From 88879f8dd79eca7bea5ec622eeecf754156632f8 Mon Sep 17 00:00:00 2001
From: Michael Chirico <michaelchirico4@gmail.com>
Date: Sun, 13 Oct 2024 13:27:40 -0700
Subject: [PATCH 1/2] Fix roxygen2 issue with all/all.equal ambiguity

---
 R/class_anndata.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/class_anndata.R b/R/class_anndata.R
index 7661856..42d5e93 100644
--- a/R/class_anndata.R
+++ b/R/class_anndata.R
@@ -1084,7 +1084,8 @@ t.AnnDataR6 <- function(x) {
 #' Test if two objects objects are equal
 #' @rdname all.equal
 #' @inheritParams base::all.equal
-#' @export
+#' @method all.equal AnnDataR6
+#' @exportS3Method all.equal AnnDataR6
 all.equal.AnnDataR6 <- function(target, current, ...) {
   a <- target
   b <- current

From 700438a297908055d51a7d4a1ff2d5df8be1f7be Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 14 Nov 2024 17:32:14 +0100
Subject: [PATCH 2/2] apply fix to other functions and run roxygen

---
 NAMESPACE        | 6 +++---
 R/class_layers.R | 3 ++-
 R/class_raw.R    | 3 ++-
 man/all.equal.Rd | 6 +++---
 4 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 0b689e7..6d91fd5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,9 +11,9 @@ S3method("[[",collections.abc.Mapping)
 S3method("[[<-",LayersR6)
 S3method("[[<-",collections.abc.MutableMapping)
 S3method("dimnames<-",AnnDataR6)
-S3method(all,equal.AnnDataR6)
-S3method(all,equal.LayersR6)
-S3method(all,equal.RawR6)
+S3method(all.equal,AnnDataR6)
+S3method(all.equal,LayersR6)
+S3method(all.equal,RawR6)
 S3method(as.data.frame,AnnDataR6)
 S3method(as.matrix,AnnDataR6)
 S3method(as.matrix,RawR6)
diff --git a/R/class_layers.R b/R/class_layers.R
index c18fa2f..b31e3ca 100644
--- a/R/class_layers.R
+++ b/R/class_layers.R
@@ -205,7 +205,8 @@ py_to_r.anndata._core.aligned_mapping.LayersBase <- function(x) {
 
 
 #' @rdname all.equal
-#' @export
+#' @method all.equal LayersR6
+#' @exportS3Method all.equal LayersR6
 all.equal.LayersR6 <- function(target, current, ...) {
   a <- target
   b <- current
diff --git a/R/class_raw.R b/R/class_raw.R
index 8235af5..aa455af 100644
--- a/R/class_raw.R
+++ b/R/class_raw.R
@@ -281,7 +281,8 @@ py_to_r.anndata._core.raw.Raw <- function(x) {
 }
 
 #' @rdname all.equal
-#' @export
+#' @method all.equal RawR6
+#' @exportS3Method all.equal RawR6
 all.equal.RawR6 <- function(target, current, ...) {
   a <- target
   b <- current
diff --git a/man/all.equal.Rd b/man/all.equal.Rd
index 0542047..510ea92 100644
--- a/man/all.equal.Rd
+++ b/man/all.equal.Rd
@@ -7,11 +7,11 @@
 \alias{all.equal.RawR6}
 \title{Test if two objects objects are equal}
 \usage{
-\method{all}{equal.AnnDataR6}(target, current, ...)
+\method{all.equal}{AnnDataR6}(target, current, ...)
 
-\method{all}{equal.LayersR6}(target, current, ...)
+\method{all.equal}{LayersR6}(target, current, ...)
 
-\method{all}{equal.RawR6}(target, current, ...)
+\method{all.equal}{RawR6}(target, current, ...)
 }
 \arguments{
 \item{target}{\R object.}