* installing *source* package ‘flipflop’ ...
** libs
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c FileSplitter.cpp -o FileSplitter.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_flipflop.c -o R_init_flipflop.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c align.cpp -o align.o
align.cpp: In function ‘std::ostream& operator<<(std::ostream&, Align&)’:
align.cpp:11:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<a.start.size();i++) out<<a.start[i]<<"-"<<a.end[i]<<",";
^
align.cpp: In member function ‘int Align::getReadLen() const’:
align.cpp:19:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++)
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c auxiliaryio.cpp -o auxiliaryio.o
In file included from structdef.h:11:0,
from auxiliaryio.h:11,
from auxiliaryio.cpp:6:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
int orientation;
^
In file included from structdef.h:11:0,
from auxiliaryio.h:11,
from auxiliaryio.cpp:6:
readgroup.h:24:18: warning: ‘const Samples* ReadGroup::samples’ [-Wreorder]
const Samples* samples; // 2015-01-15 ELSA
^
In file included from structdef.h:11:0,
from auxiliaryio.h:11,
from auxiliaryio.cpp:6:
readgroup.h:119:3: warning: when initialized here [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool hasPairEnd(){for(int i=0;i<pairs.size();i++) if(pairs[i]!=-1)return true; return false; }
^
In file included from auxiliaryio.h:11:0,
from auxiliaryio.cpp:6:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool isEnd(){return index>=range.size();}
^
auxiliaryio.cpp: In function ‘void prepareAuxFile(std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string, bool&)’:
auxiliaryio.cpp:52:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<args.size();i++){
^
auxiliaryio.cpp:53:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i<args.size()-1 && (string(args[i])=="-o" || string(args[i])=="--prefix") ){
^
auxiliaryio.cpp:63:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<args.size();i++){
^
auxiliaryio.cpp:158:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0;i<args.size();i++)
^
auxiliaryio.cpp: In function ‘void write2os(std::ostream&, std::__cxx11::string, int, std::vector<long int>&, std::vector<long int>&, bool)’:
auxiliaryio.cpp:216:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<startpos.size();i++){
^
auxiliaryio.cpp:218:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i!=startpos.size()-1)
^
auxiliaryio.cpp:223:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<endpos.size();i++){
^
auxiliaryio.cpp:225:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i!=endpos.size()-1)
^
auxiliaryio.cpp: In function ‘void writeBound(std::ostream&, std::__cxx11::string, std::vector<long int>&, std::vector<long int>&)’:
auxiliaryio.cpp:240:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=1;i<startpos.size();i++){
^
auxiliaryio.cpp:244:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<endpos.size()-1;i++){
^
auxiliaryio.cpp: In function ‘void writeannotation(ReadGroup&, int)’:
auxiliaryio.cpp:318:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i++){
^
auxiliaryio.cpp:339:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i++){
^
auxiliaryio.cpp:342:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<rpoolstart[i].size()-1;j++){
^
auxiliaryio.cpp: In function ‘void writeboundfs(range_t, int, std::__cxx11::string, std::vector<std::pair<long int, long int> >&, int, int)’:
auxiliaryio.cpp:410:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<allrange.size();i++){
^
auxiliaryio.cpp:434:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<lencod.size();i++){
^
auxiliaryio.cpp:436:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i<lencod.size()-1)boundfs<<",";
^
auxiliaryio.cpp:441:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<startcod.size();i++){
^
auxiliaryio.cpp:443:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i<startcod.size()-1)boundfs<<",";
^
auxiliaryio.cpp:450:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int n=0;n<startcod.size();n++){
^
auxiliaryio.cpp:453:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(n+1<startcod.size() && startcod[n]+lencod[n]==startcod[n+1])needplot=true;
^
auxiliaryio.cpp: In function ‘int write2rangeandinstance(ReadGroup&, range_t&)’:
auxiliaryio.cpp:522:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<subg.size();i++){
^
auxiliaryio.cpp:534:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<subg.size();i++){
^
auxiliaryio.cpp: In function ‘void write2Instance(range_t&, std::vector<std::vector<long int> >&, std::vector<std::vector<long int> >&, int, int, std::__cxx11::string, int, std::vector<std::vector<long int> >&, std::vector<std::vector<long int> >&, bool, bool)’:
auxiliaryio.cpp:609:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<annostart.size();i++){
^
auxiliaryio.cpp:611:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<annostart[i].size();j++) {
^
auxiliaryio.cpp:616:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<annostart[i].size();j++) {
^
auxiliaryio.cpp:724:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<currentstat.size();i++)
^
auxiliaryio.cpp:736:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<refseriestype.size();i++){
^
auxiliaryio.cpp:738:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<refseriestype[i].size();j++) exonbin[refseriestype[i][j]]=1;
^
auxiliaryio.cpp:767:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<seriestype.size();i++){
^
auxiliaryio.cpp:769:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<seriestype[i].size();j++){
^
auxiliaryio.cpp:788:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<seriestype.size();i++){
^
auxiliaryio.cpp:791:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<seriestype[i].size();j++){
^
auxiliaryio.cpp:808:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i+=2){
^
auxiliaryio.cpp:825:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<(apitr->second).size();i++){
^
auxiliaryio.cpp:844:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=pst;i<rpoolstart.size();i+=step){
^
auxiliaryio.cpp:849:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<allstartrange.size();i++){
^
auxiliaryio.cpp:854:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<allstartrange[i].size();j++){
^
auxiliaryio.cpp: In function ‘int readgenerangefile(std::__cxx11::string, GeneRange&)’:
auxiliaryio.cpp:904:9: warning: unused variable ‘id’ [-Wunused-variable]
int id;
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c bedio.cpp -o bedio.o
bedio.cpp: In function ‘int writeBed(std::ostream&, bedrec)’:
bedio.cpp:61:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(rec.nsegs!=rec.segstart.size())rec.nsegs=rec.segstart.size();
^
bedio.cpp:76:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rec.segend.size();i++){
^
bedio.cpp:78:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i<rec.segend.size()-1) out<<",";
^
bedio.cpp:82:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rec.segstart.size();i++){
^
