cleanup a bunch of compiler warnings (#3849)

* cleanup a bunch of g++ warnings

* make it work with clang

* remove some additional warnings based on CI builds

* fix that version number

* stop being verbose when building

External/GA/ga/BinaryStringChromosomePolicy.cpp

@@ -12,18 +12,20 @@
 
 namespace GapeGa {
 
-BinaryStringChromosomePolicy::BinaryStringChromosomePolicy(GarethUtil::RandomUtil & rng_) : rng(rng_){
-}
+BinaryStringChromosomePolicy::BinaryStringChromosomePolicy(
+    GarethUtil::RandomUtil& rng_)
+    : rng(rng_) {}
 
-BinaryStringChromosomePolicy::~BinaryStringChromosomePolicy() {
-}
+BinaryStringChromosomePolicy::~BinaryStringChromosomePolicy() {}
 
 bool BinaryStringChromosomePolicy::mutate(int pos, bool currentValue) const {
-    return ! currentValue;
-}
-    
-bool BinaryStringChromosomePolicy::initialize(int pos) const {
-    return rng.randomBoolean();
+  (void)pos;  // not used
+  return !currentValue;
 }
 
+bool BinaryStringChromosomePolicy::initialize(int pos) const {
+  (void)pos;  // not used
+  return rng.randomBoolean();
 }
+
+}  // namespace GapeGa

External/GA/ga/LinkedPopLinearSel.h

@@ -141,6 +141,8 @@ LinkedPopLinearSel<Chromosome, PopulationPolicy>::LinkedPopLinearSel(
   assert(abs(totalScaledFitness - predictTotalScaledFitness) < 1.0e-5);
 
   double predictEndFitness = SELECT_START + (popsize - 1.0) * scaledFitnessStep;
+  (void)predictEndFitness;  // suppress warnings when building with
+                            // assertions disabled
 #ifdef INCLUDE_REPORTER
   REPORT(Reporter::TRACE) << "endFitness " << endFitness
                           << " predictEndFitness " << predictEndFitness;

External/INCHI-API/inchi.cpp

@@ -93,11 +93,11 @@ bool assignBondDirs(RWMol& mol, INT_PAIR_VECT& zBondPairs,
                     INT_PAIR_VECT& eBondPairs) {
   // bonds to assign
   std::set<int> pending;
-  for (const auto pair : zBondPairs) {
+  for (const auto& pair : zBondPairs) {
     pending.insert(pair.first);
     pending.insert(pair.second);
   }
-  for (const auto pair : eBondPairs) {
+  for (const auto& pair : eBondPairs) {
     pending.insert(pair.first);
     pending.insert(pair.second);
   }
@@ -138,7 +138,7 @@ bool assignBondDirs(RWMol& mol, INT_PAIR_VECT& zBondPairs,
         for (int _ = 0; _ < 2; _++) {
           INT_PAIR_VECT* _rules = _ == 0 ? &zBondPairs : &eBondPairs;
           Bond::BondDir _dir = _ == 0 ? dir : otherDir;
-          for (const auto pair : *_rules) {
+          for (const auto& pair : *_rules) {
             int other = -1;
             if (pair.first == curBondIdx) {
               other = pair.second;
@@ -1872,7 +1872,7 @@ std::string MolToInchi(const ROMol& mol, ExtraInchiReturnValues& rv,
       // std::sort(neighbors.begin(), neighbors.end());
       unsigned char nid = 0;
       // std::cerr<<" at: "<<atom->getIdx();
-      for (const auto p : neighbors) {
+      for (const auto& p : neighbors) {
         stereo0D.neighbor[nid++] = p.second;
         // std::cerr<<" "<<p.second;
       }