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INSTALL report for flipflop on tokay1

This page was generated on 2019-04-13 11:23:21 -0400 (Sat, 13 Apr 2019).

Package 522/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flipflop 1.20.0
Elsa Bernard
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/flipflop
Branch: RELEASE_3_8
Last Commit: 5e4e92e
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flipflop
Version: 1.20.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/flipflop_1.20.0.tar.gz && rm -rf flipflop.buildbin-libdir && mkdir flipflop.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flipflop.buildbin-libdir flipflop_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flipflop_1.20.0.zip && rm flipflop_1.20.0.tar.gz flipflop_1.20.0.zip
StartedAt: 2019-04-12 19:36:25 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 19:38:09 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 103.6 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/flipflop_1.20.0.tar.gz && rm -rf flipflop.buildbin-libdir && mkdir flipflop.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flipflop.buildbin-libdir flipflop_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flipflop_1.20.0.zip && rm flipflop_1.20.0.tar.gz flipflop_1.20.0.zip
###
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##############################################################################


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100  262k  100  262k    0     0  6462k      0 --:--:-- --:--:-- --:--:-- 7092k

install for i386

* installing *source* package 'flipflop' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -c FileSplitter.cpp -o FileSplitter.o
In file included from FileSplitter.cpp:1:0:
FileSplitter.h: In member function 'void FileSplitter::endWritingInstance()':
FileSplitter.h:52:64: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iosfwd:40:0,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:38,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iostream:39,
                 from FileSplitter.h:2,
                 from FileSplitter.cpp:1:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/postypes.h:192:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int; std::streamoff = long long int]
       operator-(streamoff __off) const
       ^
In file included from FileSplitter.cpp:1:0:
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_flipflop.c -o R_init_flipflop.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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++)
                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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();}
                            ^
In file included from auxiliaryio.cpp:11:0:
FileSplitter.h: In member function 'void FileSplitter::endWritingInstance()':
FileSplitter.h:52:64: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iosfwd:40:0,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:38,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/istream:38,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/fstream:38,
                 from auxiliaryio.cpp:1:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/postypes.h:192:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int; std::streamoff = long long int]
       operator-(streamoff __off) const
       ^
In file included from auxiliaryio.cpp:11:0:
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
auxiliaryio.cpp: In function 'void prepareAuxFile(std::vector<std::basic_string<char> >, std::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::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::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::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::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::string, GeneRange&)':
auxiliaryio.cpp:904:9: warning: unused variable 'id' [-Wunused-variable]
     int id;
         ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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<<",";
         ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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();}
                            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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;
            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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();}
                            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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){
                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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::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++){
                                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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;
        ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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;
              ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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();}
                            ^
In file included from samio.cpp:16:0:
FileSplitter.h: In member function 'void FileSplitter::endWritingInstance()':
FileSplitter.h:52:64: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iosfwd:40:0,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:38,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
                 from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iostream:39,
                 from samio.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/postypes.h:192:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int; std::streamoff = long long int]
       operator-(streamoff __off) const
       ^
In file included from samio.cpp:16:0:
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
samio.cpp: In function 'int readSamFile(std::string, std::string, std::vector<std::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;
       ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -c samples.cpp -o samples.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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]
In file included from spams.cpp:1314:0:
./Rinterface.h: At global scope:
./Rinterface.h:53:12: warning: 'R_DirtyImage' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
 extern int R_DirtyImage; /* Current image dirty */
            ^
In file included from spams.h:6:0,
                 from spams.cpp:1303:
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:480:140:   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:1065:101:   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:3692:73:   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:480:140:   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:3719:93:   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:480:140:   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:3735:84:   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:480:140:   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:3751:107:   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:480:140:   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:3757:84:   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:480:140:   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:3796:81:   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:480:140:   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:3800:82:   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:480:140:   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:3620:99:   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:3735:84:   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:480:140:   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:3624:100:   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:3735:84:   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:480:140:   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:3662:99:   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:3757:84:   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:480:140:   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:3666:100:   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:3757:84:   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:480:140:   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:1065:101:   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:1065:101:   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 '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;
      ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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++)
                ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flipflop.dll tmp.def 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++ -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRblas -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRlapack -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/flipflop.buildbin-libdir/flipflop/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flipflop'
