From 919ecd3bfbf9ef55c269e6cdd2e1a4c870e783dd Mon Sep 17 00:00:00 2001
From: jorainer <johannes.rainer@gmail.com>
Date: Wed, 20 May 2020 13:12:39 +0200
Subject: [PATCH] fix: issue #471

---
 R/functions-XCMSnExp.R | 7 ++++++-
 inst/NEWS              | 2 ++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/R/functions-XCMSnExp.R b/R/functions-XCMSnExp.R
index fbcbdc7ad..4f937da8f 100644
--- a/R/functions-XCMSnExp.R
+++ b/R/functions-XCMSnExp.R
@@ -54,7 +54,12 @@ dropGenericProcessHistory <- function(x, fun) {
     xs@rt <- rts
 
     ## @phenoData
-    xs@phenoData <- pData(from)
+    pd <- pData(from)
+    if (nrow(pd) != length(fileNames(from))) {
+        pd <- data.frame(file_name = basename(fileNames(from)))
+        rownames(pd) <- pd$file_name
+    }
+    xs@phenoData <- pd
     ## @filepaths
     xs@filepaths <- fileNames(from)
 
diff --git a/inst/NEWS b/inst/NEWS
index a8641b0d3..e7f9dc9c2 100644
--- a/inst/NEWS
+++ b/inst/NEWS
@@ -1,5 +1,7 @@
 Changes in version 3.10.1
 
+- Fix for issue #471. Thanks for Andris Jankevics for reporting and providing a
+  solution.
 - Fix issue #475.
 - Fix problem in converting an XCMSnExp into an xcmsSet object (issue #464).