compiling with -std=c++11 -- various warnings fixed

bayesiancook · Oct 7, 2020 · fbd6393 · fbd6393
1 parent dca7bdf
commit fbd6393
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Showing 19 changed files with 29 additions and 86 deletions.
diff --git a/sources/AACodonMutSelFinitePhyloProcess.cpp b/sources/AACodonMutSelFinitePhyloProcess.cpp
@@ -245,7 +245,6 @@ void AACodonMutSelFinitePhyloProcess::ReadPB(int argc, char* argv[])	{
 	// 3 : compositional statistic
 
 	int cv = 0;
-	int sel = 0;
 	int map = 0;
 	int mapstats = 0;
 	string testdatafile = "";
@@ -267,10 +266,7 @@ void AACodonMutSelFinitePhyloProcess::ReadPB(int argc, char* argv[])	{
 		int i = 1;
 		while (i < argc)	{
 			string s = argv[i];
-			if (s == "-sel")	{
-				sel = 1;
-			}
-			else if (s == "-cv")	{
+			if (s == "-cv")	{
 				cv = 1;
 				i++;
 				testdatafile = argv[i];
@@ -441,7 +437,6 @@ void AACodonMutSelFinitePhyloProcess::ReadMapStats(string name, int burnin, int
 		FromStream(is);
 		i++;
 
-		MPI_Status stat;
 		MESSAGE signal = BCAST_TREE;
 		MPI_Bcast(&signal,1,MPI_INT,0,MPI_COMM_WORLD);
 		GlobalBroadcastTree();

diff --git a/sources/AACodonMutSelSBDPPhyloProcess.cpp b/sources/AACodonMutSelSBDPPhyloProcess.cpp
@@ -264,7 +264,6 @@ void AACodonMutSelSBDPPhyloProcess::ReadPB(int argc, char* argv[])	{
 	// 3 : compositional statistic
 
 	int cv = 0;
-	int sel = 0;
 	int map = 0;
 	int mapstats = 0;
 	string testdatafile = "";
@@ -286,10 +285,7 @@ void AACodonMutSelSBDPPhyloProcess::ReadPB(int argc, char* argv[])	{
 		int i = 1;
 		while (i < argc)	{
 			string s = argv[i];
-			if (s == "-sel")	{
-				sel = 1;
-			}
-			else if (s == "-cv")	{
+			if (s == "-cv")	{
 				cv = 1;
 				i++;
 				testdatafile = argv[i];
@@ -460,7 +456,6 @@ void AACodonMutSelSBDPPhyloProcess::ReadMapStats(string name, int burnin, int ev
 		FromStream(is);
 		i++;
 
-		MPI_Status stat;
 		MESSAGE signal = BCAST_TREE;
 		MPI_Bcast(&signal,1,MPI_INT,0,MPI_COMM_WORLD);
 		GlobalBroadcastTree();

diff --git a/sources/CodonMutSelFinitePhyloProcess.cpp b/sources/CodonMutSelFinitePhyloProcess.cpp
@@ -28,7 +28,6 @@ void CodonMutSelFinitePhyloProcess::SlaveUpdateParameters()	{
 	int i,j,L1,L2,ni,nd,nbranch = GetNbranch(),nnucrr = GetNnucrr(),nnucstat = 4;
 	L1 = GetNmodeMax();
 	L2 = GetDim();
-	int nstate = data->GetNstate();
 	nd = 2+ nbranch + nnucrr + nnucstat + L2 + L1*(L2+1); // check if these last terms are correct in this context...
 	ni = 1 + ProfileProcess::GetNsite();
 	int* ivector = new int[ni];
@@ -117,7 +116,6 @@ void CodonMutSelFinitePhyloProcess::GlobalUpdateParameters() {
 	nnucstat = 4;	
 	L1 = GetNmodeMax();
 	L2 = GetDim();
-	int nstate = data->GetNstate();
 	nd = 2 + nbranch + nnucrr + nnucstat + L2 + L1*(L2+1);  // check if these last terms are correct in this context...
 	ni = 1 + ProfileProcess::GetNsite(); // 1 for the number of componenets, and the rest for allocations
 	int ivector[ni];
@@ -182,7 +180,6 @@ void CodonMutSelFinitePhyloProcess::ReadPB(int argc, char* argv[])	{
 	// 3 : compositional statistic
 
 	int cv = 0;
-	int sel = 0;
 	int map = 0;
 	string testdatafile = "";
 	int rateprior = 0;
@@ -203,10 +200,7 @@ void CodonMutSelFinitePhyloProcess::ReadPB(int argc, char* argv[])	{
 		int i = 1;
 		while (i < argc)	{
 			string s = argv[i];
-			if (s == "-sel")	{
-				sel = 1;
-			}
-			else if (s == "-cv")	{
+			if (s == "-cv")	{
 				cv = 1;
 				i++;
 				testdatafile = argv[i];