    finding HTML links ... done
    flipflop                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flipflop' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -c FileSplitter.cpp -o FileSplitter.o
In file included from FileSplitter.cpp:1:0:
FileSplitter.h: In member function 'void FileSplitter::endWritingInstance()':
FileSplitter.h:52:64: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
In file included from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/iosfwd:40:0,
                 from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/ios:38,
                 from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/ostream:38,
                 from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/iostream:39,
                 from FileSplitter.h:2,
                 from FileSplitter.cpp:1:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/postypes.h:192:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int; std::streamoff = long long int]
       operator-(streamoff __off) const
       ^
In file included from FileSplitter.cpp:1:0:
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_flipflop.c -o R_init_flipflop.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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++)
                ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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();}
                            ^
In file included from auxiliaryio.cpp:11:0:
FileSplitter.h: In member function 'void FileSplitter::endWritingInstance()':
FileSplitter.h:52:64: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
In file included from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/iosfwd:40:0,
                 from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/ios:38,
                 from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/istream:38,
                 from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/fstream:38,
                 from auxiliaryio.cpp:1:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/postypes.h:192:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int; std::streamoff = long long int]
       operator-(streamoff __off) const
       ^
In file included from auxiliaryio.cpp:11:0:
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
auxiliaryio.cpp: In function 'void prepareAuxFile(std::vector<std::basic_string<char> >, std::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::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::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::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::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::string, GeneRange&)':
auxiliaryio.cpp:904:9: warning: unused variable 'id' [-Wunused-variable]
     int id;
         ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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<<",";
         ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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();}
                            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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;
            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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();}
                            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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){
                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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::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++){
                                ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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;
        ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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;
              ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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();}
                            ^
In file included from samio.cpp:16:0:
FileSplitter.h: In member function 'void FileSplitter::endWritingInstance()':
FileSplitter.h:52:64: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
In file included from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/iosfwd:40:0,
                 from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/ios:38,
                 from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/ostream:38,
                 from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/iostream:39,
                 from samio.cpp:2:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/postypes.h:192:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int; std::streamoff = long long int]
       operator-(streamoff __off) const
       ^
In file included from samio.cpp:16:0:
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
       instance_info.size = instance_os.tellp() - instance_info.offset; // attention piquet !!!
                                                                ^
samio.cpp: In function 'int readSamFile(std::string, std::string, std::vector<std::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;
       ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -c samples.cpp -o samples.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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]
In file included from spams.cpp:1314:0:
./Rinterface.h: At global scope:
./Rinterface.h:53:12: warning: 'R_DirtyImage' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
 extern int R_DirtyImage; /* Current image dirty */
            ^
In file included from spams.h:6:0,
                 from spams.cpp:1303:
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:480:140:   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:1065:101:   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:3692:73:   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:480:140:   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:3719:93:   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:480:140:   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:3735:84:   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:480:140:   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:3751:107:   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:480:140:   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:3757:84:   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:480:140:   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:3796:81:   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:480:140:   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:3800:82:   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:480:140:   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:3620:99:   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:3735:84:   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:480:140:   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:3624:100:   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:3735:84:   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:480:140:   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:3662:99:   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:3757:84:   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:480:140:   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:3666:100:   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:3757:84:   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:480:140:   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:1065:101:   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:1065:101:   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;
                                           ^
spams/prox/project.h: In member function 'bool DoubleMinCostFlow<T>::topological_sort(bool, bool*, T*) [with T = double]':
spams/prox/project.h:3750:43: warning: 'tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
spams/prox/project.h:3737:6: note: 'tmp' was declared here
    T 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 '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;
      ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=generic -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++)
                ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flipflop.dll tmp.def 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++ -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRblas -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRlapack -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/flipflop.buildbin-libdir/flipflop/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flipflop' as flipflop_1.20.0.zip
* DONE (flipflop)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'flipflop' successfully unpacked and MD5 sums checked
In R CMD INSTALL