From 643cdf74ccd4fc2d565168716fb5645917dee834 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Mon, 11 Apr 2011 19:32:07 +0000
Subject: [PATCH] 1.18.0 - fixed make.shared abort issue

---
 Mothur.xcodeproj/project.pbxproj |  4 ++--
 sharedcommand.cpp                | 12 +++++++-----
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 5a384ce..dbe9347 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -2018,7 +2018,7 @@
 		1DEB928B08733DD80010E9CD /* Release */ = {
 			isa = XCBuildConfiguration;
 			buildSettings = {
-				ARCHS = "$(NATIVE_ARCH_ACTUAL)";
+				ARCHS = "$(ARCHS_STANDARD_64_BIT)";
 				DEPLOYMENT_LOCATION = NO;
 				GCC_C_LANGUAGE_STANDARD = gnu99;
 				GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
@@ -2048,7 +2048,7 @@
 					"-lreadline",
 				);
 				PREBINDING = NO;
-				SDKROOT = "";
+				SDKROOT = macosx10.5;
 			};
 			name = Release;
 		};
diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index d153543..2b4d56e 100644
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -124,7 +124,7 @@ SharedCommand::SharedCommand(string option)  {
 			 
 			 //check for required parameters
 			 listfile = validParameter.validFile(parameters, "list", true);
-			 if (listfile == "not open") { abort = true; }
+			 if (listfile == "not open") { listfile = ""; abort = true; }
 			 else if (listfile == "not found") { 
 				 listfile = m->getListFile(); 
 				 if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
@@ -176,11 +176,11 @@ SharedCommand::SharedCommand(string option)  {
 			//getting output filename
 			filename = listfile;
 			if (outputDir == "") { outputDir += m->hasPath(filename); }
-			
+					
 			filename = outputDir + m->getRootName(m->getSimpleName(filename));
 			filename = filename + "shared";
 			outputTypes["shared"].push_back(filename);
-			
+				
 			m->openOutputFile(filename, out);
 			pickedGroups = false;
 						
@@ -196,10 +196,10 @@ SharedCommand::SharedCommand(string option)  {
 				temp = new ofstream;
 				filehandles[Groups[i]] = temp;
 			}
-			
+				
 			//set fileroot
 			fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
-			
+				
 			//clears file before we start to write to it below
 			for (int i=0; i<Groups.size(); i++) {
 				remove((fileroot + Groups[i] + ".rabund").c_str());
@@ -220,6 +220,8 @@ SharedCommand::SharedCommand(string option)  {
 int SharedCommand::execute(){
 	try {
 		
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+		
 		//lookup.clear();
 		string errorOff = "no error";
 		//errorOff = "";
-- 
2.39.2