bedio.cpp:84:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i<rec.segstart.size()-1) out<<",";
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c common.cpp -o common.o
In file included from structdef.h:11:0,
from common.cpp:5:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
int orientation;
^
In file included from structdef.h:11:0,
from common.cpp:5:
readgroup.h:24:18: warning: ‘const Samples* ReadGroup::samples’ [-Wreorder]
const Samples* samples; // 2015-01-15 ELSA
^
In file included from structdef.h:11:0,
from common.cpp:5:
readgroup.h:119:3: warning: when initialized here [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool hasPairEnd(){for(int i=0;i<pairs.size();i++) if(pairs[i]!=-1)return true; return false; }
^
In file included from common.cpp:5:0:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool isEnd(){return index>=range.size();}
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c cvganalysis.cpp -o cvganalysis.o
In file included from structdef.h:11:0,
from cvganalysis.h:9,
from cvganalysis.cpp:2:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
int orientation;
^
In file included from structdef.h:11:0,
from cvganalysis.h:9,
from cvganalysis.cpp:2:
readgroup.h:24:18: warning: ‘const Samples* ReadGroup::samples’ [-Wreorder]
const Samples* samples; // 2015-01-15 ELSA
^
In file included from structdef.h:11:0,
from cvganalysis.h:9,
from cvganalysis.cpp:2:
readgroup.h:119:3: warning: when initialized here [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool hasPairEnd(){for(int i=0;i<pairs.size();i++) if(pairs[i]!=-1)return true; return false; }
^
In file included from cvganalysis.h:9:0,
from cvganalysis.cpp:2:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool isEnd(){return index>=range.size();}
^
cvganalysis.cpp: In function ‘void getconnectedcoverage(std::map<long int, int>&, std::vector<std::vector<long int> >&, std::vector<std::vector<long int> >&, int)’:
cvganalysis.cpp:20:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i++){
^
cvganalysis.cpp:25:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i+=2){
^
cvganalysis.cpp:33:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i++){
^
cvganalysis.cpp:44:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i+=2){
^
cvganalysis.cpp: In function ‘void getcoverage(std::map<long int, int>&, std::vector<std::vector<long int> >&, std::vector<std::vector<long int> >&)’:
cvganalysis.cpp:78:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i++){
^
cvganalysis.cpp:79:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<rpoolstart[i].size();j++){
^
cvganalysis.cpp:85:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i++){
^
cvganalysis.cpp:86:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<rpoolstart[i].size();j++){
^
cvganalysis.cpp: In function ‘int cutcvg(const std::map<long int, int>&, std::vector<std::pair<long int, long int> >&, int, int)’:
cvganalysis.cpp:157:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<cvgranges.size();i++){
^
cvganalysis.cpp:156:12: warning: unused variable ‘prevjump’ [-Wunused-variable]
bool prevjump=false;
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c ffProcesssam.cpp -o ffProcesssam.o
In file included from structdef.h:11:0,
from samio.h:10,
from ffProcesssam.cpp:3:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
int orientation;
^
In file included from structdef.h:11:0,
from samio.h:10,
from ffProcesssam.cpp:3:
readgroup.h:24:18: warning: ‘const Samples* ReadGroup::samples’ [-Wreorder]
const Samples* samples; // 2015-01-15 ELSA
^
In file included from structdef.h:11:0,
from samio.h:10,
from ffProcesssam.cpp:3:
readgroup.h:119:3: warning: when initialized here [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool hasPairEnd(){for(int i=0;i<pairs.size();i++) if(pairs[i]!=-1)return true; return false; }
^
In file included from samio.h:10:0,
from ffProcesssam.cpp:3:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool isEnd(){return index>=range.size();}
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c instanceio.cpp -o instanceio.o
In file included from structdef.h:11:0,
from instanceio.h:7,
from instanceio.cpp:2:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
int orientation;
^
In file included from structdef.h:11:0,
from instanceio.h:7,
from instanceio.cpp:2:
readgroup.h:24:18: warning: ‘const Samples* ReadGroup::samples’ [-Wreorder]
const Samples* samples; // 2015-01-15 ELSA
^
In file included from structdef.h:11:0,
from instanceio.h:7,
from instanceio.cpp:2:
readgroup.h:119:3: warning: when initialized here [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool hasPairEnd(){for(int i=0;i<pairs.size();i++) if(pairs[i]!=-1)return true; return false; }
^
In file included from instanceio.h:7:0,
from instanceio.cpp:2:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool isEnd(){return index>=range.size();}
^
instanceio.cpp: In function ‘void getallbound(std::map<long int, int>&, range_t, vpos_t&, vpos_t&, std::map<long int, std::vector<double> >&, bool)’:
instanceio.cpp:25:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i++){
^
instanceio.cpp:27:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=1;j<rpoolstart[i].size();j++) boundfilter[rpoolstart[i][j]]++;
^
instanceio.cpp:28:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<rpoolend[i].size()-1;j++) boundfilter[rpoolend[i][j]+1]++;
^
instanceio.cpp:57:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<cutpoint.size();i++){
^
instanceio.cpp: In function ‘void getalltypeorders(std::map<std::vector<int>, int>&, std::map<std::vector<int>, int>&, std::vector<std::vector<int> >&, std::vector<int>&, std::map<long int, int>&, std::vector<std::vector<long int> >&, std::vector<std::vector<long int> >&, std::map<long int, int>&)’:
instanceio.cpp:87:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i++){
^
instanceio.cpp:90:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<rpoolstart[i].size();j++){
^
instanceio.cpp:95:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( (j>0 && allbound.count(a)==0) || (j<rpoolstart[i].size()-1 && allbound.count(b+1)==0)){
^
instanceio.cpp:125:9: warning: unused variable ‘currenttypeorder’ [-Wunused-variable]
int currenttypeorder=-1;
^
instanceio.cpp: In function ‘void removeoutofrangereads(range_t&, std::vector<std::vector<long int> >&, std::vector<std::vector<long int> >&, int)’:
instanceio.cpp:151:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i++){
^
instanceio.cpp:158:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i++)
^
instanceio.cpp:165:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i+=2){
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c parseopt.cpp -o parseopt.o
In file included from structdef.h:11:0,
from parseopt.h:9,
from parseopt.cpp:1:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
int orientation;
^
In file included from structdef.h:11:0,
from parseopt.h:9,
from parseopt.cpp:1:
readgroup.h:24:18: warning: ‘const Samples* ReadGroup::samples’ [-Wreorder]
const Samples* samples; // 2015-01-15 ELSA
^
