Makefile

@@ -25,7 +25,7 @@ LOGFILE_NAME ?= 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\""
-VERSION = "\"1.40.2\""
+VERSION = "\"1.40.3\""
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
     CXXFLAGS += -DBIT_VERSION

Mothur.xcodeproj/project.pbxproj

@@ -3685,10 +3685,10 @@
 				GCC_C_LANGUAGE_STANDARD = "compiler-default";
 				GCC_DYNAMIC_NO_PIC = NO;
 				GCC_MODEL_TUNING = G5;
-				GCC_OPTIMIZATION_LEVEL = 0;
+				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
-					"VERSION=\"\\\"1.40.0\\\"\"",
+					"VERSION=\"\\\"1.40.3\\\"\"",
 					"LOGFILE_NAME=\"\\\"silent\\\"\"",
 				);
 				GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3718,10 +3718,10 @@
 				DSTROOT = TARGET_BUILD_DIR;
 				GCC_C_LANGUAGE_STANDARD = "compiler-default";
 				GCC_MODEL_TUNING = G5;
-				GCC_OPTIMIZATION_LEVEL = 0;
+				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
-					"VERSION=\"\\\"1.40.0\\\"\"",
+					"VERSION=\"\\\"1.40.3\\\"\"",
 					"LOGFILE_NAME=\"\\\"./mothur.logfile\\\"\"",
 				);
 				GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3761,10 +3761,10 @@
 				GCC_ENABLE_SSE41_EXTENSIONS = NO;
 				GCC_ENABLE_SSE42_EXTENSIONS = NO;
 				GCC_NO_COMMON_BLOCKS = YES;
-				GCC_OPTIMIZATION_LEVEL = 0;
+				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
-					"VERSION=\"\\\"1.39.5\\\"\"",
+					"VERSION=\"\\\"1.40.3\\\"\"",
 					"LOGFILE_NAME=\"\\\"./mothur.logfile\\\"\"",
 				);
 				GCC_VERSION = "";
@@ -3828,9 +3828,9 @@
 				GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
 				GCC_MODEL_TUNING = "";
 				GCC_NO_COMMON_BLOCKS = YES;
-				GCC_OPTIMIZATION_LEVEL = 0;
+				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.39.5\\\"\"",
+					"VERSION=\"\\\"1.40.3\\\"\"",
 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
 					"LOGFILE_NAME=\"\\\"./mothur.logfile\\\"\"",
 				);

debian/changelog

-mothur (1.40.2-1) unstable; urgency=medium
+mothur (1.40.3-1) unstable; urgency=medium
 
   [ Steffen Moeller ]
   * debian/upstream/metadata:
@@ -8,9 +8,13 @@ mothur (1.40.2-1) unstable; urgency=medium
   [ Tomasz Buchert ]
   * fix insecure-copyright-format-uri
   * use debhelper compat 11
-  * New upstream version 1.40.2
+  * New upstream version 1.40.3
 
- -- Tomasz Buchert <tomasz@debian.org>  Wed, 25 Apr 2018 22:32:28 +0200
+  [ Andreas Tille ]
+  * Spacing
+  * Remove invalid fields from debian/upstream/metadata
+
+ -- Tomasz Buchert <tomasz@debian.org>  Sat, 19 May 2018 15:48:02 +0200
 
 mothur (1.39.5-2) unstable; urgency=medium
 

debian/patches/0002-update-version-numbers-everywhere.patch

-From: Tomasz Buchert <tomasz@debian.org>
-Date: Wed, 25 Apr 2018 22:47:30 +0200
-Subject: update version numbers everywhere
-
----
- Mothur.xcodeproj/project.pbxproj | 4 ++--
- makefile-internal                | 2 +-
- 2 files changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
-index f3ac5a2..da83469 100644
---- a/Mothur.xcodeproj/project.pbxproj
-+++ b/Mothur.xcodeproj/project.pbxproj
-@@ -3764,7 +3764,7 @@
- 				GCC_OPTIMIZATION_LEVEL = 0;
- 				GCC_PREPROCESSOR_DEFINITIONS = (
- 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
--					"VERSION=\"\\\"1.39.5\\\"\"",
-+					"VERSION=\"\\\"1.40.2\\\"\"",
- 					"LOGFILE_NAME=\"\\\"./mothur.logfile\\\"\"",
- 				);
- 				GCC_VERSION = "";
-@@ -3830,7 +3830,7 @@
- 				GCC_NO_COMMON_BLOCKS = YES;
- 				GCC_OPTIMIZATION_LEVEL = 0;
- 				GCC_PREPROCESSOR_DEFINITIONS = (
--					"VERSION=\"\\\"1.39.5\\\"\"",
-+					"VERSION=\"\\\"1.40.2\\\"\"",
- 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
- 					"LOGFILE_NAME=\"\\\"./mothur.logfile\\\"\"",
- 				);
-diff --git a/makefile-internal b/makefile-internal
-index ebeb566..49a14d9 100644
---- a/makefile-internal
-+++ b/makefile-internal
-@@ -2,7 +2,7 @@
- USEREADLINE ?= no
- USEBOOST ?= no
- LOGFILE_NAME ?= yes
--VERSION = "\"1.39.5\""
-+VERSION = "\"1.40.2\""
- 
- # Optimize to level 3:
-     CXXFLAGS += -O3 -std=c++11

