RevolutionAnalytics · andrie · Jun 26, 2017 · Apr 12, 2017 · Apr 12, 2017 · May 17, 2017
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -15,8 +15,8 @@ Description: The goal of checkpoint is to solve the problem of package
     server (<https://mran.microsoft.com/>). Immediately after completion
     of the rsync mirror process, the process takes a snapshot, thus creating the
     archive. Snapshot archives exist starting from 2014-09-17.
-Version: 0.4.0
-Date: 2017-04-10
+Version: 0.4.1
+Date: 2017-06-26
 Author: Microsoft Corporation
 Maintainer: Andrie de Vries <adevries@microsoft.com>
 Copyright: Microsoft
@@ -31,7 +31,8 @@ Suggests:
     knitr,
     rmarkdown,
     testthat(>= 0.9),
-    MASS
+    MASS,
+    darts
 VignetteBuilder: knitr
 RoxygenNote: 6.0.1
 Roxygen: list(markdown = TRUE)
diff --git a/NAMESPACE b/NAMESPACE
@@ -6,6 +6,7 @@ export(checkpointRemove)
 export(getAccessDate)
 export(getValidSnapshots)
 export(mranUrl)
+export(scanForPackages)
 export(setSnapshot)
 export(unCheckpoint)
 importFrom(utils,Stangle)

diff --git a/R/checkpoint.R b/R/checkpoint.R
@@ -114,11 +114,11 @@ checkpoint <- function(snapshotDate, project = getwd(),
     }
   }
 
-  authorizeFileSystemUse(checkpointLocation)
-
   fixRstudioBug()
 
+
   # Create checkpoint folders
+  authorizeFileSystemUse(checkpointLocation)
   if(!createFolders(snapshotDate = snapshotDate, 
                     checkpointLocation = checkpointLocation))
     stop("Unable to create checkpoint folders at checkpointLocation = \"",
@@ -152,9 +152,10 @@ checkpoint <- function(snapshotDate, project = getwd(),
   if(isTRUE(scanForPackages)){
     mssg(verbose, "Scanning for packages used in this project")
     pkgs <- scanForPackages(project, use.knitr = use.knitr, 
-                                scan.rnw.with.knitr = scan.rnw.with.knitr,
-                                auto.install.knitr = auto.install.knitr
-                                )
+                            scan.rnw.with.knitr = scan.rnw.with.knitr,
+                            auto.install.knitr = auto.install.knitr,
+                            verbose = verbose
+    )
     packages.detected <- pkgs[["pkgs"]]
     mssg(verbose, "- Discovered ", length(packages.detected), " packages")
 

diff --git a/R/checkpoint_internals.R b/R/checkpoint_internals.R
@@ -2,7 +2,9 @@
 setMranMirror <- function(
   snapshotDate, 
   snapshotUrl = checkpoint:::getSnapshoturl(/sitelet?url=https%3A%2F%2Fgithub.com%2FRevolutionAnalytics%2Fcheckpoint%2Fpull%2F246%2FsnapshotDate)){
-  options(repos = snapshotUrl)}
+  options(repos = snapshotUrl)
+}
+
 
 setLibPaths <- function(checkpointLocation, libPath){
   newLoc <- c(libPath, 

diff --git a/R/checkpoint_log.R b/R/checkpoint_log.R
@@ -42,4 +42,4 @@ checkpoint_log <- function(log, snapshotDate, pkg, file = NULL){
       )
     }
   }
-}  
+}
diff --git a/R/checkpoint_paths.R b/R/checkpoint_paths.R
@@ -47,7 +47,8 @@ file.path <- function(...){
 
 # If the folder doesn't exists, ask user permission to create it
 # The argument interactive is purely for testing purposes
-authorizeFileSystemUse <- function(checkpointLocation, interactive = interactive()) {
+authorizeFileSystemUse <- function(checkpointLocation = "~/", 
+                                   interactive = base::interactive()) {
   checkpointRoot = file.path(checkpointLocation, ".checkpoint")
   if(file.exists(checkpointRoot)) {
     if(!file.info(checkpointRoot)$isdir)

diff --git a/R/scanRepoPackages.R b/R/scanRepoPackages.R
@@ -5,10 +5,18 @@ projectScanPackages <- function(...){
   scanForPackages(...)
 }
 