In file included from structdef.h:11:0,
from parseopt.h:9,
from parseopt.cpp:1:
readgroup.h:119:3: warning: when initialized here [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool hasPairEnd(){for(int i=0;i<pairs.size();i++) if(pairs[i]!=-1)return true; return false; }
^
In file included from parseopt.h:9:0,
from parseopt.cpp:1:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool isEnd(){return index>=range.size();}
^
parseopt.cpp: In function ‘int parseopt(std::vector<std::__cxx11::basic_string<char> >)’:
parseopt.cpp:13:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<args.size();i++){
^
parseopt.cpp:29:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i<args.size()-1){
^
parseopt.cpp:63:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ai=0;ai<allchr.size();ai++){
^
parseopt.cpp:65:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ri=0;ri<allr.size();ri++){
^
parseopt.cpp:94:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ai=0;ai<allchr.size();ai++){
^
parseopt.cpp:96:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ri=0;ri<allr.size();ri++){
^
parseopt.cpp:102:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<cs.size();i++){
^
parseopt.cpp:104:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<cs[i].size();j++){
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c rangeset.cpp -o rangeset.o
rangeset.cpp: In function ‘std::ostream& operator<<(std::ostream&, const RangeSet&)’:
rangeset.cpp:15:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<vr.size();i++){
^
rangeset.cpp: In member function ‘int RangeSet::add(const std::vector<std::pair<long int, long int> >&)’:
rangeset.cpp:49:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<v_r.size();i++){
^
rangeset.cpp: In member function ‘int RangeSet::add(pos_t&, pos_t&)’:
rangeset.cpp:56:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
rangeset.cpp: In member function ‘bool RangeSet::isOverlap(pos_t&, pos_t&)’:
rangeset.cpp:137:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
rangeset.cpp: In member function ‘long int RangeSet::minDist(pos_t&, pos_t&)’:
rangeset.cpp:144:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
rangeset.cpp: In member function ‘pos_t RangeSet::getEnd() const’:
rangeset.cpp:230:8: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable]
long prev=-1;
^
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(pos_t&, pos_t&)’:
rangeset.cpp:291:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(bi<start.size()&& end[bi]<prev)bi++;
^
rangeset.cpp:292:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(bi>=start.size())break;
^
rangeset.cpp:293:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(bi<start.size() && start[bi] <=mit->first){
^
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(const std::vector<std::pair<long int, long int> >&)’:
rangeset.cpp:313:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(bi<vr.size()&& vr[bi].second<prev)bi++;
^
rangeset.cpp:314:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(bi>=vr.size())break;
^
rangeset.cpp:315:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(bi<vr.size() && vr[bi].first <= mit->first){
^
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(RangeSet&)’:
rangeset.cpp:331:8: warning: unused variable ‘t’ [-Wunused-variable]
long t=0;
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c readgroup.cpp -o readgroup.o
In file included from readgroup.cpp:3:0:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
int orientation;
^
In file included from readgroup.cpp:3:0:
readgroup.h:24:18: warning: ‘const Samples* ReadGroup::samples’ [-Wreorder]
const Samples* samples; // 2015-01-15 ELSA
^
In file included from readgroup.cpp:3:0:
readgroup.h:119:3: warning: when initialized here [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool hasPairEnd(){for(int i=0;i<pairs.size();i++) if(pairs[i]!=-1)return true; return false; }
^
In file included from cvganalysis.h:9:0,
from readgroup.cpp:5:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool isEnd(){return index>=range.size();}
^
readgroup.cpp: In member function ‘void ReadGroup::getConnectedCoverage(std::map<long int, int>&)’:
readgroup.cpp:135:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp:148:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp: In member function ‘void ReadGroup::getCoverage(std::map<long int, int>&, const range_t&)’:
readgroup.cpp:205:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp:209:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<start[i].size();j++){
^
readgroup.cpp:218:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp:222:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<start[i].size();j++){
^
readgroup.cpp: In member function ‘void ReadGroup::getPointCoverage(std::map<long int, int>&)’:
readgroup.cpp:258:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++)
^
readgroup.cpp: In member function ‘range_t ReadGroup::getRange() const’:
readgroup.cpp:273:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp: In member function ‘void ReadGroup::splitByRangeSet(std::vector<ReadGroup>&, long int)’:
readgroup.cpp:288:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp:292:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<vs.size();j++){
^
readgroup.cpp:347:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i1=0;i1<vs.size();i1++){
^
readgroup.cpp:349:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i2=i1+1;i2<vs.size();i2++){
^
readgroup.cpp:357:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<vr[i2].start.size();i++){
^
readgroup.cpp:385:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<subvr.size();j++) {
^
readgroup.cpp:396:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<valid.size();i++){
^
readgroup.cpp:410:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < valid_size; i++) {
^
readgroup.cpp: In member function ‘void ReadGroup::splitByRangeSet(std::vector<ReadGroup>&, std::vector<RangeSet>&)’:
readgroup.cpp:437:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp:443:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<vs.size();j++){
^
readgroup.cpp:474:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<vr.size();i++){
^
readgroup.cpp: In member function ‘void ReadGroup::splitByDirection(std::vector<ReadGroup>&, std::vector<std::pair<long int, long int> >&)’:
readgroup.cpp:496:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp: In member function ‘void ReadGroup::calculateRangeSet()’:
readgroup.cpp:586:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp: In member function ‘void ReadGroup::setupBound(std::vector<std::pair<long int, long int> >&)’:
readgroup.cpp:595:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<jbound.size();i++){
^
readgroup.cpp: In member function ‘void ReadGroup::calculateBound(bool, int, int)’:
readgroup.cpp:637:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rpoolstart.size();i++){
^
readgroup.cpp:640:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=1;j<rpoolstart[i].size();j++) boundfilter[rpoolstart[i][j]]++;
^