diff --git a/sources/CodonMutSelSBDPPhyloProcess.cpp b/sources/CodonMutSelSBDPPhyloProcess.cpp
@@ -191,7 +191,6 @@ void CodonMutSelSBDPPhyloProcess::ReadPB(int argc, char* argv[])	{
 	// 3 : compositional statistic
 
 	int cv = 0;
-	int sel = 0;
 	int map = 0;
 	string testdatafile = "";
 	int rateprior = 0;
@@ -212,10 +211,7 @@ void CodonMutSelSBDPPhyloProcess::ReadPB(int argc, char* argv[])	{
 		int i = 1;
 		while (i < argc)	{
 			string s = argv[i];
-			if (s == "-sel")	{
-				sel = 1;
-			}
-			else if (s == "-cv")	{
+			if (s == "-cv")	{
 				cv = 1;
 				i++;
 				testdatafile = argv[i];

diff --git a/sources/CodonSubMatrix.h b/sources/CodonSubMatrix.h
@@ -92,8 +92,8 @@ class AACodonMutSelProfileSubMatrix : public CodonSubMatrix	{
 	void ComputeArray(int state);
 	void ComputeStationary();
 	double GetRate();
-	double* aaprofile;
 	double* codonprofile;
+	double* aaprofile;
 	double* omega;
 };
 

diff --git a/sources/DPProfileProcess.cpp b/sources/DPProfileProcess.cpp
@@ -113,8 +113,7 @@ double DPProfileProcess::LogHyperPrior()	{
 	else 	{
 		total = -log(kappa);
 		if ((kappa < 1e-4) || (kappa > 1e4))	{
-			// total = InfProb;
-			total -= 1.0 / 0;
+			total = -std::numeric_limits<double>::infinity();
 		}
 	}
 	double sum = 0;
@@ -123,8 +122,7 @@ double DPProfileProcess::LogHyperPrior()	{
 		sum += dirweight[k];
 	}
 	if (sum < GetMinTotWeight())	{
-		// total += InfProb;
-		total -= 1.0 / 0;
+        total = -std::numeric_limits<double>::infinity();
 	}
 	return total;
 }

diff --git a/sources/FiniteProfileProcess.cpp b/sources/FiniteProfileProcess.cpp
@@ -157,16 +157,15 @@ double FiniteProfileProcess::LogHyperPrior()	{
 		sum += dirweight[k];
 	}
 	if (sum < GetMinTotWeight())	{
-		// total += InfProb;
-		total -= 1.0 / 0;
+		total = -std::numeric_limits<double>::infinity();
 	}
 	total -= weightalpha;
 	return total;
 }
 
 double FiniteProfileProcess::MoveHyper(double tuning, int nrep)	{
 	double total = 0;
-	if ((Ncomponent > 1) || (! fixncomp) && (! dirweightprior))	{
+	if ((Ncomponent > 1) || ((! fixncomp) && (! dirweightprior)))	{
 		total += MoveDirWeights(tuning,nrep);
 	}
 	return total;

diff --git a/sources/FiniteProfileProcess.h b/sources/FiniteProfileProcess.h
@@ -84,15 +84,16 @@ class FiniteProfileProcess: public virtual MixtureProfileProcess	{
 	bool fixncomp;
 	bool empmix;
 
-	int dirweightprior;
-	// 0 : flexible
-	// 1 : rigid
-
 	int Ncat;
+
+	string mixtype;
 	double** statfix;
 	double* empweight;
 
-	string mixtype;
+	int dirweightprior;
+	// 0 : flexible
+	// 1 : rigid
+
 };
 
 #endif

diff --git a/sources/GammaBranchProcess.cpp b/sources/GammaBranchProcess.cpp
@@ -92,8 +92,8 @@ double GammaBranchProcess::LogHyperPrior()	{
 	if (betaprior == 1)	{
 		total -= log(branchbeta);
 		if ((branchbeta < 1e-4) || (branchbeta > 1e4))	{
-			total -= 1.0 / 0;
-			// total = InfProb;
+			total = -std::numeric_limits<double>::infinity();
+			// total -= 1.0 / 0;
 		}
 	}
 	else	{
@@ -152,5 +152,6 @@ double GammaBranchProcess::NonMPIMoveLength()	{
 double GammaBranchProcess::NonMPIMove(double tuning, int nrep)	{
 	NonMPIMoveLength();
 	MoveBranchBeta(tuning,nrep);
+    return 1.0;
 }
 
diff --git a/sources/Makefile b/sources/Makefile
@@ -1,5 +1,5 @@
 CC=mpic++
-CPPFLAGS= -w -O3 -c
+CPPFLAGS= -Wall -O3 -std=c++11
 LDFLAGS= -O3
 SRCS=  TaxonSet.cpp Tree.cpp Random.cpp SequenceAlignment.cpp CodonSequenceAlignment.cpp \
 	StateSpace.cpp CodonStateSpace.cpp ZippedSequenceAlignment.cpp SubMatrix.cpp \

