Fix small issues to pass R CMD check

Author: andrie

R/checkpoint.R

@@ -21,7 +21,7 @@
 #' 
 #' @section Changing the default MRAN url:
 #' 
-#' \code{checkpoint} uses https by default to download packages (see \url{https://www.r-consortium.org/news/blogs/2015/08/best-practices-using-r-securely}).
+#' \code{checkpoint} uses https by default to download packages (see \url{https://www.r-consortium.org/blog/2015/08/17/best-practices-for-using-r-securely}).
 #' \code{checkpoint} Defaults to \url{https://mran.microsoft.com/snapshot} by default in R versions 3.2.0 and later, if https support is enabled.
 #' 
 #' You can modify the default URL. To change the URL, use \code{options(checkpoint.mranUrl = ...)}

R/checkpoint_log.R

@@ -9,8 +9,6 @@ checkpoint_log <- function(log, snapshotDate, pkg, file = NULL){
     z <- gsub(ptn, "\\2", log[grep(ptn, log)])
     z <- iconv(z, to = "ASCII", sub = "") # strip quotin
     if(length(z) == 0) return(z)
-    # z <- gsub("[‘’'`‘\"]*", "", z, useBytes = FALSE)
-    # z <- gsub("[‘’'`‘\"]*", "", z, useBytes = TRUE)
     strsplit(z, ", ")[[1]]
   }
 

man/checkpoint.Rd

@@ -0,0 +1,61 @@
+## ---- eval=FALSE---------------------------------------------------------
+#  library(checkpoint)
+#  checkpoint("2015-04-26", checkpointLocation = tempdir())
+
+## ---- eval=FALSE---------------------------------------------------------
+#  library(checkpoint)
+#  checkpoint("2015-04-26", checkpointLocation = tempdir())
+#  
+#  library(MASS)
+#  hist(islands)
+#  truehist(islands)
+
+## ----setup, include=FALSE------------------------------------------------
+
+## Create temporary project and set working directory
+
+example_project <- tempdir()
+
+dir.create(example_project, recursive = TRUE)
+unlink("~/.checkpoint/2015-04-26", recursive=TRUE)
+oldRepos <- getOption("repos")
+oldLibPaths <- .libPaths()
+
+
+## Write dummy code file to project
+
+example_code <- '
+library(checkpoint)
+checkpoint("2015-04-26", checkpointLocation = tempdir())
+
+library(MASS)
+hist(islands)
+truehist(islands)
+'
+
+cat(example_code, file = file.path(example_project, "checkpoint_example_code.R"))
+
+
+## ----checkpoint----------------------------------------------------------
+## Create a checkpoint by specifying a snapshot date
+
+library(checkpoint)
+dir.create(file.path(tempdir(), ".checkpoint"))
+checkpoint("2015-04-26", project = example_project, checkpointLocation = tempdir())
+
+## ----inspect-1-----------------------------------------------------------
+getOption("repos")
+
+## ----inspect-2-----------------------------------------------------------
+normalizePath(.libPaths(), winslash = "/")
+
+## ----inspect-3-----------------------------------------------------------
+installed.packages()[, "Package"]
+
+## ----cleanup, include=FALSE----------------------------------------------
+## cleanup
+
+unlink(example_project, recursive = TRUE)
+options(repos = oldRepos)
+.libPaths(oldLibPaths)
+

vignettes/checkpoint.R

@@ -23,7 +23,7 @@ RRT is a collection of R packages and the checkpoint server that together make y
 
 ### The checkpoint server
 
-To achieve reproducibility, daily snapshots of CRAN are stored on our checkpoint server. At midnight UTC each day, our [mirror](http://cran.revolutionanalytics.com/) of Austria CRAN is refreshed. When the rsync process is complete, the checkpoint server takes and stores a snapshot of the CRAN mirror as it was at that very moment. These daily snapshots can then be accessed on the [MRAN website](http://mran.microsoft.com/snapshot) or using the `checkpoint` package, which installs and consistently use these packages just as they existed at midnight UTC on a specified snapshot date. Daily snapshots are available as far back as `2014-09-17`. For more information, visit the [checkpoint server GitHub site](https://github.com/RevolutionAnalytics/checkpoint-server).
+To achieve reproducibility, daily snapshots of CRAN are stored on our checkpoint server. At midnight UTC each day, our [mirror](http://mran.microsoft.com/) of Austria CRAN is refreshed. When the rsync process is complete, the checkpoint server takes and stores a snapshot of the CRAN mirror as it was at that very moment. These daily snapshots can then be accessed on the [MRAN website](http://mran.microsoft.com/snapshot) or using the `checkpoint` package, which installs and consistently use these packages just as they existed at midnight UTC on a specified snapshot date. Daily snapshots are available as far back as `2014-09-17`. For more information, visit the [checkpoint server GitHub site](https://github.com/RevolutionAnalytics/checkpoint-server).
 
 ![checkpoint server](checkpoint-server.png)