+#' Scans a project (or folder) for references to packages.
+#' 
+#' @inheritParams checkpoint
+#' @return A list with two elements:
+#' * pkgs: a character vector with the names of identified packages
+#' * error: a character vector with information about files that could not be parsed
+#' @export
 scanForPackages <- function(project = getwd(), verbose = TRUE, 
-                                use.knitr = FALSE, 
-                                auto.install.knitr = FALSE, 
-                                scan.rnw.with.knitr = FALSE){
+                            use.knitr = FALSE, 
+                            auto.install.knitr = FALSE, 
+                            scan.rnw.with.knitr = FALSE
+                          ){
   # detect all package dependencies for a project
   dir <- normalizePath(project, winslash='/', mustWork=FALSE)
   pattern <- if(!use.knitr) "\\.[rR]$|\\.[rR]nw$" else

diff --git a/man/scanForPackages.Rd b/man/scanForPackages.Rd
diff --git a/tests/testthat/test-3-checkpoint.R b/tests/testthat/test-3-checkpoint.R
@@ -11,7 +11,8 @@ test.start <- switch(current.R,
                      "3.1" = "2014-10-01",
                      "3.2" = "2015-05-01",
                      "3.3" = "2016-04-01",
-                     "2016-04-01"
+                     "3.4" = "2017-04-24",
+                     "2017-04-24"
 )
 
 MRAN.default = test.start[1] # ensure only a single value

diff --git a/vignettes/using-checkpoint-with-knitr.Rmd → ...s/archive/using-checkpoint-with-knitr.Rmd b/vignettes/using-checkpoint-with-knitr.Rmd → ...s/archive/using-checkpoint-with-knitr.Rmd
@@ -17,31 +17,42 @@ vignette: >
 
 Sometimes you want to use create a report using `markdown`, and you want to `checkpoint` the code in this document.
 
-However, running this as part of a `RMarkdown` process is problematic, since the knitting process runs inside a temporary folder that is different from the current working directory.
+However, running this as part of a `R Markdown` process is problematic, since the knitting process runs inside a temporary folder that is different from the current working directory.
 
 To resolve this, I propose a hacky solution: create a "manifest" file in the same folder that contains all of the `library()` calls.
 
 # Example
 
-Imagine you have a small script that you want to put in an Rmarkdown document with a checkpoint.
+Imagine you have a small script that you want to put in an R Markdown document with a checkpoint.
 
 ```r
 # demo script
-library(MASS)
-hist(islands)
+# Example from ?darts
+library(darts)
+x = c(12,16,19,3,17,1,25,19,17,50,18,1,3,17,2,2,13,18,16,2,25,5,5,
+      1,5,4,17,25,25,50,3,7,17,17,3,3,3,7,11,10,25,1,19,15,4,1,5,12,17,16,
+      50,20,20,20,25,50,2,17,3,20,20,20,5,1,18,15,2,3,25,12,9,3,3,19,16,20,
+      5,5,1,4,15,16,5,20,16,2,25,6,12,25,11,25,7,2,5,19,17,17,2,12)
+mod = simpleEM(x, niter=100)
+e = simpleExpScores(mod$s.final)
+oldpar <- par(mfrow=c(1, 2))
+drawHeatmap(e)
+drawBoard(new=TRUE)
+drawAimSpot(e, cex = 5)
+par(oldpar)
 ```
 
 # The checkpoint solution
 
-The only way I've found to get `checkpoint()` to work inside an RMardown document, is really a bit of a hack. The workaround is to create a manifest of required packages, and write this to an R file in the working directory.
+The only way I've found to get `checkpoint()` to work inside an R Markdown document, is really a bit of a hack. The workaround is to create a manifest of required packages, and write this to an R file in the working directory.
 
