Move rmarkdown::render action to happen in a temp directory (#330)

Author: bburns632

NEWS.md

@@ -4,6 +4,7 @@
 ## CHANGES  
 
 ## BUGFIXES
+* Moved `rmarkdown::render` interium files to occur within a temp directory, not the installed package directory (#329 Thanks @jcarbaut!) 
 
 # pkgnet 0.5.0
 ## NEW FEATURES

R/CreatePackageReport.R

@@ -67,13 +67,28 @@ PackageReport <- R6::R6Class(
         , render_report = function() {
             log_info("Rendering package report...")
 
+            # copy Rmd files to temp directory to avoid writing interim files to package repo
+            tmp_dir <- tempfile("package_report") # subdir within temp directory
+            tmp_package_report_rmd <- file.path(tmp_dir, "package_report.Rmd")
+
+            orig_package_report_rmd <- system.file(file.path("package_report", "package_report.Rmd"), package = "pkgnet")
+            orig_files <- list.files(dirname(orig_package_report_rmd), full.names = TRUE)
+
+            dir.create(tmp_dir)
+            file.copy(
+                from = orig_files,
+                to = tmp_dir,
+                recursive = TRUE,
+                overwrite = TRUE
+            )
+
+            # render report
             rmarkdown::render(
-                input = system.file(
-                    file.path("package_report", "package_report.Rmd")
-                    , package = "pkgnet"
-                )
+                input = tmp_package_report_rmd
                 , output_dir = dirname(self$report_path)
                 , output_file = basename(self$report_path)
+                , intermediates_dir = tmp_dir
+                , knit_root_dir = tmp_dir
                 , quiet = TRUE
                 , params = list(
                     reporters = private$reporters
@@ -86,6 +101,9 @@ PackageReport <- R6::R6Class(
                 , sprintf("It is available at %s", self$report_path)
             ))
 
+            # Clean up tmp
+            unlink(tmp_dir, recursive = TRUE)
+
             # If suppress flag is unset, then env variable will be emptry string ""
             if (identical(Sys.getenv("PKGNET_SUPPRESS_BROWSER"), "")) {
                 utils::browseURL(self$report_path)

R/testing_utils.R

@@ -104,3 +104,29 @@
 
     return(invisible(TRUE))
 }
+
+
+# Get Files with Modification Date after a specific date
+# Used to provide more verbose logging in the event package directory is modified.
+# Will not list files created and deleted in the interium but it helps.
+.printModifiedFiles <- function(dir_path, after_posixct){
+    file_list <- list.files(
+        path = dir_path,
+        full.names = TRUE
+    )
+
+    print(sprintf("FILE INFO FOR UPDATES AFTER %s", as.character(after_posixct)))
+    for (file in file_list){
+        info <- as.list(file.info(file))
+        if (info['mtime'] > after_posixct){
+            msg <- sprintf(
+                "%s %s %s %s",
+                file,
+                info['mtime'],
+                info['mode'],
+                info['isdir']
+            )
+            print(msg)
+        }
+    }
+}

tests/testthat/test-0-test-package-installation.R

@@ -12,4 +12,9 @@ test_that('Test packages installed correctly',{
             , info = sprintf("Test package %s is not installed.", thisTestPkg)
         )
     }
-})
+})
+
+# Record modifaction time of package directory to be checked at end of testing 
+# in test-Z-test-no-source-modifcations.R
+tmp_pkgnet_path <- file.path(Sys.getenv('PKGNET_TEST_LIB'), 'pkgnet')
+Sys.setenv(PKGNET_LATEST_MOD = as.character(file.info(tmp_pkgnet_path)$mtime))

tests/testthat/test-Z-test-no-source-modifcations.R

@@ -0,0 +1,21 @@
+# Inditended to be run last, this is to confirm that no files 
+# within the package directory are modified during the normal 
+# operation of pkgnet during these tests.  This includes the 
+# creation and deletion of temp files for rendering. 
+
+test_that('No modification to pkgnet directory during testing',{
+    startModTime <- as.POSIXct(Sys.getenv('PKGNET_LATEST_MOD'))
+    
+    tmp_pkgnet_path <- file.path(Sys.getenv('PKGNET_TEST_LIB'), 'pkgnet')
+    currentModTime <- file.info(tmp_pkgnet_path)$mtime
+
+    if (as.character(startModTime) != as.character(currentModTime)){
+        pkgnet:::.printModifiedFiles(tmp_pkgnet_path, startModTime)
+    }
+
+    expect_equal(object = currentModTime
+                 , expected = startModTime
+                 , info = "The source directory was modified during the execution of tests."
+                 )
+
+})