read_csv: add warning if duplicate col or row names

- This is related to the problem that underlies Issue rqtl#209

NEWS.md

@@ -11,6 +11,9 @@
 - Give a better error message in `genoprob_to_snpprob()` if `snpinfo`
   is missing the `sdp` column (Issue #207).
 
+- In `read_cross()`, give warnings if there are duplicate column names
+  or duplicate row names in the file.
+
 
 ## qtl2 0.28 (2021-10-11)
 

R/read_csv.R

@@ -50,10 +50,17 @@ read_csv <-
         }
     }
 
+    if(length(unique(colnames(x))) != ncol(x))
+        warning("duplicate column names in file ", filename)
+
     # move first column to row names
-    if(rownames_included)
+    if(rownames_included) {
         x <- firstcol2rownames(x, filename)
 
+        if(length(unique(rownames(x))) != nrow(x))
+            warning("duplicate row names in file ", filename)
+    }
+
     # transpose if requested
     if(transpose)
         x <- as.data.frame(t(x), stringAsFactors=FALSE)