Include tangled source code in tarballs.

git-svn-id: https://svn.r-project.org/R/trunk@62368 00db46b3-68df-0310-9c12-caf00c1e9a41

doc/NEWS.Rd

@@ -625,6 +625,12 @@
       \item Package vignettes can now be processed by other engines
       besides \code{Sweave}; see \sQuote{Writing R Extensions} and the
       \code{tools::vignetteEngine} help topic for details.
+      
+      \item The \file{*.R} tangled \command{R CMD build} source code
+      for vignettes is now included in tarballs when \command{R CMD
+      build} is used to produce them. In \R 3.0.0, missing \file{*.R}
+      files will be produced at install time, but eventually this 
+      will be dropped.
 
       \item The package type \code{"mac.binary"} now results in a path
       without Mac subtype (which used to be \code{"universal"}).  This

src/library/tools/R/admin.R

@@ -521,12 +521,14 @@ function(dir, outDir, encoding = "")
 
 	loadVignetteBuilder(dir, mustwork = FALSE)
 
-        ## install tangled versions of Sweave vignettes.  FIXME:  Custom
-        ## engine vignettes should have been included when the package was built,
+        ## install tangled versions of Sweave vignettes.  FIXME:  Vignette
+        ## *.R files should have been included when the package was built,
         ## but in the interim before they are all built with the new code,
-        ## this is needed for all packages.
+        ## this is needed.
         for(i in seq_along(vigns$docs)) {
             file <- vigns$docs[i]
+            if (!is.null(vigns$sources) && !is.null(vigns$sources[i])) # already there?
+            	next
             file <- basename(file)
             enc <- getVignetteEncoding(file, TRUE)
             if(enc %in% c("non-ASCII", "unknown")) enc <- encoding
@@ -537,6 +539,7 @@ function(dir, outDir, encoding = "")
 	    engine <- try(vignetteEngine(vigns$engines[i]), silent = TRUE)
 	    if (!inherits(engine, "try-error"))
             	engine$tangle(file, quiet = TRUE, encoding = enc)
+            setwd(outVignetteDir) # just in case some strange tangle function changed it
         }
         setwd(cwd)
 

src/library/tools/R/build.R

@@ -344,16 +344,13 @@ get_exclude_patterns <- function()
                     Sys.setenv(R_LIBS = libdir)
                 }
 
-                # If a custom builder is used, we tangle all vignettes now in 
-                # case the tangler is not available at INSTALL time.
-                # We could just tangle the custom ones, but mixed Sweave/custom
-                # vignettes are likely to be rare, and this is simpler
+                # Tangle all vignettes now.  We'll try again at INSTALL time in 3.0.0,
+                # but eventually this is the only place the tangling will happen.
 
-                custom <- !is.na(desc["VignetteBuilder"])
                 cmd <- file.path(R.home("bin"), "Rscript")
                 args <- c("--vanilla",
                           "--default-packages=", # some vignettes assume methods
-                          "-e", shQuote(paste0("tools::buildVignettes(dir = '.', tangle=", custom, ")")))
+                          "-e", shQuote("tools::buildVignettes(dir = '.', tangle = TRUE)"))
                 ## since so many people use 'R CMD' in Makefiles,
                 oPATH <- Sys.getenv("PATH")
                 Sys.setenv(PATH = paste(R.home("bin"), oPATH,
@@ -369,33 +366,15 @@ get_exclude_patterns <- function()
                     vigns <- pkgVignettes(dir = '.', output = TRUE, source = TRUE)
                     stopifnot(!is.null(vigns))
 
-                    if (!custom) {
-			## Do any of the .R files which will be generated at install time
-			## exist in inst/doc?  If so the latter should be removed.
-			sources <- basename(list_files_with_exts(doc_dir, "R"))
-			if (length(sources)) {
-			    new_sources <- unlist(vigns$sources)
-			    dups <- sources[sources %in% new_sources]
-			    if(length(dups)) {
-				warningLog(Log)
-				printLog(Log,
-					 paste(c("  Unused files in inst/doc which are pointless or misleading",
-						 "  as they will be re-created from the vignettes on installation:",
-						 paste("  ", dups),
-						 "  have been removed", ""),
-					       collapse = "\n"))
-				unlink(file.path(doc_dir, dups))
-			    } else resultLog(Log, "OK")
-			} else resultLog(Log, "OK")
-                    } else resultLog(Log, "OK")
+                    resultLog(Log, "OK")
                 }
 
                 ## We may need to install them.
                 if (basename(vigns$dir) == "vignettes") {
                     ## inst may not yet exist
                     dir.create(doc_dir, recursive = TRUE, showWarnings = FALSE)
-                    file.copy(c(vigns$docs, vigns$outputs), doc_dir)
-                    unlink(vigns$outputs)
+                    file.copy(c(vigns$docs, vigns$outputs, unlist(vigns$sources)), doc_dir)
+                    unlink(c(vigns$outputs, unlist(vigns$sources)))
                     extras_file <- file.path("vignettes", ".install_extras")
                     if (file.exists(extras_file)) {
                         extras <- readLines(extras_file, warn = FALSE)