Fixed small errors to prevent notes in R CMD check

.Rbuildignore

@@ -3,9 +3,8 @@
 ^\.Rprofile$
 ^\.travis\.yml$
 ^README\.Rmd$
-^under_constr$
+^under_constr
 ^_crash_test\.R$
-^gfiles$
-^methods$
-^data-raw$
+^methods
+^data-raw
 ^diagnostics

.gitignore

@@ -11,7 +11,6 @@ src/*.dll
 inst/doc
 *.bk
 *.desc
-gfiles
 Gac
 gemino_*.tgz
 *.pdf

NAMESPACE

@@ -12,4 +12,5 @@ export(ref_genome)
 export(variants)
 export(write_fasta)
 importFrom(Rcpp,evalCpp)
+importFrom(utils,read.csv)
 useDynLib(gemino, .registration = TRUE)

R/illumina.R

@@ -2,6 +2,9 @@
 
 #' Return table of information about built-in Illumina profiles.
 #'
+#'
+#' @importFrom utils read.csv
+#'
 #' @noRd
 #'
 builtin_illumina_profiles <- function() {
@@ -505,8 +508,12 @@ check_illumina_args <- function(seq_object, n_reads,
 #' sequencing read simulator. \emph{Bioinformatics} \strong{28}:593–594.
 #'
 #' @examples
-#'
-#'
+#' \dontrun{
+#' rg <- create_genome(10, 100e3, 100)
+#' illumina(rg, "illumina_reads", n_reads = 100,
+#'          read_length = 100, paired = FALSE,
+#'          frag_mean = 400, frag_sd = 100)
+#' }
 #'
 illumina <- function(seq_object,
                      out_prefix,

R/pacbio.R

@@ -168,8 +168,10 @@ check_pacbio_args <- function(seq_object,
 #' read data. \emph{Bioinformatics} \strong{32}:2704–2706.
 #'
 #' @examples
-#'
-#'
+#' \dontrun{
+#' rg <- create_genome(10, 100e3, 100)
+#' pacbio(rg, "pacbio_reads", n_reads = 100)
+#' }
 #'
 pacbio <- function(seq_object,
                    out_prefix,