[Phylobase-commits] r738 - in pkg: . src src/ncl

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

Author: edd
Date: 2010-02-08 18:07:13 +0100 (Mon, 08 Feb 2010)
New Revision: 738

Removed:
   pkg/configure.win
   pkg/src/Makevars.in
Modified:
   pkg/cleanup
   pkg/src/ncl/nxscharactersblock.h
   pkg/src/nxscharactersblock.cpp
   pkg/src/nxsemptyblock.cpp
Log:
rearranged build once more -- now all of NCL is in pkg/src and 'simply gets built' when phylobase is built


Modified: pkg/cleanup
===================================================================
--- pkg/cleanup	2010-02-08 16:52:51 UTC (rev 737)
+++ pkg/cleanup	2010-02-08 17:07:13 UTC (rev 738)
@@ -1,5 +1,4 @@
 rm -f confdefs.h config.log config.status a.out.dSYM
-rm -f src/Makevars
 rm -rf src/bin
 rm -f src/*.o src/*.so
 rm -f src/RcppSrc/*.o src/RcppSrc/*.a inst/Rcpp-version.txt

Deleted: pkg/configure.win
===================================================================
--- pkg/configure.win	2010-02-08 16:52:51 UTC (rev 737)
+++ pkg/configure.win	2010-02-08 17:07:13 UTC (rev 738)
@@ -1,5 +0,0 @@
-echo "Configuring phylobase -- starting to build NCL"
-cd src/ncl/ncl
-make -f Makefile.win
-echo "Configuring phylobase -- finished building NCL"
-cd ../../..

Deleted: pkg/src/Makevars.in
===================================================================
--- pkg/src/Makevars.in	2010-02-08 16:52:51 UTC (rev 737)
+++ pkg/src/Makevars.in	2010-02-08 17:07:13 UTC (rev 738)
@@ -1,2 +0,0 @@
-PKG_CXXFLAGS=@CPPFLAGS@
-PKG_LIBS=@LDFLAGS@

Modified: pkg/src/ncl/nxscharactersblock.h
===================================================================
--- pkg/src/ncl/nxscharactersblock.h	2010-02-08 16:52:51 UTC (rev 737)
+++ pkg/src/ncl/nxscharactersblock.h	2010-02-08 17:07:13 UTC (rev 738)
@@ -926,7 +926,7 @@
 		/* will return NXS_INVALID_STATE_CODE if the char is unknown */
 		int				 GetStateCodeStored(char currChar) const 
 			{
-			return cLookup[currChar];
+			  return cLookup[static_cast<int>(currChar)];
 			}
 		bool			 IsPolymorphic(int stateCode) const;
 		int				 PositionInSymbols(const char currChar) const;

Modified: pkg/src/nxscharactersblock.cpp
===================================================================
--- pkg/src/nxscharactersblock.cpp	2010-02-08 16:52:51 UTC (rev 737)
+++ pkg/src/nxscharactersblock.cpp	2010-02-08 17:07:13 UTC (rev 738)
@@ -926,7 +926,7 @@
 	aaInd[62] = 9;
 	aaInd[63] = 4;
 	if (codeIndex == NXS_GCODE_VERT_MITO) {
-		aaInd[8] = 20;
+	        aaInd[8] = 20;
 		aaInd[10] = 20;
 		aaInd[12] = 10;
 		aaInd[56] = 18;
@@ -2840,7 +2840,7 @@
   const NxsDiscreteStateRow * firstTaxonRow, 
   const NxsString & nameStr) const
   	{
-  	int currState = cLookup[currChar];
+	int currState = cLookup[static_cast<int>(currChar)];
 	if (currState == NXS_INVALID_STATE_CODE)
 		{
 		NxsString emsg;

Modified: pkg/src/nxsemptyblock.cpp
===================================================================
--- pkg/src/nxsemptyblock.cpp	2010-02-08 16:52:51 UTC (rev 737)
+++ pkg/src/nxsemptyblock.cpp	2010-02-08 17:07:13 UTC (rev 738)
@@ -19,6 +19,9 @@
 
 #include "ncl/ncl.h"
 
+// not used in phylobase
+#if 0
+
 using namespace std;
 /*----------------------------------------------------------------------------------------------------------------------
 |	Sets the base class data member `id' to the name of the block (i.e. "EMPTY") in NEXUS data files.
@@ -120,3 +123,5 @@
 	return 0;
 	}
 
+
+#endif