Version bump

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,header)
 export(GDCdownload)
 export(GDCprepare)
 export(GDCprepare_clinic)

R/TCGAbiolinks-package.R

@@ -0,0 +1,18 @@
+#' The aim of TCGAbiolinks is : i) facilitate the TCGA open-access data retrieval,
+#' ii) prepare the data using the appropriate pre-processing strategies,
+#'  iii) provide the means to carry out different standard analyses and
+#'  iv) allow the user to download a specific version of the data and thus to easily reproduce earlier research results.
+#'   In more detail, the package provides multiple methods for analysis
+#' (e.g., differential expression analysis, identifying differentially methylated regions)
+#' and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.
+#'
+#' The functions you're likely to need from \pkg{TCGAbiolinks} is
+#' \code{\link{GDCdownload}}, \code{\link{GDCquery}}.
+#' Otherwise refer to the vignettes to see
+#' how to format the documentation.
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL

R/TCGAbiolinks.R

@@ -1,20 +1,3 @@
-#' The aim of TCGAbiolinks is : i) facilitate the TCGA open-access data retrieval,
-#' ii) prepare the data using the appropriate pre-processing strategies,
-#'  iii) provide the means to carry out different standard analyses and
-#'  iv) allow the user to download a specific version of the data and thus to easily reproduce earlier research results.
-#'   In more detail, the package provides multiple methods for analysis
-#' (e.g., differential expression analysis, identifying differentially methylated regions)
-#' and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.
-#'
-#' The functions you're likely to need from \pkg{TCGAbiolinks} is
-#' \code{\link{GDCdownload}}, \code{\link{GDCquery}}.
-#' Otherwise refer to the vignettes to see
-#' how to format the documentation.
-#'
-#' @docType package
-#' @name TCGAbiolinks
-NULL
-
 #' Clinical data TCGA BRCA
 #' @docType data
 #' @keywords internal

R/internal.R

@@ -691,7 +691,7 @@ get.mut.gistc.information <- function(
     return(df)
 }
 
-
+#' @export
 print.header <- function(text, type ="section"){
     message(paste(rep("-",nchar(text) + 3),collapse = ""))
     message(paste(ifelse(type=="section","o","oo"),text))

R/prepare.R

@@ -1288,7 +1288,7 @@ colDataPrepare <- function(barcode){
         # is TARGET-30-PAPKXS-01A-01D and not TARGET-30-PAPKXS-01A
         if(all(is.na(idx))){
             idx <- match(
-                stringr::str_sub(barcode,1,unique(stringr::str_length(ret$bcr_patient_barcode))),
+                stringr::str_sub(barcode,1,min(stringr::str_length(ret$bcr_patient_barcode))),
                 ret$bcr_patient_barcode
             )
         }