From 36c3f0930457eac5677f64547ab0985410e96445 Mon Sep 17 00:00:00 2001
From: pormr <61189905+pormr@users.noreply.github.com>
Date: Tue, 25 Feb 2025 07:06:57 +0000
Subject: [PATCH 1/5] Fix compatiblity issue for comparing versions

---
 R/supercell_2_Seurat.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/supercell_2_Seurat.R b/R/supercell_2_Seurat.R
index 481c72d..4f9a792 100644
--- a/R/supercell_2_Seurat.R
+++ b/R/supercell_2_Seurat.R
@@ -94,7 +94,7 @@ supercell_2_Seurat <- function(SC.GE, SC, fields = c(),
   }
   m.seurat <- Seurat::CreateSeuratObject(counts = SC.GE, meta.data = meta)
   
-  if(packageVersion("Seurat") >= 5){
+  if(packageVersion("Seurat") >= "5"){
     m.seurat[["RNA"]] <- as(object = m.seurat[["RNA"]], Class = "Assay")
   }
   
@@ -173,7 +173,7 @@ supercell_2_Seurat <- function(SC.GE, SC, fields = c(),
     warning("Super-cell graph was not found in SC object, no super-cell graph was added to Seurat object")
   }
   
-  if(packageVersion("Seurat") >= 5 & output.assay.version == "v5"){
+  if(packageVersion("Seurat") >= "5" & output.assay.version == "v5"){
     m.seurat[["RNA"]] <- as(object = m.seurat[["RNA"]], Class = "Assay5")
   }
   return(m.seurat)

From beb9826c4f2be057b5c09f9da8bcb58541b60fdd Mon Sep 17 00:00:00 2001
From: Yufei Chen <61189905+pormr@users.noreply.github.com>
Date: Tue, 17 Mar 2026 15:55:12 +0000
Subject: [PATCH 2/5] Fix Seurat v5 compatibility by setting compatibility mode
 to v3

---
 R/supercell_2_Seurat.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/supercell_2_Seurat.R b/R/supercell_2_Seurat.R
index 4f9a792..c575eee 100644
--- a/R/supercell_2_Seurat.R
+++ b/R/supercell_2_Seurat.R
@@ -92,11 +92,12 @@ supercell_2_Seurat <- function(SC.GE, SC, fields = c(),
   if(length(SC.fields) > 0){
     meta <- cbind(meta, SC.fields)
   }
-  m.seurat <- Seurat::CreateSeuratObject(counts = SC.GE, meta.data = meta)
   
-  if(packageVersion("Seurat") >= "5"){
-    m.seurat[["RNA"]] <- as(object = m.seurat[["RNA"]], Class = "Assay")
+  if(packageVersion("Seurat") >= 5) {
+    withr::local_options(list(Seurat.object.assay.version = "v3"))
   }
+
+  m.seurat <- Seurat::CreateSeuratObject(counts = SC.GE, meta.data = meta)
   
   if(!do.preproc) return(m.seurat)
   

From 76c2f7d8e2ed47d810abcc257bd304a0ccadbfe7 Mon Sep 17 00:00:00 2001
From: Yufei Chen <61189905+pormr@users.noreply.github.com>
Date: Tue, 17 Mar 2026 15:59:34 +0000
Subject: [PATCH 3/5] Fix regression in previous commit that caused version
 check failure.

---
 R/supercell_2_Seurat.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/supercell_2_Seurat.R b/R/supercell_2_Seurat.R
index c575eee..e55b3a5 100644
--- a/R/supercell_2_Seurat.R
+++ b/R/supercell_2_Seurat.R
@@ -93,7 +93,7 @@ supercell_2_Seurat <- function(SC.GE, SC, fields = c(),
     meta <- cbind(meta, SC.fields)
   }
   
-  if(packageVersion("Seurat") >= 5) {
+  if(packageVersion("Seurat") >= "5.0.0") {
     withr::local_options(list(Seurat.object.assay.version = "v3"))
   }
 

From 94b775fd7511c1912b248c396734431e2402e6c6 Mon Sep 17 00:00:00 2001
From: Yufei Chen <61189905+pormr@users.noreply.github.com>
Date: Wed, 18 Mar 2026 11:10:02 +0000
Subject: [PATCH 4/5] style: update formatting to match existing style

---
 R/supercell_2_Seurat.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/supercell_2_Seurat.R b/R/supercell_2_Seurat.R
index e55b3a5..0fbfda7 100644
--- a/R/supercell_2_Seurat.R
+++ b/R/supercell_2_Seurat.R
@@ -93,7 +93,7 @@ supercell_2_Seurat <- function(SC.GE, SC, fields = c(),
     meta <- cbind(meta, SC.fields)
   }
   
-  if(packageVersion("Seurat") >= "5.0.0") {
+  if(packageVersion("Seurat") >= "5.0.0"){
     withr::local_options(list(Seurat.object.assay.version = "v3"))
   }
 
@@ -174,7 +174,7 @@ supercell_2_Seurat <- function(SC.GE, SC, fields = c(),
     warning("Super-cell graph was not found in SC object, no super-cell graph was added to Seurat object")
   }
   
-  if(packageVersion("Seurat") >= "5" & output.assay.version == "v5"){
+  if(packageVersion("Seurat") >= "5.0.0" & output.assay.version == "v5"){
     m.seurat[["RNA"]] <- as(object = m.seurat[["RNA"]], Class = "Assay5")
   }
   return(m.seurat)

From 69ea74d71dba9ad74a235c48225204ab98b1fd11 Mon Sep 17 00:00:00 2001
From: Yufei Chen <61189905+pormr@users.noreply.github.com>
Date: Wed, 18 Mar 2026 11:28:43 +0000
Subject: [PATCH 5/5] fix: update DESCRIPTION

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1fbd481..5734ef4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -37,6 +37,7 @@ Imports:
     proxy,
     methods,
     rlang,
+    withr,
 RoxygenNote: 7.2.3
 Suggests:
     SingleCellExperiment,