[Phylobase-commits] r933 - pkg/R

[noreply at r-forge.r-project.org]

Author: francois
Date: 2014-05-06 22:26:32 +0200 (Tue, 06 May 2014)
New Revision: 933

Modified:
   pkg/R/phylobase.options.R
   pkg/R/zzz.R
Log:
changing default to fail for reticulated trees as they are not supported enough currently

Modified: pkg/R/phylobase.options.R
===================================================================
--- pkg/R/phylobase.options.R	2014-05-06 20:25:41 UTC (rev 932)
+++ pkg/R/phylobase.options.R	2014-05-06 20:26:32 UTC (rev 933)
@@ -44,6 +44,9 @@
     current <- lapply(current, function(foo) {
         foo <- match.arg(foo, c("warn", "fail", "ok"))
     })
+    if (!identical(current$retic, "fail")) {
+        stop("Currently reticulated trees are not handled by phylobase.")
+    }
     ## options are always global
     env <- asNamespace("phylobase")
     assign(".phylobase.Options", current, envir = env)

Modified: pkg/R/zzz.R
===================================================================
--- pkg/R/zzz.R	2014-05-06 20:25:41 UTC (rev 932)
+++ pkg/R/zzz.R	2014-05-06 20:26:32 UTC (rev 933)
@@ -1,6 +1,6 @@
 
 ".phylobase.Options" <-
-    list(retic = "warn",
+    list(retic = "fail",
          singleton = "warn",
          multiroot = "warn",
          poly = "ok",