fixed warnings on new GCC compiler (8.3)

common.mk

@@ -1,6 +1,6 @@
 # Definitions common to all Makefiles
 # This file is included from other Makefiles in the augustus project.
-AUGVERSION = 3.3.2
+AUGVERSION = 3.3.3
 
 # make this a comment if you get compilation errors about the boost iostreams library
 # cannot install this library and do not need to input gzipped input genome files

include/extrinsicinfo.hh

@@ -329,7 +329,7 @@ public:
 	try {
 	    ssList += Properties::getProperty("allow_hinted_splicesites");
 	    ssList += ",";
-	} catch (KeyNotFoundError) {}
+	} catch (KeyNotFoundError &) {}
 	SequenceFeatureCollection::initHintedSplicesites(ssList);
 
 	if (offset < 0)

include/pp_fastBlockSearcher.hh

@@ -367,7 +367,7 @@ namespace PP {
 		    putSeedsToEntries(forval + aa, false);
 		if (aab >= 0 && revval >= 0)
 		    putSeedsToEntries(revval + 400*aab, true);
-	    } catch (InvalidNucleotideError e) {
+	    } catch (InvalidNucleotideError &e) {
 		aa = aab = -2;
 	    }
 	    nextPattern[0] = nextPattern[1];

include/properties.hh

@@ -244,37 +244,37 @@ class Properties{
     static void assignProperty(string name, Integer& target) {
 	try {
 	    target = getIntProperty(name);
- 	} catch (KeyNotFoundError e) {}
+ 	} catch (KeyNotFoundError &e) {}
     }
     static void assignProperty(string name, unsigned& target) {
 	try {
 	    target = (unsigned) getIntProperty(name);
- 	} catch (KeyNotFoundError e) {}
+ 	} catch (KeyNotFoundError &e) {}
     }
     static void assignProperty(string name, Double& target) {
 	try {
 	    target = getDoubleProperty(name);
- 	} catch (KeyNotFoundError e) {}
+ 	} catch (KeyNotFoundError &e) {}
     }
     static void assignProperty(string name, double& target) {
 	try {
 	    target = getdoubleProperty(name);
-	} catch (KeyNotFoundError e) {}
+	} catch (KeyNotFoundError &e) {}
     }
     static void assignProperty(string name, Boolean& target) {
 	try {
 	    target = getBoolProperty(name);
-	} catch (KeyNotFoundError e) {}
+	} catch (KeyNotFoundError &e) {}
     }
     static void assignProperty(string name, string& target) {
 	try {
 	    target = getProperty(name);
-	} catch (KeyNotFoundError e) {}
+	} catch (KeyNotFoundError &e) {}
     }
     static void assignProperty(string name, const char*& target) {
 	try {
 	    target = getProperty(name);
-	} catch (KeyNotFoundError e) {}
+	} catch (KeyNotFoundError &e) {}
     }
 
 

include/types.hh

@@ -57,7 +57,7 @@ ostream& operator<< (ostream& strm, const Strand s);
 #define MODEL_SUBDIR "model/"
 #define EXTRINSIC_SUBDIR "extrinsic/"
 
-#define VERSION "3.3.2"
+#define VERSION "3.3.3"
 
 #define PREAMBLE "# This output was generated with AUGUSTUS (version " VERSION ").\n\
 # AUGUSTUS is a gene prediction tool written by M. Stanke ([email protected]),\n\

include/vitmatrix.hh

@@ -510,7 +510,7 @@ public:
 	if (substate.undef()) return get(state);
 	try {
 	    return getSubstates(state).get(substate);
-	} catch (NoSubmapFoundError) {
+	} catch (NoSubmapFoundError &) {
 	    return 0;
 	}
     }
@@ -643,7 +643,7 @@ inline void ViterbiColumnType::getMaxSubstate(int state, SubstateId& substate, D
 	submap.getMaxSubstate(substate, value);
 	if (value > mainval)
 	    return;
-    } catch (NoSubmapFoundError) {}
+    } catch (NoSubmapFoundError &) {}
     substate.set(0); value = mainval;
 }
 

src/Makefile

@@ -7,7 +7,7 @@ CXX	= g++
 # Notes: - "-Wno-sign-compare" eliminates a high number of warnings (see footnote below). Please adopt
 #          a strict signed-only usage strategy to avoid mistakes since we are not warned about this.
 #        - The order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh)
-CXXFLAGS := -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -g -ggdb -O3 ${CXXFLAGS}# -DDEBUG -g -ggdb -pg -DDEBUG_STATES
+CXXFLAGS := -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 ${CXXFLAGS}# -DDEBUG -g -ggdb -pg -DDEBUG_STATES
 ifdef SQLITE
 	COMPGENEPRED = true
 endif