readgroup.cpp:641:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<rpoolend[i].size()-1;j++) boundfilter[rpoolend[i][j]+1]++;
^
readgroup.cpp:689:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<cutpoint.size();i++){
^
readgroup.cpp: In member function ‘type_t ReadGroup::getType(const pos_t&, const pos_t&) const’:
readgroup.cpp:727:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<sn.size();i++){
^
readgroup.cpp:728:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<segs.size();j++){
^
readgroup.cpp:736:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( i==sn.size()-1 && sn[i]<segs[j].first
^
readgroup.cpp: In member function ‘void ReadGroup::calculateType()’:
readgroup.cpp:796:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp:809:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<cty.size();j++){
^
readgroup.cpp:830:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (vtc.size() <= tn) {
^
readgroup.cpp:832:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t nn = vtc.size(); nn <= tn; ++nn) {
^
readgroup.cpp:841:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alltype.size();i++){
^
readgroup.cpp: In member function ‘int ReadGroup::validSize() const’:
readgroup.cpp:848:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<validRead.size();i++)
^
readgroup.cpp: In member function ‘void ReadGroup::removeWeakSegs(float)’:
readgroup.cpp:860:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alltype.size();i++){
^
readgroup.cpp:867:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=1;j<alltype[i].size()-1;j++){
^
readgroup.cpp:874:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<segs.size();j++){
^
readgroup.cpp:886:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(j<segs.size()-1 && cvgstat.count(segs[j+1].first)>0){
^
readgroup.cpp: In member function ‘void ReadGroup::calculateValidSegs()’:
readgroup.cpp:912:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alltype.size();i++){
^
readgroup.cpp:914:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<alltype[i].size();j++){
^
readgroup.cpp:922:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<read2type.size();j++){
^
readgroup.cpp:926:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<segsCnt.size();i++) segsCnt[i]=0;
^
readgroup.cpp:928:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp:931:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<alltype[ttype].size();j++)
^
readgroup.cpp:936:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<segs.size();j++){
^
readgroup.cpp: In member function ‘std::vector<int> ReadGroup::getReadsContainingSegs(int)’:
readgroup.cpp:958:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alltype.size();i++){
^
readgroup.cpp:959:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<alltype[i].size();j++)
^
readgroup.cpp:964:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<read2type.size();i++)
^
readgroup.cpp: In member function ‘std::vector<std::pair<long int, long int> > ReadGroup::getSegs() const’:
readgroup.cpp:976:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<segs.size();i++)
^
readgroup.cpp: In member function ‘int ReadGroup::getReadLen(int) const’:
readgroup.cpp:983:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
int l=0; if(n>=start.size())return l;
^
readgroup.cpp:984:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start[n].size();i++)
^
readgroup.cpp: In member function ‘void ReadGroup::toStream(std::ostream&)’:
readgroup.cpp:1003:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<segs.size();i++) if (validSeg[i]==1)nsg++;
^
readgroup.cpp:1005:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<segs.size();i++){
^
readgroup.cpp:1013:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<st->second.size();j++)out<<"\t"<<st->second.at(j);
^
readgroup.cpp:1030:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<crt.size();j++) crtbin[crt[j]]=1;
^
readgroup.cpp:1031:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<crtbin.size();j++){
^
readgroup.cpp:1033:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(j!=crtbin.size()-1)out<<" ";
^
readgroup.cpp:1042:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i<rg.readid.size())out<<rg.readid[i];
^
readgroup.cpp:1053:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<validSeg.size();i++){
^
readgroup.cpp:1064:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alltype.size();i++) {
^
readgroup.cpp:1073:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alltype.size();i++){
^
readgroup.cpp:1079:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<alltype[i].size();j++) {
^
readgroup.cpp:1083:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<exonbin.size();j++) {
^
readgroup.cpp:1098:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
out << (*begin).first << '=' << (v.size()>i?v[i]:0) << ' ';
^
readgroup.cpp:1118:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<pairs.size();i++){
^
readgroup.cpp:1147:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<(apitr->second).size();i++)
^
readgroup.cpp: In member function ‘int ReadGroup::peSize() const’:
readgroup.cpp:1219:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<pairs.size();i++){
^
readgroup.cpp: In member function ‘void ReadGroup::removeTooLongReads(long int, int)’:
readgroup.cpp:1249:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp:1251:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=1;j<start[i].size();j++){
^
readgroup.cpp:1267:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<pairs.size();i++)
^
readgroup.cpp: In member function ‘int ReadGroup::getDirSum()’:
readgroup.cpp:1276:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<start.size();i++){
^
readgroup.cpp:1278:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=1;j<start[i].size();j++){
^
readgroup.cpp:1273:7: warning: unused variable ‘r’ [-Wunused-variable]
int r=0;
^
readgroup.cpp:1274:7: warning: unused variable ‘npos’ [-Wunused-variable]
int npos=0,nneg=0;
^
readgroup.cpp:1274:14: warning: unused variable ‘nneg’ [-Wunused-variable]
int npos=0,nneg=0;
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c samio.cpp -o samio.o
In file included from structdef.h:11:0,
from samio.h:10,
from samio.cpp:12:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
int orientation;
^
In file included from structdef.h:11:0,
from samio.h:10,
from samio.cpp:12:
readgroup.h:24:18: warning: ‘const Samples* ReadGroup::samples’ [-Wreorder]
const Samples* samples; // 2015-01-15 ELSA
^
In file included from structdef.h:11:0,
from samio.h:10,
from samio.cpp:12:
readgroup.h:119:3: warning: when initialized here [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool hasPairEnd(){for(int i=0;i<pairs.size();i++) if(pairs[i]!=-1)return true; return false; }
^
In file included from samio.h:10:0,
from samio.cpp:12:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool isEnd(){return index>=range.size();}
^
samio.cpp: In function ‘int readSamFile(std::__cxx11::string, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >)’:
