Fixes error when outputdir set in rename.file

Adds file mismatch check to summary.seqs
Fixes makefile for linux
mothur · mothur-westcott · mothur-westcott · mothur-westcott · mothur-westcott · mothur-westcott
diff --git a/Makefile b/Makefile
@@ -7,6 +7,13 @@
 #
 # Macros
 #
+# 64BIT_VERSION - set to no if you are using a 32bit arch.
+# OPTIMIZE - yes will increase speed of executable.
+# USEREADLINE - link with readline libraries.  Must have readline installed. Windows set to no.
+# USEBOOST - link with boost libraries. Must install boost. Allows the make.contigs command to read .gz files.
+# BOOST_LIBRARY_DIR - location of boost libraries
+# BOOST_INCLUDE_DIR - location of boost include files
+# MOTHUR_FILES - default location for mothur to look for input files at runtime. Most often used for reference files.
 
 64BIT_VERSION ?= yes
 OPTIMIZE ?= yes
@@ -15,8 +22,8 @@ USEBOOST ?= yes
 BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
 BOOST_INCLUDE_DIR="\"Enter_your_boost_include_path_here\""
 MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"1/23/2017\""
-VERSION = "\"1.39.0\""
+RELEASE_DATE = "\"3/20/2017\""
+VERSION = "\"1.39.5\""
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
     CXXFLAGS += -DBIT_VERSION
@@ -27,10 +34,8 @@ ifeq  ($(strip $(OPTIMIZE)),yes)
     CXXFLAGS += -O3
 endif
 
-#CPP_11
-    CXXFLAGS += -std=c++11
-
-CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION} -O3
+CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION} -std=c++0x
+LDFLAGS += -std=c++0x
 
 ifeq  ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
 else
diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
@@ -806,7 +806,6 @@
 		481623E31B58267D004C60B7 /* INSTALL.md */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = net.daringfireball.markdown; path = INSTALL.md; sourceTree = SOURCE_ROOT; };
 		481FB5191AC0A63E0076CFF3 /* TestMothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = TestMothur; sourceTree = BUILT_PRODUCTS_DIR; };
 		481FB51B1AC0A63E0076CFF3 /* main.cpp */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.cpp.cpp; name = main.cpp; path = TestMothur/main.cpp; sourceTree = SOURCE_ROOT; };
-		481FB5201AC0A6B60076CFF3 /* catch.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; name = catch.hpp; path = TestMothur/catch.hpp; sourceTree = SOURCE_ROOT; };
 		481FB5281AC19F8B0076CFF3 /* setseedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = setseedcommand.cpp; path = source/commands/setseedcommand.cpp; sourceTree = SOURCE_ROOT; };
 		481FB5291AC19F8B0076CFF3 /* setseedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = setseedcommand.h; path = source/commands/setseedcommand.h; sourceTree = SOURCE_ROOT; };
 		481FB52D1AC1B0CB0076CFF3 /* testsetseedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = testsetseedcommand.cpp; path = TestMothur/testcommands/testsetseedcommand.cpp; sourceTree = SOURCE_ROOT; };
@@ -1661,8 +1660,6 @@
 				A7E9B73A12D37EC400DA6239 /* libshuff.h */,
 				A7FC480C12D788F20055BC5C /* linearalgebra.h */,
 				A7FC480D12D788F20055BC5C /* linearalgebra.cpp */,
-				A7D9378B17B15215001E90B0 /* wilcox.h */,
-				A7D9378917B146B5001E90B0 /* wilcox.cpp */,
 				A7E9BA5612D39BD800DA6239 /* metastats */,
 				A7E9B75B12D37EC400DA6239 /* mothur.cpp */,
 				A7E9B75C12D37EC400DA6239 /* mothur.h */,
@@ -1722,6 +1719,8 @@
 				A7E9B87912D37EC400DA6239 /* venn.h */,
 				489B55701BCD7F0100FB7DC8 /* vsearchfileparser.cpp */,
 				489B55711BCD7F0100FB7DC8 /* vsearchfileparser.h */,
