[Phylobase-commits] r806 - in pkg: R src

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

Author: francois
Date: 2010-08-04 15:10:18 +0200 (Wed, 04 Aug 2010)
New Revision: 806

Modified:
   pkg/R/readNCL.R
   pkg/src/GetNCL.cpp
Log:
return NxsException messages to R without crashing

Modified: pkg/R/readNCL.R
===================================================================
--- pkg/R/readNCL.R	2010-07-28 19:25:48 UTC (rev 805)
+++ pkg/R/readNCL.R	2010-08-04 13:10:18 UTC (rev 806)
@@ -39,6 +39,11 @@
  ##  $stateLabels: the labels for the states of the characters, i.e. the levels of the factors to be returned
  ##  $dataChr: string that contains the data to be returned
  ncl <- .Call("GetNCL", fileName, parameters, PACKAGE="phylobase")
+
+ ## Return Error message
+ if (length(ncl) == 1 && names(ncl) == "ErrorMsg") {
+   stop(ncl$ErrorMsg)
+ }
  
  if (!quiet) print(ncl)
 

Modified: pkg/src/GetNCL.cpp
===================================================================
--- pkg/src/GetNCL.cpp	2010-07-28 19:25:48 UTC (rev 805)
+++ pkg/src/GetNCL.cpp	2010-08-04 13:10:18 UTC (rev 806)
@@ -83,6 +83,7 @@
     std::vector<std::string> trees;          //vector of Newick strings holding the names
     std::vector<std::string> treeNames;      //vector of tree names
     std::vector<std::string> taxaNames;      //vector of taxa names
+    std::string errorMsg;                    //error message
 
     std::vector<bool> test(3);
     test[0] = charall;
@@ -103,7 +104,14 @@
     nexusReader.cullIdenticalTaxaBlocks(true);
     /* End of making NCL less strict */
     
-    nexusReader.ReadFilepath(const_cast < char* > (filename.c_str()), MultiFormatReader::NEXUS_FORMAT);  
+    try {
+	nexusReader.ReadFilepath(const_cast < char* > (filename.c_str()), MultiFormatReader::NEXUS_FORMAT);  
+    }
+    catch (NxsException &x) {
+	errorMsg = x.msg;
+	Rcpp::List res = Rcpp::List::create(Rcpp::Named("ErrorMsg") = errorMsg);
+	return res;
+    }
 
     const unsigned nTaxaBlocks = nexusReader.GetNumTaxaBlocks();
     for (unsigned t = 0; t < nTaxaBlocks; ++t) {