samio.cpp:111:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<args.size();i++){
^
samio.cpp:112:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(args[i]=="--samples" && i<args.size()-1){
^
samio.cpp:145:11: warning: variable ‘dp2’ set but not used [-Wunused-but-set-variable]
range_t dp2=dp;
^
samio.cpp:149:7: warning: unused variable ‘rangecounter’ [-Wunused-variable]
int rangecounter=1;
^
samio.cpp:153:7: warning: unused variable ‘currentreadlen’ [-Wunused-variable]
int currentreadlen=0;
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c samples.cpp -o samples.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c spams.cpp -o spams.o
spams.cpp: In function ‘SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)’:
spams.cpp:955:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
const char *p = typeName;
^
In file included from spams/prox/fista.h:24:0,
from spams.h:6,
from spams.cpp:1303:
spams/prox/project.h: In function ‘void print_loss_flow(const loss_flow&)’:
spams/prox/project.h:3450:11: warning: enumeration value ‘FLOW_LINEAR’ not handled in switch [-Wswitch]
switch (loss) {
^
spams/prox/project.h:3450:11: warning: enumeration value ‘FLOW_SQUARE’ not handled in switch [-Wswitch]
spams/prox/project.h:3450:11: warning: enumeration value ‘FLOW_SQUARE_POS’ not handled in switch [-Wswitch]
spams/prox/project.h:3450:11: warning: enumeration value ‘FLOW_SQUARE_WEIGHTS’ not handled in switch [-Wswitch]
spams/prox/project.h:3450:11: warning: enumeration value ‘FLOW_SQUARE_POS_WEIGHTS’ not handled in switch [-Wswitch]
spams/prox/project.h:3450:11: warning: enumeration value ‘FLOW_POISSON’ not handled in switch [-Wswitch]
spams/prox/project.h:3450:11: warning: enumeration value ‘FLOW_POISSON_POS’ not handled in switch [-Wswitch]
spams/prox/project.h:3450:11: warning: enumeration value ‘FLOW_POISSON_WEIGHTS’ not handled in switch [-Wswitch]
spams/prox/project.h:3450:11: warning: enumeration value ‘FLOW_POISSON_WEIGHTS_POS’ not handled in switch [-Wswitch]
spams/prox/project.h:3450:11: warning: enumeration value ‘INCORRECT_LOSS_FLOW’ not handled in switch [-Wswitch]
In file included from spams.h:6:0,
from spams.cpp:1303:
spams/prox/fista.h: In function ‘void FISTA::print_loss(const FISTA::loss_t&)’:
spams/prox/fista.h:83:14: warning: enumeration value ‘SQUARE’ not handled in switch [-Wswitch]
switch (loss) {
^
spams/prox/fista.h:83:14: warning: enumeration value ‘SQUARE_MISSING’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘LOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘LOGWEIGHT’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘MULTILOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘CUR’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘HINGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘POISSON’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch [-Wswitch]
spams/prox/fista.h: In function ‘void FISTA::print_regul(const FISTA::regul_t&)’:
spams/prox/fista.h:101:14: warning: enumeration value ‘L0’ not handled in switch [-Wswitch]
switch (regul) {
^
spams/prox/fista.h:101:14: warning: enumeration value ‘L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘RIDGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1CONSTRAINT’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘ELASTICNET’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘FUSEDLASSO’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GROUPLASSO_L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GROUPLASSO_LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GROUPLASSO_L2_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GROUPLASSO_LINF_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1L2_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1LINF_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TREE_L0’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TREE_L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TREE_LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH_RIDGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH_L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TREEMULT’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPHMULT’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1LINFCR’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘NONE’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TRACE_NORM’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TRACE_NORM_VEC’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘RANK’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘RANK_VEC’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘INCORRECT_REG’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH_PATH_L0’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH_PATH_CONV’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH_PATH_CONV2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘LOG_DC’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘NA’ not handled in switch [-Wswitch]
spams/prox/fista.h: In instantiation of ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’:
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:3693:16: warning: enumeration value ‘SQUARE_MISSING’ not handled in switch [-Wswitch]
switch (param.loss) {
^
spams/prox/fista.h:3693:16: warning: enumeration value ‘LOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:3693:16: warning: enumeration value ‘LOGWEIGHT’ not handled in switch [-Wswitch]
spams/prox/fista.h:3693:16: warning: enumeration value ‘MULTILOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:3693:16: warning: enumeration value ‘CUR’ not handled in switch [-Wswitch]
spams/prox/fista.h:3693:16: warning: enumeration value ‘POISSON’ not handled in switch [-Wswitch]
spams/prox/fista.h:3693:16: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3720:19: warning: enumeration value ‘MULTILOG’ not handled in switch [-Wswitch]
switch (param.loss) {
^
spams/prox/fista.h:3720:19: warning: enumeration value ‘CUR’ not handled in switch [-Wswitch]
spams/prox/fista.h:3720:19: warning: enumeration value ‘HINGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:3720:19: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3752:19: warning: enumeration value ‘SQUARE’ not handled in switch [-Wswitch]
switch (param.loss) {
^
spams/prox/fista.h:3752:19: warning: enumeration value ‘SQUARE_MISSING’ not handled in switch [-Wswitch]
spams/prox/fista.h:3752:19: warning: enumeration value ‘LOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:3752:19: warning: enumeration value ‘LOGWEIGHT’ not handled in switch [-Wswitch]
spams/prox/fista.h:3752:19: warning: enumeration value ‘CUR’ not handled in switch [-Wswitch]
spams/prox/fista.h:3752:19: warning: enumeration value ‘HINGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:3752:19: warning: enumeration value ‘POISSON’ not handled in switch [-Wswitch]
spams/prox/fista.h:3752:19: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3772:16: warning: enumeration value ‘MULTILOG’ not handled in switch [-Wswitch]
switch (param.loss) {
^
