Merge branch 'fix-check' into develop

DESCRIPTION

@@ -41,4 +41,5 @@ RoxygenNote: 7.1.1
 Suggests:
     testthat (>= 2.1.0)
 Imports:
-    methods
+    methods,
+    ape

NAMESPACE

@@ -50,7 +50,10 @@ export(uigetfile)
 export(uiputfile)
 export(writeMixtureInfo)
 import(utils)
+importFrom(ape,as.DNAbin)
+importFrom(ape,read.FASTA)
 importFrom(methods,is)
 importFrom(stats,runif)
+importFrom(stats,sd)
 importFrom(utils,read.delim)
 importFrom(utils,write.table)

R/isGlobalEmpty.R

@@ -3,6 +3,7 @@
 #' @details For a list of global variables, check the \code{globals.R} file.
 #' @param g the global variable in quesiton.
 #' @return TRUE if the variable still contains its original values, FALSE otherwise.
+#' @importFrom stats sd
 #' @author Waldir Leoncio
 isGlobalEmpty <- function(g) {
 	return(sum(g) == 0 & sd(g) == 0)

R/load_fasta.R

@@ -9,11 +9,12 @@
 #' @return A character matrix with filtered SNP data
 #'
 #' @examples
-#' msa <- system.file("extdata", "seqs.fa", package = "rhierbaps")
+#' msa <- system.file("ext", "seqs.fa", package="rBAPS")
 #' snp.matrix <- load_fasta(msa)
 #'
 #' @author Gerry Tonkin-Hill
 #' @seealso rhierbaps::load_fasta
+#' @importFrom ape read.FASTA as.DNAbin
 #' @export
 load_fasta <- function(msa, keep.singletons=FALSE) {
 

man/load_fasta.Rd

@@ -19,7 +19,7 @@ Loads a fasta file into matrix format ready for
 running the hierBAPS algorithm.
 }
 \examples{
-msa <- system.file("extdata", "seqs.fa", package = "rhierbaps")
+msa <- system.file("ext", "seqs.fa", package="rBAPS")
 snp.matrix <- load_fasta(msa)
 
 }

tests/testthat/test-greedyMix.R

@@ -2,12 +2,14 @@ context("Auxiliary functions to greedyMix")
 
 # Defining the relative path to current inst ------------- #
 if (interactive()) {
-	path_inst <- "../../inst/ext/"
+	path_inst <- "../../inst/ext/BAPS_format_clustering_diploid.txt"
 } else {
-	path_inst <- "inst/ext/"
+	path_inst <- system.file(
+		"ext", "BAPS_format_clustering_diploid.txt", package="rBAPS"
+	)
 }
 baps_diploid <- read.delim(
-	file = file.path(path_inst, "BAPS_format_clustering_diploid.txt"),
+	file = path_inst,
 	sep = " ",
 	header = FALSE
 )