add additional deprecation functions to the list

Bioconductor · Nov 1, 2024 · 604e56c · 604e56c
1 parent cb9fcb7
commit 604e56c
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Showing 2 changed files with 10 additions and 5 deletions.
diff --git a/R/checkRcoding.R b/R/checkRcoding.R
@@ -132,7 +132,12 @@ checkCodingPractice <- function(.BiocPackage, parsedCode)
 
     # .Deprecated / .Defunct usage should be updated after every release
     msg_depr <- findSymbolsInRFiles(
-        .BiocPackage, c(".Deprecated", ".Defunct"), "SYMBOL_FUNCTION_CALL"
+        .BiocPackage,
+        c(
+            ".Deprecated", ".Defunct", "lifeCycle",
+            "deprecate_warn", "deprecate_stop"
+        ),
+        "SYMBOL_FUNCTION_CALL"
     )
     if (length(msg_depr)) {
         handleWarning(

diff --git a/vignettes/BiocCheck.Rmd b/vignettes/BiocCheck.Rmd
@@ -413,10 +413,10 @@ directory.
   ('=') for clarity in the code and legibility. Any use of the `=` will be
   flagged with a `NOTE`.
 
-* New submissions should not use any `.Deprecated` or `.Defunct` function calls
-  (`WARNING`). Existing packages should evolve `.Deprecated` and `.Defunct`
-  functions after a Bioconductor release according to the
-  [package guidelines][6].
+* New submissions should not use any `.Deprecated`, `.Defunct`, `lifeCycle`,
+  `deprecate_warn`, or `deprecate_stop` function calls (`WARNING`). Existing
+  packages should evolve these functions after a Bioconductor release according
+  to the [package guidelines][6].
 
 [6]: https://contributions.bioconductor.org/deprecation.html