spams/prox/fista.h:3772:16: warning: enumeration value ‘HINGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:3772:16: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3788:30: warning: unused variable ‘duality’ [-Wunused-variable]
const bool duality = loss->is_fenchel() && regularizer->is_fenchel();
^
spams/prox/fista.h: In instantiation of ‘void FISTA::SepLossPathCoding(const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, loss_flow, const GraphPathStruct<T>*, SpMatrix<T>*) [with T = double]’:
spams.h:1065:30: required from ‘SpMatrix<T>* _sepCostsPathCoding(Matrix<T>*, Matrix<T>*, T*, int*, int*, T*, T*, T, T, Vector<T>*, int, T, T, T, T*, char*, char*, bool, int) [with T = double]’
spams.cpp:4813:170: required from here
spams/prox/fista.h:3963:13: warning: enumeration value ‘FLOW_LINEAR’ not handled in switch [-Wswitch]
switch (loss) {
^
spams/prox/fista.h:3963:13: warning: enumeration value ‘FLOW_SQUARE_POS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3963:13: warning: enumeration value ‘FLOW_SQUARE_POS_WEIGHTS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3963:13: warning: enumeration value ‘FLOW_POISSON_POS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3963:13: warning: enumeration value ‘FLOW_POISSON_WEIGHTS_POS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3963:13: warning: enumeration value ‘INCORRECT_LOSS_FLOW’ not handled in switch [-Wswitch]
spams/prox/fista.h: In instantiation of ‘FISTA::SplittingFunction<T, SpMatrix<T> >* FISTA::setRegularizerADMM(const FISTA::ParamFISTA<T>&, const GraphStruct<T>*, const TreeStruct<T>*) [with T = double]’:
spams/prox/fista.h:3692:50: required from ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:3396:10: warning: enumeration value ‘L0’ not handled in switch [-Wswitch]
switch (param.regul) {
^
spams/prox/fista.h:3396:10: warning: enumeration value ‘L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘RIDGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘L1CONSTRAINT’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘ELASTICNET’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘FUSEDLASSO’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘GROUPLASSO_L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘GROUPLASSO_LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘GROUPLASSO_L2_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘GROUPLASSO_LINF_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘L1L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘L1LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘L1L2_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘L1LINF_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘TREE_L0’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘TREE_L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘TREE_LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘GRAPH_RIDGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘TREEMULT’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘GRAPHMULT’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘L1LINFCR’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘TRACE_NORM’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘TRACE_NORM_VEC’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘RANK’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘RANK_VEC’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘INCORRECT_REG’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘GRAPH_PATH_L0’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘GRAPH_PATH_CONV’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘GRAPH_PATH_CONV2’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘LOG_DC’ not handled in switch [-Wswitch]
spams/prox/fista.h:3396:10: warning: enumeration value ‘NA’ not handled in switch [-Wswitch]
spams/prox/fista.h: In instantiation of ‘FISTA::Regularizer<T>* FISTA::setRegularizerVectors(const FISTA::ParamFISTA<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’:
spams/prox/fista.h:3719:56: required from ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:3426:10: warning: enumeration value ‘L1L2’ not handled in switch [-Wswitch]
switch (param.regul) {
^
spams/prox/fista.h:3426:10: warning: enumeration value ‘L1LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:3426:10: warning: enumeration value ‘L1L2_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:3426:10: warning: enumeration value ‘L1LINF_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:3426:10: warning: enumeration value ‘TREEMULT’ not handled in switch [-Wswitch]
spams/prox/fista.h:3426:10: warning: enumeration value ‘GRAPHMULT’ not handled in switch [-Wswitch]
spams/prox/fista.h:3426:10: warning: enumeration value ‘L1LINFCR’ not handled in switch [-Wswitch]
spams/prox/fista.h:3426:10: warning: enumeration value ‘TRACE_NORM’ not handled in switch [-Wswitch]
spams/prox/fista.h:3426:10: warning: enumeration value ‘RANK’ not handled in switch [-Wswitch]
spams/prox/fista.h:3426:10: warning: enumeration value ‘INCORRECT_REG’ not handled in switch [-Wswitch]
spams/prox/fista.h:3426:10: warning: enumeration value ‘NA’ not handled in switch [-Wswitch]
spams/prox/fista.h: In instantiation of ‘void FISTA::solver_aux1(const Matrix<T>&, const Matrix<T>&, Matrix<T>&, Matrix<T>&, FISTA::Regularizer<T>**, FISTA::Loss<T>**, const FISTA::ParamFISTA<T>&) [with T = double]’:
spams/prox/fista.h:3735:27: required from ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:3588:24: warning: unused variable ‘duality’ [-Wunused-variable]
const bool duality = losses[0]->is_fenchel() && regularizers[0]->is_fenchel();
^
spams/prox/fista.h: In instantiation of ‘FISTA::Regularizer<T, Matrix<T> >* FISTA::setRegularizerMatrices(const FISTA::ParamFISTA<T>&, int, int, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’:
spams/prox/fista.h:3751:57: required from ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:3477:10: warning: enumeration value ‘GROUPLASSO_L2’ not handled in switch [-Wswitch]
switch (param.regul) {
^
spams/prox/fista.h:3477:10: warning: enumeration value ‘GROUPLASSO_LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:3477:10: warning: enumeration value ‘GROUPLASSO_L2_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:3477:10: warning: enumeration value ‘GROUPLASSO_LINF_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:3477:10: warning: enumeration value ‘GRAPH_RIDGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:3477:10: warning: enumeration value ‘GRAPH_L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:3477:10: warning: enumeration value ‘TRACE_NORM_VEC’ not handled in switch [-Wswitch]
spams/prox/fista.h:3477:10: warning: enumeration value ‘RANK_VEC’ not handled in switch [-Wswitch]
spams/prox/fista.h:3477:10: warning: enumeration value ‘INCORRECT_REG’ not handled in switch [-Wswitch]
spams/prox/fista.h:3477:10: warning: enumeration value ‘LOG_DC’ not handled in switch [-Wswitch]
spams/prox/fista.h:3477:10: warning: enumeration value ‘NA’ not handled in switch [-Wswitch]
