update docs for size limit checks for data files, closes #167 and #67

Bioconductor · Jan 9, 2023 · 8ddcfcc · 8ddcfcc
1 parent 8562ad6
commit 8ddcfcc
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Showing 3 changed files with 9 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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]