From 43f9b883a76c44a1b982b9696d23165901bf3b7a Mon Sep 17 00:00:00 2001
From: Arsham Mikaeili Namini <92790984+Arshammik@users.noreply.github.com>
Date: Wed, 19 Nov 2025 00:42:56 -0500
Subject: [PATCH 1/5] Fixing the CRAN Note "CRAN URL not in canonical form"

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index c132dd6..44f0887 100644
--- a/README.md
+++ b/README.md
@@ -8,8 +8,8 @@
 
 ## **Requirements**
 
--   [R version 3.5.0](http://www.r-project.org/) or later.
--   R libraries: [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html), [RcppArmadillo](https://cran.r-project.org/web/packages/RcppArmadillo/index.html), [Matrix](https://cran.r-project.org/web/packages/Matrix/index.html), [data.table](https://cran.r-project.org/web/packages/data.table/index.html), [R6](https://cran.r-project.org/web/packages/R6/index.html)
+-   [R version 3.5.0](https://r-project.org/) or later.
+-   R libraries: [Rcpp](https://CRAN.R-project.org/package=Rcpp), [RcppArmadillo](https://CRAN.R-project.org/package=RcppArmadillo), [Matrix](https://CRAN.R-project.org/package=Matrix), [data.table](https://CRAN.R-project.org/package=data.table), [R6](https://CRAN.R-project.org/package=R6)
 
 
 ## Installation

From 3e92cd6c341afa41d2209273f0f7aa8eae935916 Mon Sep 17 00:00:00 2001
From: Arsham Mikaeili Namini <92790984+Arshammik@users.noreply.github.com>
Date: Wed, 19 Nov 2025 00:43:26 -0500
Subject: [PATCH 2/5] Fixing CRAN note "Possibly misspelled words in
 DESCRIPTION: scRNA"

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1701095..808d679 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: splikit
-Title: A Toolkit for Analysing RNA Splicing in scRNA-Seq Data
+Title: A Toolkit for Analysing RNA Splicing in Single-cell RNA Sequencing Data
 Version: 2.0.0
 Authors@R:
     person("Arsham", "Mikaeili Namini", , "arsham.mikaeilinamini@mail.mcgill.ca", role = c("aut", "cre"),

From 2a70a78b27d2254322effe2a5c8f5b3d17d90e8e Mon Sep 17 00:00:00 2001
From: Arsham Mikaeili Namini <92790984+Arshammik@users.noreply.github.com>
Date: Wed, 19 Nov 2025 00:48:49 -0500
Subject: [PATCH 3/5] Fixing CRAN submission note

---
 src/Makevars     | 1 -
 src/Makevars.win | 2 --
 2 files changed, 3 deletions(-)

diff --git a/src/Makevars b/src/Makevars
index 6660c7f..3a7f8ac 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -1,3 +1,2 @@
-CXX_STD = CXX14
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/src/Makevars.win b/src/Makevars.win
index 85d1c66..3a7f8ac 100644
--- a/src/Makevars.win
+++ b/src/Makevars.win
@@ -1,4 +1,2 @@
-## src/Makevars.win (Windows)
-CXX_STD = CXX14
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

From ec735c712ec440972c0779f8b01e07b2e62edadb Mon Sep 17 00:00:00 2001
From: Arsham Mikaeili Namini <92790984+Arshammik@users.noreply.github.com>
Date: Wed, 19 Nov 2025 00:55:30 -0500
Subject: [PATCH 4/5] Fixing issue with elapsed time > 10s test on CRAN

---
 man/get_pseudo_correlation.Rd | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/man/get_pseudo_correlation.Rd b/man/get_pseudo_correlation.Rd
index bbd7b6d..8bde99d 100644
--- a/man/get_pseudo_correlation.Rd
+++ b/man/get_pseudo_correlation.Rd
@@ -49,6 +49,13 @@ m1_inclusion <- m1_obj$m1_inclusion_matrix
 eventdata <- m1_obj$event_data
 m2_exclusion <- make_m2(m1_inclusion, eventdata)
 
+# filter events based on junction coverage
+index_to_keep <- which(rowSums(m1_inclusion) > 10)
+m1_inclusion <- m1_inclusion[index_to_keep, ]
+m2_exclusion <- m2_exclusion[index_to_keep, ]
+
+\donttest{
+
 # creating a dummy ZDB
 ZDB_matrix <- matrix(rnorm(n = (nrow(m1_inclusion) * ncol(m1_inclusion)), sd = 7),
 nrow = nrow(m1_inclusion),
@@ -62,12 +69,5 @@ m2_dense <- as.matrix(m2_exclusion)
 pseudo_r_square_cox <- get_pseudo_correlation(ZDB_matrix, m1_dense, m2_dense)
 print(pseudo_r_square_cox)
 
-# Example with sparse matrices (more memory efficient)
-pseudo_r_square_sparse <- get_pseudo_correlation(ZDB_matrix, m1_inclusion, m2_exclusion)
-
-# Example using Nagelkerke R² instead of Cox-Snell
-pseudo_r_square_nagel <- get_pseudo_correlation(ZDB_matrix, m1_inclusion, m2_exclusion, 
-                                                metric = "Nagelkerke")
-print(pseudo_r_square_nagel)
-
+    }
 }

From 73313a72502c324e7f5d97c23d6709b688d18d45 Mon Sep 17 00:00:00 2001
From: Arsham Mikaeili Namini <92790984+Arshammik@users.noreply.github.com>
Date: Wed, 19 Nov 2025 01:02:45 -0500
Subject: [PATCH 5/5] fix the issue with --as cran test

---
 man/get_pseudo_correlation.Rd | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/man/get_pseudo_correlation.Rd b/man/get_pseudo_correlation.Rd
index 8bde99d..227c9ac 100644
--- a/man/get_pseudo_correlation.Rd
+++ b/man/get_pseudo_correlation.Rd
@@ -49,11 +49,6 @@ m1_inclusion <- m1_obj$m1_inclusion_matrix
 eventdata <- m1_obj$event_data
 m2_exclusion <- make_m2(m1_inclusion, eventdata)
 
-# filter events based on junction coverage
-index_to_keep <- which(rowSums(m1_inclusion) > 10)
-m1_inclusion <- m1_inclusion[index_to_keep, ]
-m2_exclusion <- m2_exclusion[index_to_keep, ]
-
 \donttest{
 
 # creating a dummy ZDB