From bfd9e470b9532dfd7781268244d942f5261e7258 Mon Sep 17 00:00:00 2001
From: Tiago Silva <tiagosilva@Tiagos-MBP-2.hsd1.fl.comcast.net>
Date: Tue, 30 Jan 2024 20:05:22 -0500
Subject: [PATCH] Version bump

---
 NAMESPACE                                      |  1 +
 R/TCGAbiolinks-package.R                       | 18 ++++++++++++++++++
 R/TCGAbiolinks.R                               | 17 -----------------
 R/internal.R                                   |  2 +-
 R/prepare.R                                    |  2 +-
 ...TCGAbiolinks.Rd => TCGAbiolinks-package.Rd} | 14 ++++++++++++--
 6 files changed, 33 insertions(+), 21 deletions(-)
 create mode 100644 R/TCGAbiolinks-package.R
 rename man/{TCGAbiolinks.Rd => TCGAbiolinks-package.Rd} (74%)

diff --git a/NAMESPACE b/NAMESPACE
index 9437c6330..ef9d41ecd 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,header)
 export(GDCdownload)
 export(GDCprepare)
 export(GDCprepare_clinic)
diff --git a/R/TCGAbiolinks-package.R b/R/TCGAbiolinks-package.R
new file mode 100644
index 000000000..b5cc28ef5
--- /dev/null
+++ b/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
diff --git a/R/TCGAbiolinks.R b/R/TCGAbiolinks.R
index 18cc9f958..d599c6b82 100644
--- a/R/TCGAbiolinks.R
+++ b/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
diff --git a/R/internal.R b/R/internal.R
index dd35d78a8..cf1b96dc6 100644
--- a/R/internal.R
+++ b/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))
diff --git a/R/prepare.R b/R/prepare.R
index fbe6f44fa..6a9e7120c 100644
--- a/R/prepare.R
+++ b/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
             )
         }
diff --git a/man/TCGAbiolinks.Rd b/man/TCGAbiolinks-package.Rd
similarity index 74%
rename from man/TCGAbiolinks.Rd
rename to man/TCGAbiolinks-package.Rd
index 8a27ab40b..216d471dd 100644
--- a/man/TCGAbiolinks.Rd
+++ b/man/TCGAbiolinks-package.Rd
@@ -1,8 +1,9 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/TCGAbiolinks.R
+% Please edit documentation in R/TCGAbiolinks-package.R
 \docType{package}
-\name{TCGAbiolinks}
+\name{TCGAbiolinks-package}
 \alias{TCGAbiolinks}
+\alias{TCGAbiolinks-package}
 \title{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
@@ -16,3 +17,12 @@ The functions you're likely to need from \pkg{TCGAbiolinks} is
 Otherwise refer to the vignettes to see
 how to format the documentation.
 }
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://github.com/BioinformaticsFMRP/TCGAbiolinks}
+  \item Report bugs at \url{https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues}
+}
+
+}
+\keyword{internal}