Fixing Travis build, remove gcc warnings and bump version

5 files changed, 32 insertions, 32 deletions

diff --git a/src/fastblas.cpp b/src/fastblas.cpp
index 41ee741..efa8412 100644
--- a/src/fastblas.cpp
+++ b/src/fastblas.cpp
@@ -2,7 +2,7 @@
     Genome-wide Efficient Mixed Model Association (GEMMA)
     Copyright © 2011-2017, Xiang Zhou
     Copyright © 2017, Peter Carbonetto
-    Copyright © 2017, Pjotr Prins
+    Copyright © 2017-2020, Pjotr Prins
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -25,6 +25,7 @@
 #include "debug.h"
 #include "mathfunc.h"
 #include <string.h>
+#include "fastblas.h"
 
 const char *FastblasTrans = "T";
 const char *FastblasNoTrans = "N";
@@ -246,29 +247,27 @@ extern "C" {
   int gsl_linalg_LU_decomp(gsl_matrix * A, gsl_permutation * p, int * signum);
 }
 
-void gsl_matrix_inv(gsl_matrix *m)  
-{  
-    size_t n=m->size1;  
-  
-    gsl_matrix *temp1=gsl_matrix_calloc(n,n);  
-    gsl_matrix_memcpy(temp1,m);  
-  
-    gsl_permutation *p=gsl_permutation_calloc(n);  
-    int sign=0;  
-    gsl_linalg_LU_decomp(temp1,p,&sign);  
-    gsl_matrix *inverse=gsl_matrix_calloc(n,n);  
-  
-    gsl_linalg_LU_invert(temp1,p,inverse);  
-    gsl_matrix_memcpy(m,inverse);  
-  
-    gsl_permutation_free(p);  
-    gsl_matrix_free(temp1);  
-    gsl_matrix_free(inverse);  
-  
+void gsl_matrix_inv(gsl_matrix *m)
+{
+    size_t n=m->size1;
+
+    gsl_matrix *temp1=gsl_matrix_calloc(n,n);
+    gsl_matrix_memcpy(temp1,m);
+
+    gsl_permutation *p=gsl_permutation_calloc(n);
+    int sign=0;
+    gsl_linalg_LU_decomp(temp1,p,&sign);
+    gsl_matrix *inverse=gsl_matrix_calloc(n,n);
+
+    gsl_linalg_LU_invert(temp1,p,inverse);
+    gsl_matrix_memcpy(m,inverse);
+
+    gsl_permutation_free(p);
+    gsl_matrix_free(temp1);
+    gsl_matrix_free(inverse);
+
 }
 
 void fast_inverse(gsl_matrix *m) {
     gsl_matrix_inv(m);
 }
-
-  
diff --git a/src/fastblas.h b/src/fastblas.h
index 32253b3..b36506d 100644
--- a/src/fastblas.h
+++ b/src/fastblas.h
@@ -23,7 +23,8 @@
 
 #include <assert.h>
 #include <iostream>
-// #include "gsl/gsl_matrix.h"
+#include "gsl/gsl_cblas.h"
+#include "gsl/gsl_matrix.h"
 
 gsl_matrix *fast_copy(gsl_matrix *m, const double *mem);
 
diff --git a/src/lmm.cpp b/src/lmm.cpp
index b811594..6337116 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -278,8 +278,8 @@ void CalcPab(const size_t n_cvt, const size_t e_mode, const gsl_vector *Hi_eval,
              const gsl_matrix *Uab, const gsl_vector *unused, gsl_matrix *Pab) {
 
 
-  size_t n_index = (n_cvt + 2 + 1) * (n_cvt + 2) / 2; // result size
-  auto ni_test = Uab->size1; // inds
+  // size_t n_index = (n_cvt + 2 + 1) * (n_cvt + 2) / 2; // result size
+  // auto ni_test = Uab->size1; // inds
   assert(Uab->size1 == Hi_eval->size);
   assert(Uab->size2 == n_index);
 
@@ -593,8 +593,8 @@ $7 = 3
 $8 = 6
   */
 
-  auto Uab = p->Uab;
-  auto ab = p->ab;
+    // auto Uab = p->Uab;
+    // auto ab = p->ab;
   assert(n_index == (n_cvt + 2 + 1) * (n_cvt + 2) / 2);
   assert(Uab->size1 == ni_test);
   assert(Uab->size2 == n_index); // n_cvt == 1 -> n_index == 6?
diff --git a/src/mathfunc.cpp b/src/mathfunc.cpp
index cd74e09..aaa9431 100644
--- a/src/mathfunc.cpp
+++ b/src/mathfunc.cpp
@@ -400,7 +400,7 @@ uint count_abs_small_values(const gsl_vector *v, double min) {
 // and the ratio of max and min but one (min is expected to be zero).
 bool isMatrixIllConditioned(const gsl_vector *eigenvalues, double max_ratio) {
   auto t = abs_minmax(eigenvalues);
-  auto absmin = get<0>(t);
+  // auto absmin = get<0>(t);
   auto absmin1 = get<1>(t);
   auto absmax = get<2>(t);
   if (absmax/absmin1 > max_ratio) {
diff --git a/src/version.h b/src/version.h
index f97c9f1..6c22a1b 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1,5 +1,5 @@
-// version.h generated by GEMMA ./scripts/gen_version_info.sh
-#define GEMMA_VERSION "0.98.2"
-#define GEMMA_DATE "2020-05-28"
+// version.h generated by GEMMA scripts/gen_version_info.sh
+#define GEMMA_VERSION "0.98.3"
+#define GEMMA_DATE "2020-09-29"
 #define GEMMA_YEAR "2020"
-#define GEMMA_PROFILE ""
+#define GEMMA_PROFILE "/gnu/store/a7a35vv75zk9k23k8ws4v2wrs123dln1-profile"