diff --git a/sources/NNI.cpp b/sources/NNI.cpp
@@ -212,10 +212,7 @@ double PhyloProcess::SendRandomBranches(Link* from, double tuning, Link**& branc
 
 void PhyloProcess::SlaveNNI(Link* from, int n){
 
-
-	MPI_Status stat;
 	Link* up = from->Next();
-
 	int* br;
 	double* m;
 	if(n){

diff --git a/sources/PBTree.cpp b/sources/PBTree.cpp
@@ -165,7 +165,6 @@ void PBTree::Clone(PolyNode* node, PolyNode* fromNode)	{
 		node->down = first;
 		Clone(first, fromfirst);
 
-		PolyNode* fromcurrent = fromfirst;
 		PolyNode* fromnext = fromfirst->next;
 		PolyNode* thiscurrent = first;
 
@@ -176,7 +175,6 @@ void PBTree::Clone(PolyNode* node, PolyNode* fromNode)	{
 			thiscurrent->next = thisnext;
 			Clone(thisnext, fromnext);
 			thiscurrent = thisnext;
-			fromcurrent = fromnext;
 			fromnext = fromnext->next;
 		}
 		thiscurrent->next = first;

diff --git a/sources/PhyloProcess.cpp b/sources/PhyloProcess.cpp
@@ -707,7 +707,8 @@ void PhyloProcess::RecursiveGibbsSPRScan(Link* from, Link* fromup, Link* down, L
 		}
 		loglarray[n] = logl;
 		n++;
-		Link* tmp1 = GetTree()->Detach(down,up);
+		GetTree()->Detach(down,up);
+		// Link* tmp1 = GetTree()->Detach(down,up);
 	}
 	Link* trailer = from;
 	for (const Link* link=from->Next(); link!=from; link=link->Next())	{
@@ -820,7 +821,8 @@ void PhyloProcess::RecursiveNonMPIGibbsSPRScan(Link* from, Link* fromup, Link* d
 		Propagate(aux,GetConditionalLikelihoodVector(up->Out()),GetLength(up->GetBranch()));
 		double logl = ComputeNodeLikelihood(up->Out(),0);
 		loglmap[pair<Link*,Link*>(from,fromup)] = logl;
-		Link* tmp1 = GetTree()->Detach(down,up);
+		GetTree()->Detach(down,up);
+		// Link* tmp1 = GetTree()->Detach(down,up);
 	}
 	Link* trailer = from;
 	for (const Link* link=from->Next(); link!=from; link=link->Next())	{
@@ -1890,7 +1892,6 @@ void PhyloProcess::SlaveUpdateBranchLengthSuffStat()	{
 
 void PhyloProcess::GlobalUpdateSiteRateSuffStat()	{
 
-	MPI_Status stat;
 	MESSAGE signal = UPDATE_SRATE;
 	MPI_Bcast(&signal,1,MPI_INT,0,MPI_COMM_WORLD);
 }
@@ -1913,7 +1914,7 @@ void PhyloProcess::GlobalGetMeanSiteRate()	{
 	}
 
 	assert(myid == 0);
-	int i,width,smin[nprocs-1],smax[nprocs-1],workload[nprocs-1];
+	int i,width,smin[nprocs-1],smax[nprocs-1];
 	MPI_Status stat;
 	MESSAGE signal = SITERATE;
 
@@ -2101,7 +2102,6 @@ void PhyloProcess::AllPostPred(string name, int burnin, int every, int until, in
 	}
 
 	double* obstaxstat = new double[GetNtaxa()];
-	SequenceAlignment* datacopy  = new SequenceAlignment(GetData());
 	int nstat = 5;
 	double obsarray[nstat];
 	obsarray[0] = data->GetMeanDiversity();
@@ -2121,7 +2121,7 @@ void PhyloProcess::AllPostPred(string name, int burnin, int every, int until, in
 	double meanstatarray[nstat];
 	double varstatarray[nstat];
 	double ppstatarray[nstat];
-	for (int k=0; k<6; k++)	{
+	for (int k=0; k<nstat; k++)	{
 		meanstatarray[k] = 0;
 		varstatarray[k] = 0;
 		ppstatarray[k] = 0;
@@ -2261,7 +2261,6 @@ void PhyloProcess::PostPred(int ppredtype, string name, int burnin, int every, i
 	}
 
 	double* obstaxstat = new double[GetNtaxa()];
-	SequenceAlignment* datacopy  = new SequenceAlignment(GetData());
 	double obs = 0;
 	double obs2 = 0;
 	if (ppredtype == 2)	{
@@ -2613,7 +2612,6 @@ void PhyloProcess::ReadAncestral(string name, int burnin, int every, int until)
 		MESSAGE signal = STATEPOSTPROBS;
 		MPI_Bcast(&signal,1,MPI_INT,0,MPI_COMM_WORLD);
 