spams/prox/fista.h: In instantiation of ‘void FISTA::solver_aux2(const Matrix<T>&, const Matrix<T>&, Matrix<T>&, Matrix<T>&, FISTA::Regularizer<T, Matrix<T> >**, FISTA::Loss<T, Matrix<T> >**, const FISTA::ParamFISTA<T>&) [with T = double]’:
spams/prox/fista.h:3757:27: required from ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:3635:24: warning: unused variable ‘duality’ [-Wunused-variable]
const bool duality = losses[0]->is_fenchel() && regularizers[0]->is_fenchel();
^
spams/prox/fista.h: In instantiation of ‘void FISTA::ISTA_Generic(FISTA::Loss<T, D, E>&, FISTA::Regularizer<T, D>&, const D&, D&, Vector<T>&, const FISTA::ParamFISTA<T>&) [with T = double; D = Matrix<double>; E = Matrix<double>]’:
spams/prox/fista.h:3796:31: required from ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:2956:12: warning: unused variable ‘sec’ [-Wunused-variable]
T sec=time.getElapsed();
^
spams/prox/fista.h: In instantiation of ‘void FISTA::FISTA_Generic(FISTA::Loss<T, D, E>&, FISTA::Regularizer<T, D>&, const D&, D&, Vector<T>&, const FISTA::ParamFISTA<T>&) [with T = double; D = Matrix<double>; E = Matrix<double>]’:
spams/prox/fista.h:3800:32: required from ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:3044:12: warning: unused variable ‘sec’ [-Wunused-variable]
T sec=time.getElapsed();
^
spams/prox/fista.h: In instantiation of ‘void FISTA::ISTA_Generic(FISTA::Loss<T, D, E>&, FISTA::Regularizer<T, D>&, const D&, D&, Vector<T>&, const FISTA::ParamFISTA<T>&) [with T = double; D = Vector<double>; E = Vector<double>]’:
spams/prox/fista.h:3620:28: required from ‘void FISTA::solver_aux1(const Matrix<T>&, const Matrix<T>&, Matrix<T>&, Matrix<T>&, FISTA::Regularizer<T>**, FISTA::Loss<T>**, const FISTA::ParamFISTA<T>&) [with T = double]’
spams/prox/fista.h:3735:27: required from ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:2956:12: warning: unused variable ‘sec’ [-Wunused-variable]
T sec=time.getElapsed();
^
spams/prox/fista.h: In instantiation of ‘void FISTA::FISTA_Generic(FISTA::Loss<T, D, E>&, FISTA::Regularizer<T, D>&, const D&, D&, Vector<T>&, const FISTA::ParamFISTA<T>&) [with T = double; D = Vector<double>; E = Vector<double>]’:
spams/prox/fista.h:3624:29: required from ‘void FISTA::solver_aux1(const Matrix<T>&, const Matrix<T>&, Matrix<T>&, Matrix<T>&, FISTA::Regularizer<T>**, FISTA::Loss<T>**, const FISTA::ParamFISTA<T>&) [with T = double]’
spams/prox/fista.h:3735:27: required from ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:3044:12: warning: unused variable ‘sec’ [-Wunused-variable]
T sec=time.getElapsed();
^
spams/prox/fista.h: In instantiation of ‘void FISTA::ISTA_Generic(FISTA::Loss<T, D, E>&, FISTA::Regularizer<T, D>&, const D&, D&, Vector<T>&, const FISTA::ParamFISTA<T>&) [with T = double; D = Matrix<double>; E = Vector<double>]’:
spams/prox/fista.h:3662:28: required from ‘void FISTA::solver_aux2(const Matrix<T>&, const Matrix<T>&, Matrix<T>&, Matrix<T>&, FISTA::Regularizer<T, Matrix<T> >**, FISTA::Loss<T, Matrix<T> >**, const FISTA::ParamFISTA<T>&) [with T = double]’
spams/prox/fista.h:3757:27: required from ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:2956:12: warning: unused variable ‘sec’ [-Wunused-variable]
T sec=time.getElapsed();
^
spams/prox/fista.h: In instantiation of ‘void FISTA::FISTA_Generic(FISTA::Loss<T, D, E>&, FISTA::Regularizer<T, D>&, const D&, D&, Vector<T>&, const FISTA::ParamFISTA<T>&) [with T = double; D = Matrix<double>; E = Vector<double>]’:
spams/prox/fista.h:3666:29: required from ‘void FISTA::solver_aux2(const Matrix<T>&, const Matrix<T>&, Matrix<T>&, Matrix<T>&, FISTA::Regularizer<T, Matrix<T> >**, FISTA::Loss<T, Matrix<T> >**, const FISTA::ParamFISTA<T>&) [with T = double]’
spams/prox/fista.h:3757:27: required from ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’
spams.h:480:16: required from ‘Matrix<T>* _fistaFlat(Matrix<T>*, AbstractMatrixB<T>*, Matrix<T>*, Matrix<T>*, int, int, T, bool, T, T, T, T, T, T, T, T, T, int, int, bool, bool, bool, bool, bool, char*, char*, bool, bool, bool, bool, bool, bool, char*, bool, Vector<T>*, int, bool, bool, int) [with T = double]’
spams.cpp:3278:279: required from here
spams/prox/fista.h:3044:12: warning: unused variable ‘sec’ [-Wunused-variable]
T sec=time.getElapsed();
^
In file included from spams/prox/fista.h:24:0,
from spams.h:6,
from spams.cpp:1303:
spams/prox/project.h: In instantiation of ‘T DoubleMinCostFlow<T>::eval_flow_derivative_arc(int, int) const [with T = double]’:
spams/prox/project.h:3991:72: required from ‘T DoubleMinCostFlow<T>::check_reduced_costs() const [with T = double]’
spams/prox/project.h:3804:7: required from ‘void DoubleMinCostFlow<T>::solve_min_cost(T, bool) [with T = double]’
spams/prox/project.h:4660:4: required from ‘void DoubleGraphPath<T>::sep_costs_conv(T*, T, loss_flow, List<Path<Int>*>*, const T*, T, T) [with T = double]’
spams/prox/fista.h:3991:13: required from ‘void FISTA::SepLossPathCoding(const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, loss_flow, const GraphPathStruct<T>*, SpMatrix<T>*) [with T = double]’
spams.h:1065:30: required from ‘SpMatrix<T>* _sepCostsPathCoding(Matrix<T>*, Matrix<T>*, T*, int*, int*, T*, T*, T, T, Vector<T>*, int, T, T, T, T*, char*, char*, bool, int) [with T = double]’
spams.cpp:4813:170: required from here
spams/prox/project.h:3738:4: warning: enumeration value ‘INCORRECT_LOSS_FLOW’ not handled in switch [-Wswitch]
switch (loss) {
^
spams/prox/project.h: In instantiation of ‘T DoubleMinCostFlow<T>::eval_flow_saturate_arc(int, int, T) const [with T = double]’:
spams/prox/project.h:4019:81: required from ‘void DoubleMinCostFlow<T>::saturate_arc(int, int) [with T = double]’
spams/prox/project.h:3859:10: required from ‘void DoubleMinCostFlow<T>::refine(T) [with T = double]’
spams/prox/project.h:3817:7: required from ‘void DoubleMinCostFlow<T>::solve_min_cost(T, bool) [with T = double]’
spams/prox/project.h:4660:4: required from ‘void DoubleGraphPath<T>::sep_costs_conv(T*, T, loss_flow, List<Path<Int>*>*, const T*, T, T) [with T = double]’
spams/prox/fista.h:3991:13: required from ‘void FISTA::SepLossPathCoding(const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, loss_flow, const GraphPathStruct<T>*, SpMatrix<T>*) [with T = double]’
spams.h:1065:30: required from ‘SpMatrix<T>* _sepCostsPathCoding(Matrix<T>*, Matrix<T>*, T*, int*, int*, T*, T*, T, T, Vector<T>*, int, T, T, T, T*, char*, char*, bool, int) [with T = double]’
spams.cpp:4813:170: required from here
spams/prox/project.h:3761:4: warning: enumeration value ‘INCORRECT_LOSS_FLOW’ not handled in switch [-Wswitch]
switch (loss) {
^
In file included from spams.h:6:0,
from spams.cpp:1303:
spams/prox/fista.h: In instantiation of ‘FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double; Reg = FISTA::normLINF<double>]’:
spams.cpp:5545:1: required from here
spams/prox/fista.h:1807:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i<_groups.size(); ++i) delete(_groups[i]);
^
spams/prox/fista.h: In instantiation of ‘void FISTA::GroupProx<T, Reg>::prox(const Vector<T>&, Vector<T>&, T) [with T = double; Reg = FISTA::normLINF<double>]’:
spams.cpp:5545:1: required from here