src/augustus.cc

@@ -233,7 +233,7 @@ int main( int argc, char* argv[] ){
     } catch( ProjectError& err ){
         cerr << "\n" <<  argv[0] << ": ERROR\n\t" << err.getMessage( ) << "\n\n";
         errorcode=1;
-    } catch ( HelpException help ) {
+    } catch ( HelpException &help ) {
     	cerr << help.message << endl;
     }
     if (outputfile.is_open())
@@ -424,7 +424,7 @@ void predictOnInputSequences(AnnoSequence *seq, NAMGene &namgene, FeatureCollect
 			cout << "# joint probability of gene structure and sequence in " << 
 			    Properties::getProperty(SPECIES_KEY) << " model: " << curseq->anno->emiProb << endl;
 			curseq->anno = olda;
-		    } catch (ProjectError e){
+		    } catch (ProjectError &e){
 			cerr << e.getMessage() << endl << "Error: Could not compute the emission probabilities (--emiprobs)" << endl;
 		    }
 		}
@@ -459,7 +459,7 @@ void setParameters(){
     } catch (...) {} 
     try {
 	checkExAcc = Properties::getBoolProperty("checkExAcc");
-    } catch (ProjectError e) {
+    } catch (ProjectError &e) {
 	cerr << e.getMessage();
     }
     try {

src/codonMSA.cc

@@ -133,7 +133,7 @@ void CodonMSA::readAlignment(string filename){
 	}
       }
       // cout << "species name: " << speciesName << "\t rowseq: " << rowseq << endl;
-    } catch (std::ios_base::failure e) {
+    } catch (std::ios_base::failure &e) {
       throw ProjectError(string("Could not open file ") + filename + ". Make sure this is not a directory.\n");
     }
     if(aliLen){

src/compgenepred.cc

@@ -204,7 +204,7 @@ void CompGenePred::start(){
 		throw ProjectError("Is not numeric.");
 	    dd_factors.push_back(pos);
 	}
-    } catch (ProjectError e) {
+    } catch (ProjectError &e) {
 	throw ProjectError("Format error parsing parameter --/CompPred/dd_factor=" + dd_param_s +".\n" + e.getMessage());
     }
     bool onlySampling = false;
@@ -221,7 +221,7 @@ void CompGenePred::start(){
 	}else{
 	  cout << "# No outfile for logReg parameters specified. Writing parameters to " << Constant::configPath <<  "/cgp/log_reg_parameters_trained.cfg" << endl;
 	}
-      } catch (ProjectError e) {
+      } catch (ProjectError &e) {
 	throw ProjectError("For parameter training a reference species must be specified. Use --refSpecies=<SPECIES> and note, that <SPECIES> must be identical to one of the species names provided in the alignment and tree files.");
       }
     }

src/etraining.cc

@@ -67,7 +67,7 @@ int main( int argc, char* argv[] ){
 
 	try {
 	    Properties::init( argc, argv );
-	} catch (ProjectError e) {
+	} catch (ProjectError &e) {
 	    cout << e.getMessage() << endl << endl;
 	    exit(1);
 	}

