From 5694c92fbf646fe01abc87bde2af59e14a9a56b6 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Wed, 5 Jan 2011 13:07:39 +0000
Subject: [PATCH] removed various build warnings
---
clearcut.cpp | 4 ++--
clusterclassic.cpp | 2 ++
clustersplitcommand.cpp | 2 +-
distancecommand.cpp | 2 ++
engine.cpp | 2 +-
getgroupscommand.cpp | 2 ++
getotuscommand.cpp | 2 +-
metastats2.c | 8 ++++----
parsimony.cpp | 1 -
phylodiversitycommand.cpp | 2 +-
phylosummary.cpp | 4 ++--
phylotree.cpp | 2 ++
pipelinepdscommand.cpp | 2 ++
rarefact.cpp | 2 +-
removegroupscommand.cpp | 2 ++
removeotuscommand.cpp | 1 +
shhhercommand.cpp | 4 ----
splitmatrix.cpp | 2 ++
subsamplecommand.cpp | 4 ++++
summarysharedcommand.cpp | 1 +
trimflowscommand.cpp | 3 ---
trimseqscommand.cpp | 4 +---
unifracweightedcommand.cpp | 1 -
unweighted.cpp | 4 ----
weighted.cpp | 4 +---
25 files changed, 35 insertions(+), 32 deletions(-)
diff --git a/clearcut.cpp b/clearcut.cpp
index b06aa5b..a4bd450 100644
--- a/clearcut.cpp
+++ b/clearcut.cpp
@@ -230,8 +230,8 @@ int clearcut_main(int argc, char *argv[]) {
printf("Relaxed NJ tree(s) in %s\n", nj_args->outfilename);
}
}
-
- //exit(0);
+
+ return 0;
}
diff --git a/clusterclassic.cpp b/clusterclassic.cpp
index 287332a..7f6e97e 100644
--- a/clusterclassic.cpp
+++ b/clusterclassic.cpp
@@ -215,6 +215,8 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
rabund = new RAbundVector(list->getRAbundVector());
fileHandle.close();
+
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "ClusterClassic", "readPhylipFile");
diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 5998726..0aceb8b 100644
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -1112,7 +1112,7 @@ int ClusterSplitCommand::createMergedDistanceFile(vector< map<string, string> >
}
#endif
-
+ return 0;
}
diff --git a/distancecommand.cpp b/distancecommand.cpp
index 3711a1d..a3cebe2 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -1151,6 +1151,8 @@ bool DistanceCommand::sanityCheck() {
remove(outputFile.c_str()); //temp file is bad because file mismatch above
}
+ return good;
+
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "sanityCheck");
diff --git a/engine.cpp b/engine.cpp
index a90bb7e..2b1c802 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -181,7 +181,7 @@ string Engine::getCommand() {
if(nextCommand != NULL) { add_history(nextCommand); }
else{ //^D causes null string and we want it to quit mothur
- nextCommand = "quit";
+ strcpy(nextCommand, "quit");
mout->mothurOut(nextCommand);
}
diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index 266fc52..1832f96 100644
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -587,6 +587,8 @@ int GetGroupsCommand::fillNames(){
names.insert(seqs[i]);
}
}
+
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "GetGroupsCommand", "fillNames");
diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index ba9a5e7..fd7c8d1 100644
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -381,7 +381,7 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream
m->mothurOut(newList.getLabel() + " - selected " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();
-
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "GetOtusCommand", "processList");
diff --git a/metastats2.c b/metastats2.c
index de2a930..6601b09 100644
--- a/metastats2.c
+++ b/metastats2.c
@@ -5,13 +5,13 @@
int metastat_main (char* outputFileName, int numRows, int numCols, double threshold, int numPermutations, double** data, int secondGroupingStart){
- int size,c=0,i=0,j=0,k,counter=0, bflag=0;
+ int size,c=0,i=0,j=0,counter=0, bflag=0;
int B=numPermutations;
int row = numRows;
int col = numCols;
int g = secondGroupingStart;
double thresh=threshold;
- double placeholder=0,min=0;
+ double min=0;
char output[1024];
strcpy(output, outputFileName);
@@ -24,7 +24,7 @@ int metastat_main (char* outputFileName, int numRows, int numCols, double thresh
// Initialize the matrices
size = row*col;
double matrix[row][col];
- double pmatrix[size],pmatrix2[size],permuted[size];
+ double pmatrix[size],permuted[size];
double storage[row][9];
for (i=0;i<row;i++){
@@ -343,7 +343,7 @@ void testp(double *permuted_ttests,int *B,double *permuted,
*ps) {
double Tvalues[*nr];
- int a, b, n, i, j,k=0;
+ int a, b, n, j;
a = *B;
b = *nr;
diff --git a/parsimony.cpp b/parsimony.cpp
index 4ec5e1b..11abb94 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -92,7 +92,6 @@ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGr
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
- int num = 0;
vector<int> processIDS;
EstOutput results;
diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index a97e095..80d9090 100644
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -290,7 +290,7 @@ int PhyloDiversityCommand::createProcesses(vector<int>& procIters, Tree* t, map<
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
- int num = 0;
+
vector<int> processIDS;
map< string, vector<float> >::iterator itSum;
diff --git a/phylosummary.cpp b/phylosummary.cpp
index a9a170b..26ae3a8 100644
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -200,7 +200,7 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
for (int k = level; k < maxLevel; k++) { seqTaxonomy += "unclassified;"; }
}
}
-
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "addSeqToTree");
@@ -310,7 +310,7 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
for (int k = level; k < maxLevel; k++) { seqTaxonomy += "unclassified;"; }
}
}
-
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "addSeqToTree");
diff --git a/phylotree.cpp b/phylotree.cpp
index 1fd4e5d..891cca4 100644
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -275,6 +275,8 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
if (seqTaxonomy == "") { uniqueTaxonomies[currentNode] = currentNode; }
}
+
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "PhyloTree", "addSeqToTree");
diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index b7ba7d3..f95b928 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -525,6 +525,8 @@ int PipelineCommand::runUsersPipeline(){
}
in.close();
+
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "PipelineCommand", "runUsersPipeline");
diff --git a/rarefact.cpp b/rarefact.cpp
index ec77dd5..032cd93 100644
--- a/rarefact.cpp
+++ b/rarefact.cpp
@@ -116,7 +116,7 @@ int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd,
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
- int num = 0;
+
vector<int> processIDS;
EstOutput results;
diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 6042bbe..2c98e81 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -588,6 +588,8 @@ int RemoveGroupsCommand::fillNames(){
names.insert(seqs[i]);
}
}
+
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "fillNames");
diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 0e7d302..1a7d3bd 100644
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -388,6 +388,7 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr
m->mothurOut(newList.getLabel() + " - removed " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();
+ return 0;
}
catch(exception& e) {
diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index f9b3429..d1732cd 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -1160,7 +1160,6 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){
double clusterCutoff = cutoff;
while (matrix->getSmallDist() <= clusterCutoff && matrix->getNNodes() > 0){
cluster->update(clusterCutoff);
- float dist = matrix->getSmallDist();
}
list->setLabel(toString(cutoff));
@@ -1411,7 +1410,6 @@ void ShhherCommand::calcCentroidsDriver(int start, int finish){
for(int j=0;j<nSeqsPerOTU[i];j++){
int index = cumNumSeqs[i] + j;
int nI = seqIndex[index];
- int nIU = mapSeqToUnique[nI];
double tauValue = singleTau[seqNumber[index]];
@@ -1483,7 +1481,6 @@ double ShhherCommand::getNewWeights(){
for(int j=0;j<nSeqsPerOTU[i];j++){
int index = cumNumSeqs[i] + j;
- int nI = seqIndex[index];
double tauValue = singleTau[seqNumber[index]];
weight[i] += tauValue;
}
@@ -1902,7 +1899,6 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
vector<vector<int> > qualities(numOTUs);
vector<double> pr(HOMOPS, 0);
- int index = 0;
for(int i=0;i<numOTUs;i++){
int index = 0;
diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index 1f23ec3..80f311d 100644
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -66,6 +66,8 @@ int SplitMatrix::splitDistance(){
if (large) { splitDistanceLarge(); }
else { splitDistanceRAM(); }
+
+ return 0;
}
catch(exception& e) {
diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index ac45d2f..b8bb7ad 100644
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -521,6 +521,8 @@ int SubSampleCommand::getNames() {
}
in.close();
+ return 0;
+
}
catch(exception& e) {
m->errorOut(e, "SubSampleCommand", "getNames");
@@ -559,6 +561,8 @@ int SubSampleCommand::readNames() {
}
in.close();
+ return 0;
+
}
catch(exception& e) {
m->errorOut(e, "SubSampleCommand", "readNames");
diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index b3f7729..029ca26 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -665,6 +665,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
outDist.close();
}
}
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "SummarySharedCommand", "process");
diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index b098f8f..e4d0165 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -661,7 +661,6 @@ int TrimFlowsCommand::stripBarcode(Sequence& seq, int& group){
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
- int newStart=0;
int numDiff = countDiffs(oligo, temp);
if(numDiff < minDiff){
@@ -959,10 +958,8 @@ vector<unsigned long int> TrimFlowsCommand::getFlowFileBreaks() {
m->openInputFile(flowFileName, in);
in.seekg(spot);
- unsigned long int newSpot = spot;
string dummy = m->getline(in);
-
//there was not another sequence before the end of the file
unsigned long int sanityPos = in.tellg();
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 2000204..d5df473 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -455,7 +455,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
try {
ofstream outFASTA;
- int able = m->openOutputFile(trimFile, outFASTA);
+ m->openOutputFile(trimFile, outFASTA);
ofstream scrapFASTA;
m->openOutputFile(scrapFile, scrapFASTA);
@@ -1095,7 +1095,6 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
- int newStart=0;
int numDiff = countDiffs(oligo, temp);
// cout << oligo << '\t' << temp << '\t' << numDiff << endl;
@@ -1220,7 +1219,6 @@ int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
- int newStart=0;
int numDiff = countDiffs(oligo, temp);
// cout << oligo << '\t' << temp << '\t' << numDiff << endl;
diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 4ded9c5..b2fd628 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -332,7 +332,6 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > na
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
- int num = 0;
vector<int> processIDS;
EstOutput results;
diff --git a/unweighted.cpp b/unweighted.cpp
index ef9e521..24b41a1 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -87,7 +87,6 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
- int num = 0;
vector<int> processIDS;
EstOutput results;
@@ -340,7 +339,6 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
- int num = 0;
vector<int> processIDS;
EstOutput results;
@@ -423,8 +421,6 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
EstOutput results; results.resize(num);
int count = 0;
- int total = num;
- int twentyPercent = (total * 0.20);
int numLeaves = t->getNumLeaves();
Tree* copyTree = new Tree;
diff --git a/weighted.cpp b/weighted.cpp
index 24adbba..30e4a76 100644
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -294,9 +294,7 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
D += weightedSum;
}
-
- int numLeaves = t->getNumLeaves();
-
+
//calculate u for the group comb
for(int i=0;i<t->getNumNodes();i++){
--
2.39.5