From 6cd5d966c7d44cbd3cf7a13d7bad72aaaed1b622 Mon Sep 17 00:00:00 2001
From: muschellij2 <muschellij2@gmail.com>
Date: Wed, 28 Aug 2019 12:28:51 -0400
Subject: [PATCH] updated the docs and help for robex main

---
 .gitignore   |  1 +
 R/robex.R    | 34 +++++++++++++++++++++-------------
 man/robex.Rd |  4 ++--
 3 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/.gitignore b/.gitignore
index 28b5631..064aef8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@ inst/runROBEX.sh
 inst/ROBEX
 src/
 ROBEX/
+ROBEX.zip
diff --git a/R/robex.R b/R/robex.R
index d15fcdd..ef8c1e2 100644
--- a/R/robex.R
+++ b/R/robex.R
@@ -9,10 +9,10 @@
 #' @examples
 #' result = robex(infile = "", outfile = "")
 #'
-#' if (requireNamespace("kirby21.t1")) {
+#' if (requireNamespace("kirby21.t1", quietly = TRUE)) {
 #'    infile = kirby21.t1::get_t1_filenames(id = "113", visit = 1)
 #'    if (is.null(infile)) {
-#'    infile = ""
+#'       infile = ""
 #'    }
 #'    if (!file.exists(infile)) {
 #'       outdir = tempdir()
@@ -37,20 +37,27 @@ robex = function(
   ...){
 
 
-  infile = neurobase::checkimg(infile)
   xinfile = infile
-  infile = shQuote(infile)
+  if (file.exists(infile)) {
+    infile = neurobase::checkimg(infile)
+    infile = normalizePath(infile)
+    infile = shQuote(infile)
+  }
   xoutfile = outfile
-  outfile = path.expand(outfile)
-  outfile = normalizePath(outfile, "/")
-  outfile = file.path(normalizePath(dirname(outfile), "/"),
-                      basename(outfile))
-  if (.Platform$OS.type == "windows") {
-    outfile = gsub("\\", "/", outfile, fixed = TRUE)
-    outfile = gsub("/+", "/", outfile)
-    outfile = gsub("/", "\\\\", outfile)
+  if (length(outfile) > 0) {
+    if (nchar(outfile) > 0) {
+      outfile = path.expand(outfile)
+      outfile = normalizePath(outfile, winslash = "/")
+      outfile = file.path(normalizePath(dirname(outfile), "/"),
+                          basename(outfile))
+      if (.Platform$OS.type == "windows") {
+        outfile = gsub("\\", "/", outfile, fixed = TRUE)
+        outfile = gsub("/+", "/", outfile)
+        outfile = gsub("/", "\\\\", outfile)
+      }
+      outfile = shQuote(outfile)
+    }
   }
-  outfile = shQuote(outfile)
 
   # install_robex()
 
@@ -83,3 +90,4 @@ robex = function(
          outfile = xoutfile)
   )
 } ## end robex
+
diff --git a/man/robex.Rd b/man/robex.Rd
index d88309a..0f3c498 100644
--- a/man/robex.Rd
+++ b/man/robex.Rd
@@ -26,10 +26,10 @@ Executes Robust Brain Extraction
 \examples{
 result = robex(infile = "", outfile = "")
 
-if (requireNamespace("kirby21.t1")) {
+if (requireNamespace("kirby21.t1", quietly = TRUE)) {
    infile = kirby21.t1::get_t1_filenames(id = "113", visit = 1)
    if (is.null(infile)) {
-   infile = ""
+      infile = ""
    }
    if (!file.exists(infile)) {
       outdir = tempdir()