From 6cb4bd16c04ce01462d0899261fc46abbd50861f Mon Sep 17 00:00:00 2001
From: theHumanBorch <ncborch@gmail.com>
Date: Wed, 1 May 2024 13:29:36 -0500
Subject: [PATCH] working through check()

---
 .Rbuildignore        | 1 +
 DESCRIPTION          | 4 ++++
 NAMESPACE            | 2 ++
 R/getIR.R            | 1 +
 R/one.hot.encoder.R  | 1 +
 R/property.encoder.R | 6 +++---
 tests/testthat.R     | 4 ++--
 7 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 4be4cfa..7264d31 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,2 +1,3 @@
 ^codecov\.yml$
 ^\.github$
+^www$
diff --git a/DESCRIPTION b/DESCRIPTION
index eaebe3a..b8ebd1f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -14,12 +14,16 @@ biocViews: Software, ImmunoOncology, SingleCell, Classification, Annotation, Seq
 Depends: 
 	R (>= 4.0)
 Imports: keras,
+	methods,
 	SingleCellExperiment,
+	stats,
 	stringi,
 	stringr
 Suggests: 
 	BiocStyle,
 	knitr,
+	scRepertoire,
+	spelling,
         testthat
 VignetteBuilder: knitr
 Language: en-US
diff --git a/NAMESPACE b/NAMESPACE
index a39b0f4..d69b86e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,5 +9,7 @@ export(property.encoder)
 export(tokenize.sequences)
 importFrom(SingleCellExperiment,colData)
 importFrom(keras,array_reshape)
+importFrom(methods,slot)
+importFrom(stats,setNames)
 importFrom(stringi,stri_rand_strings)
 importFrom(stringr,str_split)
diff --git a/R/getIR.R b/R/getIR.R
index dd58bb1..3e57dc0 100644
--- a/R/getIR.R
+++ b/R/getIR.R
@@ -60,6 +60,7 @@ getIR <- function(input.data,
 }
 
 #' @importFrom SingleCellExperiment colData 
+#' @importFrom methods slot
 .grabMeta <- function(sc) {
   if (inherits(x=sc, what ="Seurat")) {
     meta <- data.frame(sc[[]], slot(sc, "active.ident"))
diff --git a/R/one.hot.encoder.R b/R/one.hot.encoder.R
index 68355c9..5fd9872 100644
--- a/R/one.hot.encoder.R
+++ b/R/one.hot.encoder.R
@@ -21,6 +21,7 @@
 #' This will be overrode if using a motif approach (split.length > 1).
 #' 
 #' @importFrom keras array_reshape
+#' @importFrom stats setNames
 #' 
 #' @export
 #' @return One hot encoded amino acid sequences in a matrix or 3D array
diff --git a/R/property.encoder.R b/R/property.encoder.R
index 2333326..2d01dda 100644
--- a/R/property.encoder.R
+++ b/R/property.encoder.R
@@ -11,9 +11,9 @@
 #'                                     min.length = 8,
 #'                                     max.length = 16)
 #'                           
-#' sequence.matrix <- one.hot.encoder(new.sequences, 
-#'                                    method.to.use = "VHSE",
-#'                                    convert.to.matrix = TRUE)
+#' sequence.matrix <- property.encoder(new.sequences, 
+#'                                     method.to.use = "VHSE",
+#'                                     convert.to.matrix = TRUE)
 #'                         
 #' @param input.sequences The amino acid sequences to use
 #' @param max.length Additional length to pad, NULL will pad sequences 
diff --git a/tests/testthat.R b/tests/testthat.R
index c5a1ba1..7b39b16 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -7,6 +7,6 @@
 # * https://testthat.r-lib.org/reference/test_package.html#special-files
 
 library(testthat)
-library(Trex)
+library(Apex)
 
-test_check("Trex")
+test_check("Apex")