make vignette static

Author: hongooi73

vignettes/checkpoint.Rmd

@@ -83,7 +83,7 @@ To create a checkpoint project, you do:
 
     ```r
     library(checkpoint)
-    checkpoint("2015-04-26", checkpointLocation = tempdir())
+    checkpoint("<checkpoint date>", checkpointLocation = tempdir())
     ```
 
 4. Run the script.
@@ -94,7 +94,7 @@ For example, your script may look like this:
 
 ```r
 library(checkpoint)
-checkpoint("2015-04-26", checkpointLocation = tempdir())
+checkpoint("2017-04-01")
 
 # Example from ?darts
 library(darts)
@@ -116,45 +116,7 @@ par(oldpar)
 
 Next you want to run the script.  Here is what `checkpoint` does:
 
-
-```{r setup, include=FALSE, fig.asp=4/3}
-
-## Create temporary project and set working directory
-
-
-example_project <- tempfile(pattern="proj")
-
-dir.create(example_project, recursive = TRUE, showWarnings = FALSE)
-oldRepos <- getOption("repos")
-oldLibPaths <- .libPaths()
-
-
-## Write dummy code file to project
-
-example_code <- '
-library(checkpoint)
-checkpoint("2015-04-26", checkpointLocation = tempdir())
-
-# 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"))
-
-```
-
-```{r checkpoint, warning=FALSE}
+```r
 ## Create a folder to contain the checkpoint
 ## This is optional - the default is to use ~/.checkpoint
 
@@ -167,36 +129,47 @@ checkpoint("2017-04-01", project = example_project,
            checkpointLocation = tempdir())
 ```
 
+```
+## Scanning for packages used in this project
+## - Discovered 2 packages
+## Installing packages used in this project
+##  - Installing 'darts'
+## darts
+## Package which is only available in source form, and may need
+##   compilation of C/C++/Fortran: 'darts'
+## installing the source package 'darts'
+## checkpoint process complete
+## ---
+```
+
 ### Inspecting the results
 
 Now inspect the results. First, check that your CRAN mirror is set to MRAN snapshot:
 
 
-```{r inspect-1}
+```r
 getOption("repos")
 ```
-
+```
+## [1] "https://mran.microsoft.com/snapshot/2017-04-01"
+```
 
 Next, check that the library path is set to `~/.checkpoint`:
 
-```{r inspect-2}
+```r
 normalizePath(.libPaths(), winslash = "/")
 ```
+```
+## [1] "C:/Users/hongo/AppData/Local/Temp/RtmpEPckx0/.checkpoint/2017-04-01/lib/x86_64-w64-mingw32/3.6.1"
+## [2] "C:/Users/hongo/AppData/Local/Temp/RtmpEPckx0/.checkpoint/R-3.6.1"                                
+## [3] "C:/Program Files/R/R-3.6.1/library"
+```
 
 Finally, check which packages are installed in checkpoint library:
 
-```{r inspect-3, eval=FALSE}
+```r
 installed.packages(.libPaths()[1])[, "Package"]
 ```
-
-
-```{r cleanup, include=TRUE}
-## cleanup
-
-unlink(example_project, recursive = TRUE)
-unlink(file.path(example_project, "checkpoint_example_code.R"))
-unlink(file.path(tempdir(), ".checkpoint"), recursive = TRUE)
-options(repos = oldRepos)
-unCheckpoint(oldLibPaths)
-.libPaths()
+```
+## [1] "darts"
 ```