDetachString(to.detach), unload = TRUE, force = TRUE, character.only = TRUE)
+      },
+      silent = TRUE
+      )
+    }
+    n <- n + 1
+    if(n > max.n) break
+  }
+}

README.md

@@ -34,7 +34,7 @@ This means the remainder of your script will run with the packages from a specif
 Sharing your script to be reproducible is as easy as:
 
 - Load the `checkpoint` package using `library(checkpoint)`
-- Ensure you specify `checkpoint()` with your checkpoint date, e.g. `checkpoint("2014-09-17")`
+- Ensure you specify `checkpoint()` with your checkpoint date, e.g. `checkpoint("2014-10-01")`
 
 Then send this script to your collaborators.  When they run this script on their machine, `checkpoint` will perform the same steps of installing the necessary packages, creating the `checkpoint` snapshot folder and producing the same results.
 
@@ -67,7 +67,7 @@ cat("library(MASS)", "library(foreach)",
 # Create a checkpoint by specifying a snapshot date
 
 library(checkpoint)
-checkpoint("2014-09-17")
+checkpoint("2014-10-01")
 
 # Check that CRAN mirror is set to MRAN snapshot
 getOption("repos")
@@ -98,7 +98,7 @@ To install `checkpoint` directly from github, use the `devtools` package.  In yo
 
 ```
 install.packages("devtools")
-devtools::install_github("RevolutionAnalytics/checkpoint", ref="v0.3.3")
+devtools::install_github("RevolutionAnalytics/checkpoint", ref="v0.3.4")
 library("checkpoint")
 ```
 

tests/testthat/test-1-checkpoint.R

@@ -1,55 +1,73 @@
 # tests for initialize
 context("checkpoint")
 
+Sys.setenv("R_TESTS" = "") # Configure Travis for tests https://github.com/RevolutionAnalytics/checkpoint/issues/139
+
 MRAN.start = as.Date("2014-09-17")
 MRAN.default = as.Date("2014-10-01")
 MRAN.dates = as.Date(MRAN.start:(Sys.Date()-1), origin = as.Date("1970-01-01"))
+
+packages.to.test = c("MASS", "plyr", "XML", "httr","checkpoint", "stats", "stats4", "compiler")
+
 for(snap_date in as.character(c(MRAN.default, MRAN.dates[sample(length(MRAN.dates), 10, replace = FALSE)]))) {
   project_root <- file.path(tempfile(), "checkpointtemp")
   dir.create(project_root, recursive = TRUE)
-
-  test_that("snapshot functions return correct results", {
+  
+  test_that(paste("snapshot functions work correctly with snapshot", snap_date), {
     skip_on_cran()
-    Sys.setenv("R_TESTS" = "") # Need this line to configure Travis for tests https://github.com/RevolutionAnalytics/checkpoint/issues/139
-
+    message("\n", "Snapshot date: ", snap_date)
+    
     checkpoint:::cleanCheckpointFolder(snap_date)
-
+    
     expect_equal(
       checkpoint:::getSnapshotUrl(snap_date),
       file.path("http://mran.revolutionanalytics.com/snapshot", snap_date))
-
+    
     expect_message(
       checkpoint(snap_date, project = project_root),
       "No packages found to install")
-
+    
     # Write dummy code file to project
-    packages.to.test = c("MASS", "plyr", "XML", "httr","checkpoint", "stats", "stats4")
     code = paste("library('", packages.to.test, "')", sep ="", collapse ="\n")
     cat(code, file = file.path(project_root, "code.R"))
-
+    
     expect_message(
       checkpoint(snap_date, project = project_root),
       "Installing packages used in this project")
-
-    x <- installed.packages(fields = "Date/Publication")
-    expect_equivalent(
-      sort(x[, "Package"]),
-      sort(c("bitops", "digest", "httr", "jsonlite", "MASS", "plyr", "Rcpp",
-             "RCurl", "stringr", "XML")))
+    
+    x <- installed.packages(fields = "Date/Publication", noCache = TRUE)
+    
+    base.packages <- unname(installed.packages(priority = "base", lib.loc = .Library)[, "Package"])
+    packages.expected <- sort(unique(unlist(
+      
+      sapply(setdiff(packages.to.test, c("checkpoint", base.packages)), function(p){
+        z <- tools::pkgDepends(p)
+        c(z$Depends, z$Imports)
+      }, USE.NAMES = FALSE)
+    )))
+    
+    expect_true(
+      all(setdiff(packages.to.test, c("checkpoint", base.packages)) %in% unname(x[, "Package"])))
+    
+    expect_true(
+      all(setdiff(packages.expected, c("checkpoint", base.packages)) %in% unname(x[, "Package"])))   
 
     expect_true(
       all(
         na.omit(
           x[, "Date/Publication"]) <=
           as.POSIXct(snap_date, tz="UTC")))
 
+    expect_true(
+      all(sapply(setdiff(packages.to.test, "checkpoint"), require, character.only = TRUE, quietly = TRUE)))
+
     expect_equal(
       getOption("repos"),
       file.path("http://mran.revolutionanalytics.com/snapshot", snap_date))
-
+    
     expect_equal(
       checkpoint:::checkpointPath(snap_date, "lib"),
       normalizePath(.libPaths()[1]))})
   # cleanup
   checkpoint:::cleanCheckpointFolder(snap_date)
-}
+}