+				A7D9378B17B15215001E90B0 /* wilcox.h */,
+				A7D9378917B146B5001E90B0 /* wilcox.cpp */,
 				A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */,
 			);
 			name = Source;
@@ -1739,7 +1738,6 @@
 		481FB51A1AC0A63E0076CFF3 /* TestMothur */ = {
 			isa = PBXGroup;
 			children = (
-				481FB5201AC0A6B60076CFF3 /* catch.hpp */,
 				481FB51B1AC0A63E0076CFF3 /* main.cpp */,
 				48F06CCA1D74BC6F004A45DD /* testclassifier */,
 				48D6E9691CA4262A008DF76B /* dataset.cpp */,
@@ -3370,8 +3368,8 @@
 			isa = XCBuildConfiguration;
 			buildSettings = {
 				ALWAYS_SEARCH_USER_PATHS = YES;
-				CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
-				CLANG_CXX_LIBRARY = "libstdc++";
+				CLANG_CXX_LANGUAGE_STANDARD = "c++14";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				CLANG_WARN_CXX0X_EXTENSIONS = YES;
 				"CLANG_WARN_CXX0X_EXTENSIONS[arch=*]" = NO;
 				CLANG_WARN_UNREACHABLE_CODE = YES;
@@ -3380,23 +3378,21 @@
 				DSTROOT = TARGET_BUILD_DIR;
 				"DSTROOT[sdk=*]" = TARGET_BUILD_DIR;
 				"DYLIB_CURRENT_VERSION[sdk=*]" = "";
+				GCC_C_LANGUAGE_STANDARD = "compiler-default";
 				GCC_DYNAMIC_NO_PIC = NO;
 				GCC_MODEL_TUNING = G5;
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.39.0\\\"\"",
-					"RELEASE_DATE=\"\\\"1/20/2017\\\"\"",
+					"VERSION=\"\\\"1.39.3\\\"\"",
+					"RELEASE_DATE=\"\\\"2/23/2017\\\"\"",
 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
 				);
 				GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
 				GCC_WARN_UNINITIALIZED_AUTOS = NO;
 				GCC_WARN_UNUSED_FUNCTION = YES;
 				"INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR;
 				LIBRARY_SEARCH_PATHS = "";
-				"LIBRARY_SEARCH_PATHS[arch=*]" = (
-					/usr/local/lib/,
-					/usr/local/include/,
-				);
+				"LIBRARY_SEARCH_PATHS[arch=*]" = /usr/local/lib/;
 				ONLY_ACTIVE_ARCH = YES;
 				PRELINK_LIBS = "";
 				PRODUCT_NAME = mothur;
@@ -3409,27 +3405,25 @@
 			isa = XCBuildConfiguration;
 			buildSettings = {
 				ALWAYS_SEARCH_USER_PATHS = YES;
-				CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
-				CLANG_CXX_LIBRARY = "libstdc++";
+				CLANG_CXX_LANGUAGE_STANDARD = "c++14";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				CLANG_WARN_CXX0X_EXTENSIONS = YES;
 				CLANG_WARN_UNREACHABLE_CODE = YES;
 				DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
 				DEPLOYMENT_LOCATION = YES;
 				DSTROOT = TARGET_BUILD_DIR;
+				GCC_C_LANGUAGE_STANDARD = "compiler-default";
 				GCC_MODEL_TUNING = G5;
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.39.0\\\"\"",
-					"RELEASE_DATE=\"\\\"1/20/2017\\\"\"",
+					"VERSION=\"\\\"1.39.3\\\"\"",
+					"RELEASE_DATE=\"\\\"2/23/2017\\\"\"",
 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
 				);
 				GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
 				GCC_WARN_UNINITIALIZED_AUTOS = NO;
 				GCC_WARN_UNUSED_VALUE = YES;
-				LIBRARY_SEARCH_PATHS = (
-					/usr/local/include/,
-					/usr/local/lib/,
-				);
+				LIBRARY_SEARCH_PATHS = /usr/local/lib/;
 				"LIBRARY_SEARCH_PATHS[arch=*]" = "";
 				ONLY_ACTIVE_ARCH = YES;
 				PRELINK_LIBS = "";
@@ -3444,19 +3438,19 @@
 			isa = XCBuildConfiguration;
 			buildSettings = {
 				CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
-				CLANG_CXX_LIBRARY = "libstdc++";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				CLANG_WARN_UNREACHABLE_CODE = YES;
 				DEPLOYMENT_LOCATION = NO;
 				ENABLE_TESTABILITY = YES;
-				GCC_C_LANGUAGE_STANDARD = c11;
+				GCC_C_LANGUAGE_STANDARD = "compiler-default";
 				GCC_ENABLE_SSE3_EXTENSIONS = NO;
