Fix CRAN note

CRAN-RELEASE

@@ -1,2 +1,2 @@
 This package was submitted to CRAN on 2021-01-08.
-Once it is accepted, delete this file and tag the release (commit c5a40bb).
+Once it is accepted, delete this file and tag the release (commit 719ddf9).

R/data.R

@@ -120,7 +120,7 @@ NULL
 
 #' A List of Simulated SBS-96 Catalog Matrix
 #'
-#' Data from <https://doi.org/10.1038/s43018-020-0027-5>.
+#' Data from \doi{10.1038/s43018-020-0027-5}.
 #' 5 simulated mutation catalogs are used by the paper but only 4 are available.
 #' The data are simulated from COSMIC mutational signatures 1, 2, 3, 5, 6, 8,
 #' 12, 13, 17 and 18. Each sample is a linear combination of 5 randomly selected

R/read_vcf.R

@@ -108,6 +108,7 @@ read_vcf <- function(vcfs, samples = NULL, genome_build = c("hg19", "hg38"), kee
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' if (requireNamespace("UCSCXenaTools")) {
 #'   library(UCSCXenaTools)
 #'   options(use_hiplot = TRUE)
@@ -119,6 +120,7 @@ read_vcf <- function(vcfs, samples = NULL, genome_build = c("hg19", "hg38"), kee
 #'   y <- sig_tally(x)
 #'   y
 #' }
+#' }
 #' @testexamples
 #' if (requireNamespace("UCSCXenaTools")) {
 #'   expect_is(y, "list")
@@ -132,14 +134,19 @@ read_xena_variants <- function(path) {
 
   data.table::setnames(
     dt,
-    old = c(detect_name("Sample_ID", "sample", colnames(dt)),
-            "gene",
-            detect_name("chrom", "chr", colnames(dt)),
-            "start", "end",
-            detect_name("ref", "reference", colnames(dt)),
-            "alt"),
-    new = c("Tumor_Sample_Barcode", "Hugo_Symbol", "Chromosome",
-            "Start_Position", "End_Position", "Reference_Allele", "Tumor_Seq_Allele2"))
+    old = c(
+      detect_name("Sample_ID", "sample", colnames(dt)),
+      "gene",
+      detect_name("chrom", "chr", colnames(dt)),
+      "start", "end",
+      detect_name("ref", "reference", colnames(dt)),
+      "alt"
+    ),
+    new = c(
+      "Tumor_Sample_Barcode", "Hugo_Symbol", "Chromosome",
+      "Start_Position", "End_Position", "Reference_Allele", "Tumor_Seq_Allele2"
+    )
+  )
 
   dt$Variant_Type <- dplyr::case_when(
     nchar(dt$Reference_Allele) == 1L & nchar(dt$Tumor_Seq_Allele2) == 1L ~ "SNP",

R/scoring.R

@@ -42,7 +42,7 @@
 #' - sTDP_size: sTDP region size (Mb).
 #' - lTDP_size: lTDP region size(Mb).
 #' - Chromoth_state: chromothripsis state score,
-#' according to reference <http://dx.doi.org/10.1016/j.cell.2013.02.023>,
+#' according to reference \doi{10.1016/j.cell.2013.02.023},
 #' chromothripsis frequently leads to massive loss of segments on
 #' the affected chromosome with segmental losses being interspersed with regions displaying
 #' normal (disomic) copy-number (e.g., copy-number states oscillating between

tests/testthat/test-roxytest-testexamples-read_vcf.R

@@ -2,7 +2,8 @@
 
 context("File R/read_vcf.R: @testexamples")
 
-test_that("Function read_xena_variants() @ L126", {
+test_that("Function read_xena_variants() @ L128", {
+
 
   if (requireNamespace("UCSCXenaTools")) {
     library(UCSCXenaTools)
@@ -15,6 +16,7 @@ test_that("Function read_xena_variants() @ L126", {
     y <- sig_tally(x)
     y
   }
+
   if (requireNamespace("UCSCXenaTools")) {
     expect_is(y, "list")
   }