From efc7ebef943599ee9486484a0097f29b644ae94c Mon Sep 17 00:00:00 2001
From: Jack Leary <j.leary@ufl.edu>
Date: Sun, 12 Nov 2023 20:14:55 -0500
Subject: [PATCH] hopefully fixed R CMD check and Bioccheck errors

---
 .github/workflows/bioc-check.yaml | 2 --
 DESCRIPTION                       | 1 -
 R/clusterGenes.R                  | 3 ++-
 R/geneProgramScoring.R            | 3 ++-
 man/clusterGenes.Rd               | 3 ++-
 man/geneProgramScoring.Rd         | 3 ++-
 6 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/bioc-check.yaml b/.github/workflows/bioc-check.yaml
index 13a952e..dd103f3 100644
--- a/.github/workflows/bioc-check.yaml
+++ b/.github/workflows/bioc-check.yaml
@@ -4,8 +4,6 @@
 on:
   push:
     branches: main
-  pull_request:
-    branches: main
 
 name: bioc-check
 
diff --git a/DESCRIPTION b/DESCRIPTION
index ef4685d..fe5a4e2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,7 +9,6 @@ Description: This package uses truncated power basis spline models to build flex
              Downstream analysis functionalities include model comparison, dynamic gene clustering, smoothed counts generation, gene set enrichment testing, & visualization. 
 License: MIT + file LICENSE
 Encoding: UTF-8
-LazyData: true
 RoxygenNote: 7.2.1
 Depends: 
   glm2, 
diff --git a/R/clusterGenes.R b/R/clusterGenes.R
index 42a61fb..c3fa9ee 100644
--- a/R/clusterGenes.R
+++ b/R/clusterGenes.R
@@ -23,8 +23,9 @@
 #' @seealso \code{\link{plotClusteredGenes}}
 #' @export
 #' @examples
-#' data(sim_pseudotime)
+#' data(sim_counts)
 #' data(scLANE_models)
+#' data(sim_pseudotime)
 #' cell_offset <- createCellOffset(sim_counts)
 #' gene_clusters <- clusterGenes(scLANE_models,
 #'                               pt = sim_pseudotime,
diff --git a/R/geneProgramScoring.R b/R/geneProgramScoring.R
index 1404ce1..b221906 100644
--- a/R/geneProgramScoring.R
+++ b/R/geneProgramScoring.R
@@ -15,8 +15,9 @@
 #' @return Either a \code{Seurat} or \code{SingleCellExperiment} object if \code{expr.mat} is in either form, or a data.frame containing per-cell program scores if \code{expr.mat} is a matrix.
 #' @export
 #' @examples
-#' data(sim_pseudotime)
+#' data(sim_counts)
 #' data(scLANE_models)
+#' data(sim_pseudotime)
 #' smoothed_dynamics <- smoothedCountsMatrix(scLANE_models,
 #'                                           pt = sim_pseudotime,
 #'                                           n.cores = 1L)
diff --git a/man/clusterGenes.Rd b/man/clusterGenes.Rd
index 67ca7cf..af590eb 100644
--- a/man/clusterGenes.Rd
+++ b/man/clusterGenes.Rd
@@ -41,8 +41,9 @@ This function takes as input the output from \code{\link{testDynamic}} and clust
 }
 }
 \examples{
-data(sim_pseudotime)
+data(sim_counts)
 data(scLANE_models)
+data(sim_pseudotime)
 cell_offset <- createCellOffset(sim_counts)
 gene_clusters <- clusterGenes(scLANE_models,
                               pt = sim_pseudotime,
diff --git a/man/geneProgramScoring.Rd b/man/geneProgramScoring.Rd
index d28e721..a807b12 100644
--- a/man/geneProgramScoring.Rd
+++ b/man/geneProgramScoring.Rd
@@ -30,8 +30,9 @@ Either a \code{Seurat} or \code{SingleCellExperiment} object if \code{expr.mat}
 This function uses \code{\link[UCell]{ScoreSignatures_UCell}} to create a per-cell module score for each of the provided gene clusters. If the
 }
 \examples{
-data(sim_pseudotime)
+data(sim_counts)
 data(scLANE_models)
+data(sim_pseudotime)
 smoothed_dynamics <- smoothedCountsMatrix(scLANE_models,
                                           pt = sim_pseudotime,
                                           n.cores = 1L)