-For example, imagine your R script uses the `MASS` package, then create a manifest file like this:
+For example, imagine your R script uses the `darts` package, then create a manifest file like this:
 
 ```{r, echo=FALSE, comment=""}
 cat("```{r, include=FALSE}", '
 # write a manifest to local folder
 cat("
-library(MASS)
+library(darts)
 ",
 file = "manifest.R")
 ', "```", sep = "")
@@ -55,10 +66,12 @@ Once this is done, the checkpoint process from here is straight-forward
 
 
 ```{r, echo=FALSE, comment=""}
+oldLibPaths <- .libPaths()
+
 cat("```{r, include=FALSE}", '
 # Create .checkpoint folder (in tempdir for this example)
 td <- tempdir()
-dir.create(file.path(td, ".checkpoint"), recursive = TRUE)
+dir.create(file.path(td, ".checkpoint"), recursive = TRUE, showWarnings = FALSE)
 
 # Create the checkpoint
 library(checkpoint)
@@ -73,12 +86,13 @@ Now you are ready to put these instructions in an actual code block to see what
 ```{r checkpoint, warning=FALSE}
 # write a manifest to local folder
 cat('
-library(MASS)
+library(darts)
 ',
 file = "manifest.R")
 
 # Create .checkpoint folder (in tempdir for this example)
-dir.create(file.path(tempdir(), ".checkpoint"), recursive = TRUE)
+dir.create(file.path(tempdir(), ".checkpoint"), recursive = TRUE, showWarnings = FALSE)
+options(install.packages.compile.from.source = "no")
 
 # Create the checkpoint
 library(checkpoint)
@@ -87,7 +101,7 @@ checkpoint("2017-03-28", checkpointLocation = tempdir())
 ```
 
 
-If this worked, you should see that the library path now points to `tempdir()` and that MASS should be one of only a few package installed:
+If this worked, you should see that the library path now points to `tempdir()` and that `darts` is one of only a few package installed:
 
 ```{r, eval=FALSE}
 .libPaths()
@@ -103,21 +117,33 @@ installed.packages()[, "Package"]
 
 Now your real R code follows, and it creates the plot, as expected:
 
-```{r, warning=FALSE}
-library(MASS)
-hist(islands)
+```{r, warning=FALSE, fig.asp=4/3}
+# Example from ?darts
+library(darts)
+x = c(12,16,19,3,17,1,25,19,17,50,18,1,3,17,2,2,13,18,16,2,25,5,5,
+      1,5,4,17,25,25,50,3,7,17,17,3,3,3,7,11,10,25,1,19,15,4,1,5,12,17,16,
+      50,20,20,20,25,50,2,17,3,20,20,20,5,1,18,15,2,3,25,12,9,3,3,19,16,20,
+      5,5,1,4,15,16,5,20,16,2,25,6,12,25,11,25,7,2,5,19,17,17,2,12)
+mod = simpleEM(x, niter=100)
+e = simpleExpScores(mod$s.final)
+oldpar <- par(mfrow=c(1, 2))
+drawHeatmap(e)
+drawBoard(new=TRUE)
+drawAimSpot(e, cex = 5)
+par(oldpar)
 ```
 
 # Conclusion
 
-This is a bit of a hack, but points in a direction for getting your RMarkdown script to be checkpointed.
+This is a bit of a hack, but points in a direction for getting your R Markdown script to be checkpointed.
 
