More warnings work

Author: michalsta

IsoSpec++/Makefile

@@ -1,9 +1,12 @@
 OPTFLAGS=-O3 -march=native -mtune=native
 DEBUGFLAGS=-O0 -g -Werror -DISOSPEC_DEBUG -DDEBUG -D_GLIBCXX_DEBUG
-CXXFLAGS=-std=c++17 -Wall -pedantic -Wextra -Wshadow -Wcast-align -Wcast-qual -Wctor-dtor-privacy -Wdisabled-optimization -Wformat=2 -Winit-self -Wmissing-include-dirs -Wno-old-style-cast -Woverloaded-virtual -Wredundant-decls -Wshadow -Wno-sign-conversion -Wsign-promo -Wswitch-default -Wundef
+CXXFLAGS=-std=c++17 -Wall -pedantic -Wextra -Wshadow -Wcast-align -Wcast-qual -Wctor-dtor-privacy -Wdisabled-optimization -Wformat=2 -Winit-self -Wmissing-include-dirs -Wno-old-style-cast -Woverloaded-virtual -Wredundant-decls -Wshadow -Wno-sign-conversion -Wsign-promo -Wswitch-default -Wundef -Wshorten-64-to-32
 SRCFILES=cwrapper.cpp allocator.cpp  dirtyAllocator.cpp  isoSpec++.cpp  isoMath.cpp  marginalTrek++.cpp  operators.cpp element_tables.cpp misc.cpp mman.cpp fixedEnvelopes.cpp fasta.cpp
 
-all: unitylib
+all: syntax
+
+syntax:
+	$(CXX) $(CXXFLAGS) unity-build.cpp -fsyntax-only
 
 unitylib:
 	$(CXX) $(CXXFLAGS) $(OPTFLAGS) unity-build.cpp -fPIC -shared -o libIsoSpec++.so

IsoSpec++/allocator.cpp

@@ -21,7 +21,7 @@ namespace IsoSpec
 {
 
 template <typename T>
-Allocator<T>::Allocator(const int dim_, const int tabSize_): currentTab(new T[dim_ * tabSize_]), currentId(-1), dim(dim_), tabSize(tabSize_) {}
+Allocator<T>::Allocator(const size_t dim_, const size_t tabSize_): currentTab(new T[dim_ * tabSize_]), currentId(-1), dim(dim_), tabSize(tabSize_) {}
 
 
 template <typename T>
@@ -34,7 +34,7 @@ Allocator<T>::~Allocator()
         delete [] currentTab;
     }
 
-    for(unsigned int i = 0; i < prevTabs.size(); ++i)
+    for(size_t i = 0; i < prevTabs.size(); ++i)
         delete [] prevTabs[i];
 }
 

IsoSpec++/allocator.h

@@ -25,21 +25,21 @@ namespace IsoSpec
 
 template <typename T> inline void copyConf(
     const T* source, T* destination,
-    int dim
+    size_t dim
 ){
     memcpy(destination, source, dim*sizeof(T));
 }
 
 template <typename T> class Allocator
 {
  private:
-    T*      currentTab;
+    T* currentTab;
     int currentId;
-    const int       dim, tabSize;
+    const size_t dim, tabSize;
     pod_vector<T*>  prevTabs;
 
  public:
-    explicit Allocator(const int dim, const int tabSize = 10000);
+    explicit Allocator(const size_t dim, const size_t tabSize = 10000);
     ~Allocator();
 
     Allocator(const Allocator& other) = delete;

IsoSpec++/dirtyAllocator.cpp

@@ -22,7 +22,7 @@ namespace IsoSpec
 {
 
 DirtyAllocator::DirtyAllocator(
-    const int dim, const int tabSize_
+    const size_t dim, const size_t tabSize_
 ): tabSize(tabSize_)
 {
     cellSize        = sizeof(double) + sizeof(int) * dim;
@@ -39,7 +39,7 @@ DirtyAllocator::DirtyAllocator(
 
 DirtyAllocator::~DirtyAllocator()
 {
-    for(unsigned int i = 0; i < prevTabs.size(); ++i) free(prevTabs[i]);
+    for(size_t i = 0; i < prevTabs.size(); ++i) free(prevTabs[i]);
     free(currentTab);
 }
 

IsoSpec++/dirtyAllocator.h

@@ -28,12 +28,12 @@ class DirtyAllocator
     void*   currentTab;
     void*   currentConf;
     void*   endOfTablePtr;
-    const int       tabSize;
+    const size_t tabSize;
     int     cellSize;
     pod_vector<void*>  prevTabs;
 
  public:
-    explicit DirtyAllocator(const int dim, const int tabSize = 10000);
+    explicit DirtyAllocator(const size_t dim, const size_t tabSize = 10000);
     ~DirtyAllocator();
 
     DirtyAllocator(const DirtyAllocator& other) = delete;

IsoSpec++/isoSpec++.h

@@ -247,7 +247,7 @@ class ISOSPEC_EXPORT_SYMBOL IsoOrderedGeneratorTemplate: public IsoGenerator
     double                      currentLProb;                       /*!< The log-probability of the current isotopologue. */
     double                      currentMass;                        /*!< The mass of the current isotopologue. */
     double                      currentProb;                        /*!< The probability of the current isotopologue. */
-    int                         ccount;
+    long int                    ccount;
 
  public:
     IsoOrderedGeneratorTemplate(const IsoOrderedGeneratorTemplate& other) = delete;
@@ -538,7 +538,7 @@ class ISOSPEC_EXPORT_SYMBOL IsoLayeredGeneratorTemplate : public IsoGenerator
 
 
     //! Recalculate the current partial log-probabilities, masses, and probabilities.
-    ISOSPEC_FORCE_INLINE void recalc(int idx)
+    ISOSPEC_FORCE_INLINE void recalc(size_t idx)
     {
         for(; idx > 0; idx--)
         {

IsoSpec++/misc.h

@@ -27,19 +27,19 @@ namespace IsoSpec
 {
 
 inline double combinedSum(
-    const int* conf, const std::vector<double>** valuesContainer, int dimNumber
+    const int* conf, const std::vector<double>** valuesContainer, size_t dimNumber
 ){
     double res = 0.0;
-    for(int i = 0; i < dimNumber; i++)
+    for(size_t i = 0; i < dimNumber; i++)
         res += (*(valuesContainer[i]))[conf[i]];
     return res;
 }
 
 inline double combinedSum(
-    const int* conf, const pod_vector<double>** valuesContainer, int dimNumber
+    const int* conf, const pod_vector<double>** valuesContainer, size_t dimNumber
 ){
     double res = 0.0;
-    for(int i = 0; i < dimNumber; i++)
+    for(size_t i = 0; i < dimNumber; i++)
         res += (*(valuesContainer[i]))[conf[i]];
     return res;
 }
@@ -135,9 +135,9 @@ template <typename T> static T* array_copy_nptr(const T* A, size_t size)
     return array_copy(A, size);
 }
 
-template<typename T> void dealloc_table(T* tbl, int dim)
+template<typename T> void dealloc_table(T* tbl, size_t dim)
 {
-    for(int i = 0; i < dim; i++)
+    for(size_t i = 0; i < dim; i++)
     {
         delete tbl[i];
     }