src/exonmodel.cc

@@ -300,62 +300,62 @@ void ExonModel::init() {
     minwindowcount=3;           // see class Smooth in commontrain.hh	
     try{
 	verbosity = Properties::getIntProperty("/ExonModel/verbosity");
-    }catch( ProjectError e) {    
+    }catch( ProjectError &e) {
 	cerr << e.getMessage();
     }
     try{
 	k = Properties::getIntProperty( "/ExonModel/k" );
-    }catch( ProjectError e) {    
+    }catch( ProjectError &e) {    
 	cerr << e.getMessage();
     }
     try{
 	patpseudo = Properties::getDoubleProperty( "/ExonModel/patpseudocount" );
-    }catch( ProjectError e) { 
+    }catch( ProjectError &e) { 
 	cerr << e.getMessage();
     }
     try{
 	exonLenD = Properties::getIntProperty( "/ExonModel/exonlengthD" );
-    }catch( ProjectError e) { 
+    }catch( ProjectError &e) { 
 	cerr << e.getMessage();
     }
     try{
 	slope_of_bandwidth = Properties::getdoubleProperty( "/ExonModel/slope_of_bandwidth");
-    }catch( ProjectError e) { 
+    }catch( ProjectError &e) { 
 	cerr << e.getMessage();
     }
     try{
 	minwindowcount = Properties::getIntProperty( "/ExonModel/minwindowcount");
-    }catch( ProjectError e) { 
+    }catch( ProjectError &e) { 
 	cerr << e.getMessage();
     }
     try{
 	min_exon_length = Properties::getIntProperty( "/ExonModel/minexonlength");
-    } catch( ProjectError e) { 
+    } catch( ProjectError &e) { 
 	// optional parameter
     }
     try{
 	minPatSum = Properties::getIntProperty( "/ExonModel/minPatSum");
-    } catch( ProjectError e) { 
+    } catch( ProjectError &e) { 
 	cerr << e.getMessage();
     }
     try{
 	etorder = Properties::getIntProperty( "/ExonModel/etorder");
-    } catch( ProjectError e) { 
+    } catch( ProjectError &e) { 
 	cerr << e.getMessage();
     }
     try{
 	etpseudocount = Properties::getIntProperty( "/ExonModel/etpseudocount");
-    } catch( ProjectError e) { 
+    } catch( ProjectError &e) { 
 	cerr << e.getMessage();
     }
     try{
 	tis_motif_memory = Properties::getIntProperty( "/ExonModel/tis_motif_memory");
-    } catch( ProjectError e) { 
+    } catch( ProjectError &e) { 
 	cerr << e.getMessage();
     }
     try{
 	tis_motif_radius = Properties::getIntProperty( "/ExonModel/tis_motif_radius");
-    } catch( ProjectError e) { 
+    } catch( ProjectError &e) { 
 	cerr << e.getMessage();
     }
     try{
@@ -364,10 +364,10 @@ void ExonModel::init() {
 	    cout << "Warning: /ExonModel/lenboostE < 0 does not make sense. Will use 0 instead." << endl;
 	    lenboostE = 0.0;
 	}
-    } catch( ProjectError e) {}
+    } catch( ProjectError &e) {}
     try{
 	lenboostL = Properties::getIntProperty( "/ExonModel/lenboostL");
-    } catch( ProjectError e) {}
+    } catch( ProjectError &e) {}
 
     trans_init_window = Constant::trans_init_window;
 
@@ -1111,7 +1111,7 @@ void ExonModel::viterbiForwardAndSampling(ViterbiMatrixType& viterbi, // matrix
 				oli.resetPredEnd();
 				oli.state = getFullStateId(predState, exonScorer->getPredSubstate());
 			    }
-			} catch(NoSubmapFoundError e) {}
+			} catch(NoSubmapFoundError &e) {}
 		} 
 		Double predProb = predVit.get(predState) * transEmiProb;
 		if (predProb > maxProb) {
@@ -1138,7 +1138,7 @@ void ExonModel::viterbiForwardAndSampling(ViterbiMatrixType& viterbi, // matrix
 	    optionslist->prepareSampling();
 	    try {
 		oli = optionslist->sample();
-	    } catch (ProjectError e) {
+	    } catch (ProjectError &e) {
 		cerr << "Sampling error in exon model. state=" << state << " base=" << base << endl;
 		throw e;
 	    }
@@ -1570,7 +1570,7 @@ Double ExonModel::notEndPartEmiProb(int beginOfStart, int right, int frameOfRigh
 	    else
 		restSeqProb = Pls[right-beginOfStart][mod3(frameOfRight + right - beginOfStart)]
 		    [s2i.rc(sequence + beginOfStart)];		
-	} catch (InvalidNucleotideError e) {
+	} catch (InvalidNucleotideError &e) {
 	    // we dont assume anything in this case, take iid uniform distribution on {a,c,g,t}
 	    restSeqProb = pow(Constant::probNinCoding, right-beginOfStart + 1); // 0.25
 	}
@@ -1600,7 +1600,7 @@ Double ExonModel::notEndPartEmiProb(int beginOfStart, int right, int frameOfRigh
 		else                  // init pattern at right side
 		    restSeqProb = Pls[k-1][mod3(frameOfRight+right-beginOfInitP)]
 			[Seq2Int(k).rc(sequence + beginOfInitP)];
-	} catch (InvalidNucleotideError e) {
+	} catch (InvalidNucleotideError &e) {
 	    restSeqProb = pow(Constant::probNinCoding, (int) k ); // 0.25
 	}
 
