From 9da5cbc2cbb22efe720c7e28a925187bf8d1b33f Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Tue, 3 Oct 2023 19:05:08 -0400
Subject: [PATCH] try to fix rcmdcheck

---
 .Rbuildignore                     |  1 +
 .github/workflows/main_check.yaml |  2 +-
 NAMESPACE                         |  1 -
 R/spdep.R                         | 16 ++++++++--------
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index b5d8c96f8..86f1b62e9 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -14,3 +14,4 @@
 ^pkgdown$
 .Rbuildignore.save
 ^\.github$
+^codecov\.yml$
diff --git a/.github/workflows/main_check.yaml b/.github/workflows/main_check.yaml
index 1445d44d8..60e988f8d 100644
--- a/.github/workflows/main_check.yaml
+++ b/.github/workflows/main_check.yaml
@@ -58,7 +58,7 @@ jobs:
           _R_CHECK_RD_XREFS: false
         with:
           dependencies: '"hard"' # do not use suggested dependencies
-          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr
+          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr, any::spdep
 
       - name: Set up dependencies (GiottoData)
         run: |
diff --git a/NAMESPACE b/NAMESPACE
index b4f744ff4..0bd26fb31 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -402,7 +402,6 @@ import(GiottoUtils)
 import(GiottoVisuals)
 import(ggplot2)
 import(methods)
-import(spdep)
 import(stats)
 import(utils)
 importClassesFrom(data.table,data.table)
diff --git a/R/spdep.R b/R/spdep.R
index ff4779957..43d1e8291 100644
--- a/R/spdep.R
+++ b/R/spdep.R
@@ -13,7 +13,7 @@
 #' @export
 
 spdepAutoCorr <- function (gobject,
-                      method = c("geary.test", "lee.test", "lm.morantest","moran.test"),
+                      method = c("geary.test", "lee.test", "lm.morantest", "moran.test"),
                       spat_unit = NULL,
                       feat_type = NULL,
                       expression_values = "normalized",
@@ -61,32 +61,32 @@ spdepAutoCorr <- function (gobject,
   feat <- resultSpdepCor$feats
   weight_matrix <- resultSpdepCor$weight_matrix
   use_values <- resultSpdepCor$use_values
-  
+
   #progressr
   nfeats = length(feat)
   step_size = ceiling(nfeats/10L)
-  
+
   result_list <- list()
   progressr::with_progress({
     if(step_size > 1) pb = progressr::progressor(steps = nfeats/step_size)
     result_list <- lapply_flex(seq_along(feat),
                                         function(feat_value){
                                          callSpdepVar <- callSpdep(method = method,
-                                                                    x = use_values[,feat_value], 
+                                                                    x = use_values[,feat_value],
                                                                     listw = mat2listw (weight_matrix, style = "W"))
                                          # Extract the estimated value from the result
-                                         result_value <- callSpdepVar$estimate[1] 
+                                         result_value <- callSpdepVar$estimate[1]
                                          temp_dt <- data.table(feat_ID = feat[feat_value], value = result_value)
                                          # increment progress
-                                         if(exists('pb')) if(feat_value %% step_size == 0) pb() 
+                                         if(exists('pb')) if(feat_value %% step_size == 0) pb()
                                          return(temp_dt)
                                         }
                                         )
   })
   result_dt <- rbindlist(result_list)
-  
+
   # Return the resulting datatable
-  
+
   if(isTRUE(return_gobject)) {
     if(isTRUE(verbose)) wrap_msg('Appending', method,
                                  'results to feature metadata: fDataDT()')