 
-```{r, include=FALSE}
+```{r, include=TRUE}
 # clean up
 
-detach("package:MASS", unload = TRUE)
+detach("package:darts", unload = TRUE)
 unlink("manifest.R")
 unlink(file.path(tempdir(), ".checkpoint"), recursive = TRUE)
-unCheckpoint()
+unCheckpoint(oldLibPaths)
+.libPaths()
 ```
diff --git a/vignettes/checkpoint.Rmd b/vignettes/checkpoint.Rmd
@@ -96,9 +96,19 @@ For example, your script may look like this:
 library(checkpoint)
 checkpoint("2015-04-26", checkpointLocation = tempdir())
 
-library(MASS)
-hist(islands)
-truehist(islands)
+# Example from ?darts
+library(darts)
+x = c(12,16,19,3,17,1,25,19,17,50,18,1,3,17,2,2,13,18,16,2,25,5,5,
+      1,5,4,17,25,25,50,3,7,17,17,3,3,3,7,11,10,25,1,19,15,4,1,5,12,17,16,
+      50,20,20,20,25,50,2,17,3,20,20,20,5,1,18,15,2,3,25,12,9,3,3,19,16,20,
+      5,5,1,4,15,16,5,20,16,2,25,6,12,25,11,25,7,2,5,19,17,17,2,12)
+mod = simpleEM(x, niter=100)
+e = simpleExpScores(mod$s.final)
+oldpar <- par(mfrow=c(1, 2))
+drawHeatmap(e)
+drawBoard(new=TRUE)
+drawAimSpot(e, cex = 5)
+par(oldpar)
 ```
 
 
@@ -107,10 +117,11 @@ truehist(islands)
 Next you want to run the script.  Here is what `checkpoint` does:
 
 
-```{r setup, include=FALSE}
+```{r setup, include=FALSE, fig.asp=4/3}
 
 ## Create temporary project and set working directory
 
+
 example_project <- tempdir()
 
 dir.create(example_project, recursive = TRUE, showWarnings = FALSE)
@@ -124,9 +135,19 @@ example_code <- '
 library(checkpoint)
 checkpoint("2015-04-26", checkpointLocation = tempdir())
 
-library(MASS)
-hist(islands)
-truehist(islands)
+# Example from ?darts
+library(darts)
+x = c(12,16,19,3,17,1,25,19,17,50,18,1,3,17,2,2,13,18,16,2,25,5,5,
+      1,5,4,17,25,25,50,3,7,17,17,3,3,3,7,11,10,25,1,19,15,4,1,5,12,17,16,
+      50,20,20,20,25,50,2,17,3,20,20,20,5,1,18,15,2,3,25,12,9,3,3,19,16,20,
+      5,5,1,4,15,16,5,20,16,2,25,6,12,25,11,25,7,2,5,19,17,17,2,12)
+mod = simpleEM(x, niter=100)
+e = simpleExpScores(mod$s.final)
+oldpar <- par(mfrow=c(1, 2))
+drawHeatmap(e)
+drawBoard(new=TRUE)
+drawAimSpot(e, cex = 5)
+par(oldpar)
 '
 
 cat(example_code, file = file.path(example_project, "checkpoint_example_code.R"))
@@ -137,12 +158,13 @@ cat(example_code, file = file.path(example_project, "checkpoint_example_code.R")
 ## Create a folder to contain the checkpoint
 ## This is optional - the default is to use ~/.checkpoint
 
-dir.create(file.path(tempdir(), ".checkpoint"), recursive = TRUE)
+dir.create(file.path(tempdir(), ".checkpoint"), recursive = TRUE, showWarnings = FALSE)
 
 ## Create a checkpoint by specifying a snapshot date
 
 library(checkpoint)
-checkpoint("2017-04-01", project = example_project, checkpointLocation = tempdir())
+checkpoint("2017-04-01", project = example_project, 
+           checkpointLocation = tempdir())
 ```
 
 ### Inspecting the results
@@ -168,12 +190,13 @@ installed.packages(.libPaths()[1])[, "Package"]
 ```
 
 
-```{r cleanup, include=FALSE}
+```{r cleanup, include=TRUE}
 ## cleanup
 
 unlink(example_project, recursive = TRUE)
 unlink(file.path(tempdir(), "checkpoint_example_code.R"))
 unlink(file.path(tempdir(), ".checkpoint"), recursive = TRUE)
 options(repos = oldRepos)
-unCheckpoint()
+unCheckpoint(oldLibPaths)
+.libPaths()
 ```
-Original file line number
+Diff line change
@@ Expand Up @@
           )
         }
       }
-    }
+    }