@@ -1946,7 +1946,7 @@ Double ExonModel::seqProb(int left, int right, int frameOfRight) const {
 		int f = reverse? mod3(frameOfRight+right-curpos) : mod3(frameOfRight-right+curpos);
 		int pn = reverse? s2i.rc(sequence+curpos) : s2i(sequence+curpos-k);
 		seqProb *= emiprobs.probs[f][pn];
-            } catch (InvalidNucleotideError e) {
+            } catch (InvalidNucleotideError &e) {
                 seqProb *= Constant::probNinCoding; //  0.25, 1/4
             }
         }
@@ -1963,7 +1963,7 @@ Double ExonModel::seqProb(int left, int right, int frameOfRight) const {
 	    seqProb  *= emiprobs.probs[f][pn];
 	    if (inCRFTraining && (countEnd < 0 || (curpos >= countStart && curpos <= countEnd)))
 		GCemiprobs[gcIdx].addCount(GCemiprobs[gcIdx].getIndex(f,pn));
-	} catch (InvalidNucleotideError e) {
+	} catch (InvalidNucleotideError &e) {
 	    seqProb  *= Constant::probNinCoding; // 0.25 1/4
 	}
     }
@@ -2001,7 +2001,7 @@ Double ExonModel::eTermSeqProb(int left, int right, int frameOfRight) const {
 		int f = reverse? mod3(frameOfRight+right-curpos) : mod3(frameOfRight-right+curpos);
 		int pn = reverse? s2i.rc(sequence+curpos) : s2i(sequence+curpos-k);
 		seqProb *= etemiprobs[f][pn];
-	    } catch (InvalidNucleotideError e) {
+	    } catch (InvalidNucleotideError &e) {
 		seqProb *= Constant::probNinCoding; // 0.25, 1/4
 	    }
 	}
@@ -2028,7 +2028,7 @@ Double ExonModel::initialSeqProb(int left, int right, int frameOfRight) const {
 	    int f = reverse? mod3(frameOfRight+right-curpos) : mod3(frameOfRight-right+curpos);
 	    int pn = reverse? s2i.rc(sequence+curpos) : s2i(sequence+curpos-k);
 	    seqProb *= initemiprobs[f][pn];
-	} catch (InvalidNucleotideError e) {
+	} catch (InvalidNucleotideError &e) {
 	    seqProb *= Constant::probNinCoding; // 0.25, 1/4
 	}
     }

src/exontrain.cc

@@ -516,7 +516,7 @@ void ExonModel::printProbabilities(int idx, BaseCount *bc, const char* suffix){
 	    */
 	    ofstrm.close();
 	}
-	catch( ProjectError ) {
+	catch( ProjectError& ) {
 	    if (verbosity)    
 		cout << "Exon model parameters not saved." << endl;
 	}
@@ -620,15 +620,15 @@ void ExonModel::processExons( const Gene* gene ){
     if( !exon->next ){
 	try{
 	    processSingleExon( exon );
-	} catch (ExonModelError e) {
+	} catch (ExonModelError &e) {
 	    if (verbosity)
 	      cerr << "gene " << gene->geneid << " transcr. " << gene->id << " in sequence " << gene->seqname << ": " << e.getMessage() << endl;
 	}
     }
     else{
 	try{
 	    processInitialExon( exon );
-	} catch( ExonModelError e ){
+	} catch( ExonModelError &e ){
 	    if (verbosity)
 	      cerr << "gene " << gene->geneid << " transcr. " << gene->id << " in sequence " << gene->seqname << ": " << e.getMessage() << endl;
 	}
@@ -637,15 +637,15 @@ void ExonModel::processExons( const Gene* gene ){
 	while( exon->next ){
 	    try{
 		processInternalExon( exon );
-	    } catch( ExonModelError e ){
+	    } catch( ExonModelError &e ){
 	      if (verbosity)
 		    cerr << "gene " << gene->geneid << " transcr. " << gene->id << " in sequence " << gene->seqname << ": " << e.getMessage() << endl;
 	    }
 	    exon = exon->next;
 	} 
 	try{
 	    processTerminalExon( exon );
-	} catch( ExonModelError e ){
+	} catch( ExonModelError &e ){
 	    if (verbosity)
 		cerr << "gene " << gene->geneid << " transcr. " << gene->id << " in sequence " << gene->seqname << ": " << e.getMessage() << endl;
 	}
@@ -805,7 +805,7 @@ void ExonModel::processInternalExon( const State* exon){
 	cout << "internal etMotif " << mod3(oldwin + length - Constant::dss_start - Constant::et_coding_len) << " " <<fenster << endl;
 	*/
 
-    } catch( ExonModelError e ){
+    } catch( ExonModelError &e ){
 	cerr << "ExonModel::processInternalExon: " << e.getMessage() << endl;
 	throw e;
     }
@@ -890,7 +890,7 @@ void ExonModel::processInnerSequence(const char *begin, const char* end, int mod
 	    else 
 		throw ProjectError("ExonModel::processInnerSequence: invalid model type");
 	    gesbasen[curwin] += gweight;
-	} catch (InvalidNucleotideError e) {}
+	} catch (InvalidNucleotideError &e) {}
 	curwin++;
     }
 }