spams/prox/fista.h:1814:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i<_groups.size(); ++i) {
^
spams/prox/fista.h: In instantiation of ‘T FISTA::GroupProx<T, Reg>::eval(const Vector<T>&) const [with T = double; Reg = FISTA::normLINF<double>]’:
spams.cpp:5545:1: required from here
spams/prox/fista.h:1843:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i<_groups.size(); ++i) {
^
spams/prox/fista.h: In instantiation of ‘void FISTA::GroupProx<T, Reg>::fenchel(const Vector<T>&, T&, T&) const [with T = double; Reg = FISTA::normLINF<double>]’:
spams.cpp:5545:1: required from here
spams/prox/fista.h:1870:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i<_groups.size(); ++i) {
^
spams/prox/fista.h: In instantiation of ‘FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double; Reg = FISTA::normL2<double>]’:
spams.cpp:5545:1: required from here
spams/prox/fista.h:1807:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i<_groups.size(); ++i) delete(_groups[i]);
^
spams/prox/fista.h: In instantiation of ‘void FISTA::GroupProx<T, Reg>::prox(const Vector<T>&, Vector<T>&, T) [with T = double; Reg = FISTA::normL2<double>]’:
spams.cpp:5545:1: required from here
spams/prox/fista.h:1814:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i<_groups.size(); ++i) {
^
spams/prox/fista.h: In instantiation of ‘T FISTA::GroupProx<T, Reg>::eval(const Vector<T>&) const [with T = double; Reg = FISTA::normL2<double>]’:
spams.cpp:5545:1: required from here
spams/prox/fista.h:1843:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i<_groups.size(); ++i) {
^
spams/prox/fista.h: In instantiation of ‘void FISTA::GroupProx<T, Reg>::fenchel(const Vector<T>&, T&, T&) const [with T = double; Reg = FISTA::normL2<double>]’:
spams.cpp:5545:1: required from here
spams/prox/fista.h:1870:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i<_groups.size(); ++i) {
^
In file included from spams/prox/fista.h:24:0,
from spams.h:6,
from spams.cpp:1303:
spams/prox/project.h: In instantiation of ‘T DoubleMinCostFlow<T>::eval_flow_arc(int, int) const [with T = double]’:
spams/prox/project.h:3696:14: required from ‘T DoubleMinCostFlow<T>::compute_cost() const [with T = double]’
spams/prox/project.h:4545:19: required from ‘T DoubleGraphPath<T>::eval_conv(const T*, List<Path<Int>*>*, bool) [with T = double]’
spams/prox/fista.h:2265:104: required from ‘T FISTA::GraphPathConv<T>::eval(const Vector<T>&) const [with T = double]’
spams.cpp:5545:1: required from here
spams/prox/project.h:3709:4: warning: enumeration value ‘INCORRECT_LOSS_FLOW’ not handled in switch [-Wswitch]
switch (loss) {
^
In file included from spams.h:6:0,
from spams.cpp:1303:
spams/prox/fista.h: In function ‘FISTA::SplittingFunction<T, SpMatrix<T> >* FISTA::setRegularizerADMM(const FISTA::ParamFISTA<T>&, const GraphStruct<T>*, const TreeStruct<T>*) [with T = double]’:
spams/prox/fista.h:3402:17: warning: ‘reg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return reg;
^
In file included from spams/prox/fista.h:24:0,
from spams.h:6,
from spams.cpp:1303:
spams/prox/project.h: In member function ‘T DoubleMinCostFlow<T>::eval_flow_derivative_arc(int, int) const [with T = double]’:
spams/prox/project.h:3750:43: warning: ‘tmp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return _capacity[pointer] > 0 ? tmp : -tmp;
^
In file included from spams.h:6:0,
from spams.cpp:1303:
spams/prox/fista.h: In function ‘FISTA::Regularizer<T>* FISTA::setRegularizerVectors(const FISTA::ParamFISTA<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’:
spams/prox/fista.h:3454:17: warning: ‘reg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return reg;
^
spams/prox/fista.h: In function ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’:
spams/prox/fista.h:3788:59: warning: ‘loss’ may be used uninitialized in this function [-Wmaybe-uninitialized]
const bool duality = loss->is_fenchel() && regularizer->is_fenchel();
^
In file included from spams/prox/fista.h:24:0,
from spams.h:6,
from spams.cpp:1303:
spams/prox/project.h: In member function ‘T DoubleMinCostFlow<T>::eval_flow_saturate_arc(int, int, T) const [with T = double]’:
spams/prox/project.h:3774:11: warning: ‘tmp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return tmp;
^
spams/prox/project.h: In member function ‘void DoubleMinCostFlow<T>::solve_min_cost(T, bool) [with T = double]’:
spams/prox/project.h:3923:59: warning: ‘tmp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
const T delta = saturated_amount-_flow[pointer];
^
spams/prox/project.h:3760:6: note: ‘tmp’ was declared here
T tmp;
^
spams/prox/project.h:3919:70: warning: ‘tmp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
const T reduced_cost=this->eval_flow_derivative_arc(node,j)-target;
^
spams/prox/project.h:3737:6: note: ‘tmp’ was declared here
T tmp;
^
spams/prox/project.h:3750:43: warning: ‘tmp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return _capacity[pointer] > 0 ? tmp : -tmp;
^
spams/prox/project.h:3737:6: note: ‘tmp’ was declared here
T tmp;
^
spams/prox/project.h:3750:43: warning: ‘tmp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return _capacity[pointer] > 0 ? tmp : -tmp;
^
spams/prox/project.h:3737:6: note: ‘tmp’ was declared here
T tmp;
^
spams/prox/project.h: In member function ‘T DoubleGraphPath<T>::eval_conv(const T*, List<Path<Int>*>*, bool) [with T = double]’:
spams/prox/project.h:3696:10: warning: ‘tmp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
cost+=this->eval_flow_arc(i,j);
^
spams/prox/project.h:3708:6: note: ‘tmp’ was declared here
T tmp;
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -Wall -c structdef.cpp -o structdef.o
In file included from structdef.h:11:0,
from structdef.cpp:6:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
int orientation;
^
In file included from structdef.h:11:0,
from structdef.cpp:6:
readgroup.h:24:18: warning: ‘const Samples* ReadGroup::samples’ [-Wreorder]
const Samples* samples; // 2015-01-15 ELSA
^
In file included from structdef.h:11:0,
from structdef.cpp:6:
readgroup.h:119:3: warning: when initialized here [-Wreorder]
ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool hasPairEnd(){for(int i=0;i<pairs.size();i++) if(pairs[i]!=-1)return true; return false; }
^
In file included from structdef.cpp:6:0:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool isEnd(){return index>=range.size();}
^
structdef.cpp: In member function ‘int GeneRange::sort()’:
structdef.cpp:47:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<chr.size();i++)
^
structdef.cpp:52:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<rangepos.size();i++)
^
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o flipflop.so FileSplitter.o R_init_flipflop.o align.o auxiliaryio.o bedio.o common.o cvganalysis.o ffProcesssam.o instanceio.o parseopt.o rangeset.o readgroup.o samio.o samples.o spams.o structdef.o -s -fopenmp -lstdc++ -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/flipflop.Rcheck/flipflop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flipflop)
