From 46aa92a94f9d102ed48c5662998aa08db38e0a21 Mon Sep 17 00:00:00 2001
From: Kent Riemondy <kent.riemondy@gmail.com>
Date: Fri, 27 Dec 2024 08:10:54 -0700
Subject: [PATCH] rtracklayer is available on Bioc, clarify NEWS and
 deprecation messages.

---
 NEWS.md      |  4 +++-
 R/read_bed.r | 18 ++++++++++++------
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 944cec90..b97a807b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,8 @@
 # valr (development version)
 
-* `read_bigwig()` and `read_gtf()` were deprecated as rtracklayer is no longer avilable on CRAN.
+* `read_bigwig()` and `read_gtf()` were deprecated. The rtracklayer package used
+for this functionality is no longer a dependency of valr due to errors from 
+CRAN AddressSantizer checks of the UCSC c-library code vendored in rtracklayer.
 
 * valr now depends on R >= 4.0.0.
 
diff --git a/R/read_bed.r b/R/read_bed.r
index cedab7a1..371e0a2c 100644
--- a/R/read_bed.r
+++ b/R/read_bed.r
@@ -201,12 +201,14 @@ read_bigwig <- function(path, set_strand = "+") {
     what = "read_bigwig()",
     details = c(
       x = paste0(
-        "read_bigwig() was removed because rtracklayer is",
-        "no longer available on CRAN"
+        "read_bigwig() was removed because rtracklayer does not pass ",
+        "CRAN AddressSantizer checks of the UCSC C-library code vendored ",
+        "in rtracklayer."
       ),
       i = paste0(
         "use `bigWigToBedGraph` to convert bw to bedGraph,",
-        "and then `read_bedgraph()`."
+        " and then `read_bedgraph()`. Alternatively use ",
+        "`rtracklayer::import()` then `gr_to_bed()`."
       )
     )
   )
@@ -238,10 +240,14 @@ read_gtf <- function(path, zero_based = TRUE) {
     what = "read_gtf()",
     details = c(
       x = paste0(
-        "read_gtf() was removed because rtracklayer is",
-        "no longer available on CRAN"
+        "read_gtf() was removed because rtracklayer does not pass ",
+        "CRAN AddressSantizer checks of the UCSC C-library code vendored ",
+        "in rtracklayer."
       ),
-      i = "convert GTF to BED, and then `read_bed()`."
+      i = paste0(
+        "convert GTF to BED, and then `read_bed()`, ",
+        "or use `rtracklayer::import()` then `gr_to_bed()`."
+      )
     )
   )
 }