passing r cmd check

calico · Sep 9, 2024 · 5cc2f44 · 5cc2f44
1 parent a217c1a
commit 5cc2f44
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Showing 4 changed files with 8 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: romic
 Type: Package
 Title: R for High-Dimensional Omic Data
-Version: 1.2.2
+Version: 1.2.3
 Authors@R: c(
     person(
       given = "Sean",

diff --git a/R/dim_reduction.R b/R/dim_reduction.R
@@ -489,7 +489,7 @@ calculate_sample_mahalanobis_distances <- function (
   ) {
 
   checkmate::assertClass(tomic, "tomic")
-  value_var <- romic:::value_var_handler(value_var, tomic$design)
+  value_var <- value_var_handler(value_var, tomic$design)
   checkmate::assertIntegerish(max_pcs, len = 1)
 
   n_features <- nrow(romic::get_tomic_table(tomic, "features"))
@@ -518,7 +518,7 @@ calculate_sample_mahalanobis_distances <- function (
     !!rlang::sym(tomic$design$sample_pk) := rownames(X_std_v),
     pc_distance = rowSums(X_std_v^2)
   ) %>%
-    arrange(desc(pc_distance))
+    dplyr::arrange(dplyr::desc(pc_distance))
 
   # validate calculation
   varex_leading_components <- sum(svd_results$d^2) * sum((svd_results$d^2 / sum(svd_results$d^2))[1:npcs])

diff --git a/R/romic-package.R b/R/romic-package.R
@@ -40,6 +40,7 @@ utils::globalVariables(c(
   "sample_label",
   "ordered_sampleId",
   "orderedId",
+  "pc_distance",
   "valid_tables",
   "NAME",
   "name",

diff --git a/man/get_design_tbl.Rd b/man/get_design_tbl.Rd