From 8ddcfcc2536f49830d0e9e604b3ed6903b05f3df Mon Sep 17 00:00:00 2001
From: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: Mon, 9 Jan 2023 21:37:21 +0000
Subject: [PATCH] update docs for size limit checks for data files, closes #167
 and #67

---
 NEWS                    | 2 ++
 R/checks.R              | 7 ++++---
 vignettes/BiocCheck.Rmd | 4 +++-
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/NEWS b/NEWS
index b0caf966..1a84736d 100644
--- a/NEWS
+++ b/NEWS
@@ -3,6 +3,8 @@ CHANGES IN VERSION 1.36.0
 
 NEW FEATURES
 
+    o Include size limit checks for data files in `data`, `inst/extdata`, and
+    `data-raw` folders (@lshep, #167, #67)
     o Source package directories that include an `inst/doc` folder with files
     are now flagged with an error. `doc` folders are generated during
     `R CMD build`.
diff --git a/R/checks.R b/R/checks.R
index 7a57c47e..bf5cea79 100644
--- a/R/checks.R
+++ b/R/checks.R
@@ -177,8 +177,9 @@ checkIndivFileSizes <- function(pkgdir)
 {
     largefiles <- .findLargeFiles(pkgdir, data_only = FALSE)
     if (length(largefiles))
-        handleWarningFiles(
-            "The 5MB size limit was exceeded in package files.",
+        handleWarning(
+            "Package files exceed the 5MB size limit.",
+            help_text = "Files over the limit: ",
             messages = largefiles
         )
 }
@@ -187,7 +188,7 @@ checkDataFileSizes <- function(pkgdir) {
     largedata <- .findLargeFiles(pkgdir, data_only = TRUE)
     if (length(largedata))
         handleWarning(
-            "The 5MB size limit was exceeded in data files.",
+            "Data files exceed the 5MB size limit.",
             help_text =
                 "Use 'ExperimentHub' or 'AnnotationHub' for the files: ",
             messages = largedata
diff --git a/vignettes/BiocCheck.Rmd b/vignettes/BiocCheck.Rmd
index 75623e6b..3ce568c9 100644
--- a/vignettes/BiocCheck.Rmd
+++ b/vignettes/BiocCheck.Rmd
@@ -158,7 +158,9 @@ Can be disabled with `--no-check-pkg-size` and `--no-check-file-size`.
   checking a source tarball. (ERROR)
 
 * **Checking individual file sizes**
-  The current size limit for all individual files is 5 MB. (WARNING)
+  The current size limit for all individual files is 5 MB. Checks inspect both
+  package-wide files and data files found in the `data`, `inst/extdata`, and
+  `data-raw` folders. (WARNING)
 
 It may be necessary to remove large files from your Git history; see
 [Remove Large Data Files and Clean Git Tree][3.1]