fix #1812: when render(run_pandoc = FALSE), exclude the .md output fi…

…le and associated figure files from the list of intermediate files, so they won't be cleaned up

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rmarkdown
 Type: Package
 Title: Dynamic Documents for R
-Version: 2.1.9
+Version: 2.1.10
 Authors@R: c(
   person("JJ", "Allaire", role = "aut", email = "[email protected]"),
   person("Yihui", "Xie", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-0645-5666")),

NEWS.md

@@ -27,6 +27,8 @@ rmarkdown 2.2
 
 - For `pandoc_convert()`, when the argument `to = 'pdf'`, it will be changed to `'latex'` internally (thanks, @JohannesFriedrich, #1802).
 
+- `render(run_pandoc = FALSE)` no longer cleans up the Markdown file (typically knitted from Rmd) (thanks, @BrianDiggs, #1812).
+
 
 rmarkdown 2.1
 ================================================================================

R/render.R

@@ -780,23 +780,21 @@ render <- function(input,
   # the knitr cache is active; clean the figure-* dir instead of the whole
   # files_dir if other subdirs are generated by another format and still needed:
   # https://github.com/rstudio/rmarkdown/issues/1472 and also #1503
-  if (output_format$clean_supporting && !dir_exists(cache_dir)) {
+  intermediates_fig <- if (output_format$clean_supporting && !dir_exists(cache_dir)) {
     # unlink does not support / at the end of file path
     fig_path <- gsub("/$", "", knitr::opts_chunk$get('fig.path'))
 
     # existing figure folder(s), can be character(0)
     # if no figure is generated, clean the whole files_dir (#1664)
     files_dir_fig <- list.files(files_dir, '^figure-.+')
 
-    intermediates <- c(
-      intermediates,
-      if (length(files_dir_fig) < 1 || identical(files_dir_fig, basename(fig_path))) {
-        files_dir
-      } else {
-        fig_path
-      }
-    )
+    if (length(files_dir_fig) < 1 || identical(files_dir_fig, basename(fig_path))) {
+      files_dir
+    } else {
+      fig_path
+    }
   }
+  intermediates <- c(intermediates, intermediates_fig)
 
   file.copy(input, utf8_input, overwrite = TRUE)
 
@@ -968,6 +966,8 @@ render <- function(input,
       attr(output_file, 'rmd_output_metadata') <- output_meta
     invisible(output_file)
   } else {
+    # make sure the markdown output and fig dir are not cleaned up
+    intermediates <- setdiff(intermediates, c(input, intermediates_fig))
     # did not run pandoc; returns the markdown output with attributes of the
     # knitr meta data and intermediate files
     structure(input, knit_meta = knit_meta, intermediates = intermediates)