allow to disable overwrite of manifest files

Author: nuest

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: codecheck
 Title: Helper Functions for CODECHECK Project
-Version: 0.0.0.9009
+Version: 0.0.0.9010
 Authors@R: 
     c(person(given = "Stephen",
             family = "Eglen",

R/codecheck.R

@@ -61,11 +61,13 @@ codecheck_metadata <- function(root = getwd()) {
 ##' @param metadata - the codecheck metadata list.
 ##' @param dest_dir - folder where outputs are to be copied to (codecheck/outputs)
 ##' @param keep_full_path - TRUE to keep relative pathname of figures.
+##' @param overwrite - TRUE to overwrite the output files even if they already exist
 ##' @return A dataframe containing one row per manifest file.
 ##' @author Stephen Eglen
 ##' @export
 copy_manifest_files <- function(root, metadata, dest_dir,
-                                keep_full_path = FALSE) {
+                                keep_full_path = FALSE,
+                                overwrite = FALSE) {
   manifest = metadata$manifest
   outputs = sapply(manifest, function(x) x$file)
   src_files = file.path(root, outputs)
@@ -87,8 +89,10 @@ copy_manifest_files <- function(root, metadata, dest_dir,
         dir.create(dir, recursive=TRUE)
     }
   }
-  file.copy(src_files, dest_files, overwrite=TRUE)
-  dest_files
+  
+  if (overwrite) message("Overwriting output files: ", toString(dest_files))
+  file.copy(src_files, dest_files, overwrite = overwrite)
+  
   manifest_df = data.frame(output=outputs,
                            comment=sapply(manifest, function(x) x$comment),
                            dest=dest_files,

inst/extdata/templates/codecheck/codecheck.Rmd

@@ -8,14 +8,14 @@ output:
 ---
 
 ```{r rsetup,eval=TRUE,include=FALSE}
-require(codecheck)
-require(knitr)
-require(rprojroot)
-require(yaml)
-require(xtable)
-require(tibble)
-require(readr)
-options(width=60)
+require("codecheck")
+require("knitr")
+require("rprojroot")
+require("yaml")
+require("xtable")
+require("tibble")
+require("readr")
+options(width = 60)
 opts_chunk$set(cache=FALSE)
 
 root = find_root("codecheck.yml")
@@ -36,7 +36,9 @@ if ( !dir.exists(dest_dir) ) {
 }
 
 manifest_df = copy_manifest_files(root, metadata,
-                                  dest_dir, keep_full_path=FALSE)
+                                  dest_dir, keep_full_path = FALSE,
+                                  overwrite = FALSE,
+                                  )
 ```
 
 ---