 				GCC_ENABLE_SSE41_EXTENSIONS = NO;
 				GCC_ENABLE_SSE42_EXTENSIONS = NO;
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
-					"VERSION=\"\\\"1.36.0\\\"\"",
-					"RELEASE_DATE=\"\\\"07/23/2015\\\"\"",
+					"VERSION=\"\\\"1.39.1\\\"\"",
+					"RELEASE_DATE=\"\\\"2/2/2017\\\"\"",
 				);
 				GCC_VERSION = "";
 				"GCC_VERSION[arch=*]" = "";
@@ -3465,8 +3459,11 @@
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
 				GCC_WARN_UNUSED_FUNCTION = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
-				HEADER_SEARCH_PATHS = /usr/local/include/;
-				"HEADER_SEARCH_PATHS[arch=*]" = "";
+				HEADER_SEARCH_PATHS = "";
+				"HEADER_SEARCH_PATHS[arch=*]" = (
+					"$(inherited)",
+					/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include,
+				);
 				INSTALL_PATH = TARGET_BUILD_DIR;
 				LIBRARY_SEARCH_PATHS = "";
 				"LIBRARY_SEARCH_PATHS[arch=*]" = /usr/local/lib/;
@@ -3475,12 +3472,10 @@
 				ONLY_ACTIVE_ARCH = YES;
 				OTHER_CPLUSPLUSFLAGS = (
 					"-DBIT_VERSION",
-					"-DUSE_BOOST",
 					"-DUNIT_TEST",
-					"-stdlib=libstdc++",
-					"-std=c++11",
 					"-DUSE_READLINE",
 					"$(OTHER_CFLAGS)",
+					"-DUSE_BOOST",
 				);
 				OTHER_LDFLAGS = (
 					"-lreadline",
@@ -3497,16 +3492,16 @@
 			isa = XCBuildConfiguration;
 			buildSettings = {
 				CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
-				CLANG_CXX_LIBRARY = "libstdc++";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				CLANG_WARN_UNREACHABLE_CODE = YES;
 				DEPLOYMENT_LOCATION = NO;
-				GCC_C_LANGUAGE_STANDARD = c11;
+				GCC_C_LANGUAGE_STANDARD = "compiler-default";
 				GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
 				GCC_MODEL_TUNING = "";
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.39.0\\\"\"",
-					"RELEASE_DATE=\"\\\"1/20/2017\\\"\"",
+					"VERSION=\"\\\"1.39.3\\\"\"",
+					"RELEASE_DATE=\"\\\"2/23/2017\\\"\"",
 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
 				);
 				GCC_VERSION = "";
@@ -3530,12 +3525,10 @@
 				MACOSX_DEPLOYMENT_TARGET = 10.12;
 				OTHER_CPLUSPLUSFLAGS = (
 					"-DUSE_READLINE",
-					"-DUSE_BOOST",
 					"-DUNIT_TEST",
-					"-std=c++11",
-					"-stdlib=libstdc++",
 					"-DBIT_VERSION",
 					"$(OTHER_CFLAGS)",
+					"-DUSE_BOOST",
 				);
 				OTHER_LDFLAGS = (
 					"-lreadline",
@@ -3553,7 +3546,7 @@
 			buildSettings = {
 				ALWAYS_SEARCH_USER_PATHS = YES;
 				CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
-				CLANG_CXX_LIBRARY = "libstdc++";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				CLANG_ENABLE_MODULES = YES;
 				CLANG_ENABLE_OBJC_ARC = YES;
 				CLANG_WARN_BOOL_CONVERSION = NO;
@@ -3568,7 +3561,7 @@
 				ENABLE_STRICT_OBJC_MSGSEND = YES;
 				GCC_C_LANGUAGE_STANDARD = "compiler-default";
 				GCC_DYNAMIC_NO_PIC = NO;
-				GCC_OPTIMIZATION_LEVEL = 0;
+				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"DEBUG=1",
 					"$(inherited)",
@@ -3591,7 +3584,7 @@
 			buildSettings = {
 				ALWAYS_SEARCH_USER_PATHS = YES;
 				CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
-				CLANG_CXX_LIBRARY = "libstdc++";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				CLANG_ENABLE_MODULES = YES;
 				CLANG_ENABLE_OBJC_ARC = YES;
 				CLANG_WARN_BOOL_CONVERSION = NO;
@@ -3607,6 +3600,7 @@
 				ENABLE_NS_ASSERTIONS = NO;
 				ENABLE_STRICT_OBJC_MSGSEND = YES;
 				GCC_C_LANGUAGE_STANDARD = "compiler-default";
+				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"VERSION=\"\\\"1.37.6\\\"\"",
 					"RELEASE_DATE=\"\\\"06/20/2016\\\"\"",