-		double total = 0;
 		for(int proc=1; proc<GetNprocs(); proc++) {
 			MPI_Recv(allocstatepostprob+smin[proc-1]*GetNnode()*GetGlobalNstate(),(smax[proc-1]-smin[proc-1])*GetNnode()*GetGlobalNstate(),MPI_DOUBLE,proc,TAG1,MPI_COMM_WORLD,&stat);
 			for (int i=smin[proc-1]; i<smax[proc-1]; i++)	{
@@ -2998,7 +2996,6 @@ void PhyloProcess::ReadMap(string name, int burnin, int every, int until){
 		ofstream sos(s.str().c_str());
 
 		// quick update and mapping on the fly
-		MPI_Status stat;
 		MESSAGE signal = BCAST_TREE;
 		MPI_Bcast(&signal,1,MPI_INT,0,MPI_COMM_WORLD);
 		GlobalBroadcastTree();
@@ -3066,7 +3063,6 @@ void PhyloProcess::ReadMap(string name, int burnin, int every, int until){
 }
 
 void PhyloProcess::GlobalWriteMappings(string name){
-	MPI_Status stat;
 	MESSAGE signal = WRITE_MAPPING;
 	MPI_Bcast(&signal,1,MPI_INT,0,MPI_COMM_WORLD);
 

diff --git a/sources/PhyloProcess.h b/sources/PhyloProcess.h
@@ -232,7 +232,6 @@ class PhyloProcess : public virtual SubstitutionProcess, public virtual BranchPr
 
 	virtual void QuickUpdate()	{
 
-		MPI_Status stat;
 		MESSAGE signal = BCAST_TREE;
 		MPI_Bcast(&signal,1,MPI_INT,0,MPI_COMM_WORLD);
 		GlobalBroadcastTree();

diff --git a/sources/RASCATGTRFiniteGammaPhyloProcess.cpp b/sources/RASCATGTRFiniteGammaPhyloProcess.cpp
@@ -472,7 +472,6 @@ void RASCATGTRFiniteGammaPhyloProcess::SlaveComputeSiteLogL()	{
 			}
 		}
 		double tot = 0;
-		double totweight = 0;
 		for (int k=0; k<GetNcomponent(); k++)	{
 			tot += weight[k] * exp(sitelogl[i][k] - max);
             cumul[k] = tot;

diff --git a/sources/RASCATGTRSBDPGammaPhyloProcess.cpp b/sources/RASCATGTRSBDPGammaPhyloProcess.cpp
@@ -205,7 +205,6 @@ void RASCATGTRSBDPGammaPhyloProcess::ReadPB(int argc, char* argv[])	{
 	// 3 : compositional statistic
 
 	int ss = 0;
-	int nocc = 0;
 	int cv = 0;
 	int sitelogl = 0;
 	int rr = 0;

diff --git a/sources/SequenceAlignment.cpp b/sources/SequenceAlignment.cpp
@@ -274,7 +274,7 @@ int FileSequenceAlignment::ReadNexus(string filespec)	{
 			}
 			delete[] Data;
 		}
-		Data = new (int *[Ntaxa]);
+		Data = new int*[Ntaxa];
 		for (int i=0; i<Ntaxa; i++)	{
 			Data[i] = new int[Nsite];
 		}
@@ -411,7 +411,7 @@ int FileSequenceAlignment::ReadSpecial(string filespec)	{
 
 		statespace = new SimpleStateSpace(Nstate, NAlphabetSet, Alphabet, AlphabetSet);
 
-		Data = new (int *[Ntaxa]);
+		Data = new int *[Ntaxa];
 		for (int i=0; i<Ntaxa; i++)	{
 			Data[i] = new int[Nsite];
 		}
@@ -637,7 +637,7 @@ void FileSequenceAlignment::ReadPhylipSequential (string filespec)	{
 		}
 		Nsite = Int(temp);
 
-		Data = new (int *[Ntaxa]);
+		Data = new int *[Ntaxa];
 		for (int i=0; i<Ntaxa; i++)	{
 			Data[i] = new int[Nsite];
 		}
@@ -877,7 +877,7 @@ FileSequenceAlignment::ReadPhylip (string filespec, int repeattaxa)	{
 		Nsite = Int(temp);
 		// cerr << Ntaxa << '\t' << Nsite << '\n';
 
-		Data = new (int *[Ntaxa]);
+		Data = new int *[Ntaxa];
 		for (int i=0; i<Ntaxa; i++)	{
 			Data[i] = new int[Nsite];
 		}