debian/patches/series

 0001-Add-hardening-flags.patch
-0002-update-version-numbers-everywhere.patch

makefile-internal

@@ -2,7 +2,7 @@
 USEREADLINE ?= no
 USEBOOST ?= no
 LOGFILE_NAME ?= yes
-VERSION = "\"1.39.5\""
+VERSION = "\"1.40.3\""
 
 # Optimize to level 3:
     CXXFLAGS += -O3 -std=c++11

source/calcsparcc.cpp

@@ -27,6 +27,7 @@ CalcSparcc::CalcSparcc(vector<vector<float> > sharedVector, int maxIterations, i
         //    unsigned long long cycTimeStart = time(NULL);
 
         for(int i=0;i<numSamplings;i++){
+
             if (m->getControl_pressed()) { break; }
             vector<float> logFractions =  getLogFractions(sharedVector, method);
             getT_Matrix(logFractions);     //this step is slow...
@@ -61,7 +62,6 @@ CalcSparcc::CalcSparcc(vector<vector<float> > sharedVector, int maxIterations, i
                 median = allCorrelations[0];
             }
         }
-//    cout << median[0][3] << '\t' << median[0][6] << endl;
     }
     catch(exception& e) {
         m->errorOut(e, "CalcSparcc", "CalcSparcc");
@@ -84,9 +84,7 @@ void CalcSparcc::addPseudoCount(vector<vector<float> >& sharedVector){
         m->errorOut(e, "CalcSparcc", "addPseudoCount");
         exit(1);
     }
-
 }
-
 /**************************************************************************************************/
 
 vector<float> CalcSparcc::getLogFractions(vector<vector<float> > sharedVector, string method){   //dirichlet by default
@@ -97,7 +95,7 @@ vector<float> CalcSparcc::getLogFractions(vector<vector<float> > sharedVector, s
             vector<float> alphas(numGroups);
             for(int i=0;i<numGroups;i++){   //iterate across the groups
                 if (m->getControl_pressed()) { return logSharedFractions; }
-                alphas = RNG.randomDirichlet(sharedVector[i]);
+                alphas = util.randomDirichlet(sharedVector[i]);
 
                 for(int j=0;j<numOTUs;j++){
 									logSharedFractions[i * numOTUs + j] = alphas[j];
@@ -137,7 +135,6 @@ void CalcSparcc::getT_Matrix(vector<float> sharedFractions){
         tMatrix.resize(numOTUs * numOTUs, 0);
 
         vector<float> diff(numGroups);
-        
         for(int j1=0;j1<numOTUs;j1++){
             for(int j2=0;j2<j1;j2++){
                 if (m->getControl_pressed()) { return; }
@@ -146,8 +143,8 @@ void CalcSparcc::getT_Matrix(vector<float> sharedFractions){
                     diff[i] = sharedFractions[i * numOTUs + j1] - sharedFractions[i * numOTUs + j2];
                     mean += diff[i];
                 }
-                mean /= float(numGroups);
 
+                mean /= float(numGroups);
                 float variance = 0.0;
                 for(int i=0;i<numGroups;i++){
                     variance += (diff[i] - mean) * (diff[i] - mean);
@@ -247,7 +244,6 @@ vector<vector<float> > CalcSparcc::getBasisCorrelations(vector<float> basisVaria
                 else if(rho[i][j] < -1.0)   {   rho[i][j] = -1.0;  }
 
                 rho[j][i] = rho[i][j];
-                
             }
         }
 

source/calcsparcc.h

@@ -13,8 +13,9 @@
 /**************************************************************************************************/
 
 //#include "sparcc.h"
-#include "randomnumber.h"
+
 #include "mothurout.h"
+#include "utils.hpp"
 
 /**************************************************************************************************/
 
@@ -25,6 +26,7 @@ public:
     vector<vector<float> > getRho()    {   return median;  }
 private:
     MothurOut* m;
+    Utils util;
     void addPseudoCount(vector<vector<float> >&);
     vector<float> getLogFractions(vector<vector<float> >, string);
     void getT_Matrix(vector<float>);
@@ -48,8 +50,6 @@ private:
     int numOTUs;
     int numGroups;
     string normalizationMethod;
-    
-    RandomNumberGenerator RNG;    
 };
 
 #endif