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CHECK report for flipflop on tokay2

This page was generated on 2019-04-09 12:13:54 -0400 (Tue, 09 Apr 2019).

Package 545/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flipflop 1.21.0
Elsa Bernard
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/flipflop
Branch: master
Last Commit: b82d464
Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  ERROR  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  ERROR  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  ERROR  ERROR  skipped  skipped 

Summary

Package: flipflop
Version: 1.21.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flipflop.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings flipflop_1.21.0.tar.gz
StartedAt: 2019-04-09 02:43:48 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:46:25 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 156.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: flipflop.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flipflop.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings flipflop_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/flipflop.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flipflop/DESCRIPTION' ... OK
* this is package 'flipflop' version '1.21.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'flipflop' can be installed ... WARNING
Found the following significant warnings:
  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:
  readgroup.h:108:7: warning: 'ReadGroup::orientation' will be initialized after [-Wreorder]
  readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
  readgroup.h:119:3: warning:   when initialized here [-Wreorder]
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/flipflop.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
  apparently using $(LAPACK_LIBS) without following $(BLAS_LIBS) in 'src/Makevars'
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/flipflop/libs/i386/flipflop.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/flipflop/libs/x64/flipflop.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/flipflop.Rcheck/00check.log'
for details.

Installation output

flipflop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/flipflop_1.21.0.tar.gz && rm -rf flipflop.buildbin-libdir && mkdir flipflop.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flipflop.buildbin-libdir flipflop_1.21.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL flipflop_1.21.0.zip && rm flipflop_1.21.0.tar.gz flipflop_1.21.0.zip
###
##############################################################################
##############################################################################


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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  260k  100  260k    0     0  3950k      0 --:--:-- --:--:-- --:--:-- 4422k

install for i386

* installing *source* package 'flipflop' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-B/R/bin/i386 -lRblas -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRlapack -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/flipflop.buildbin-libdir/00LOCK-flipflop/00new/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'flipflop' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-B/R/bin/x64 -lRblas -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRlapack -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/flipflop.buildbin-libdir/flipflop/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flipflop' as flipflop_1.21.0.zip
* DONE (flipflop)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'flipflop' successfully unpacked and MD5 sums checked

Tests output

Example timings

flipflop.Rcheck/examples_i386/flipflop-Ex.timings

nameusersystemelapsed
flipflop0.720.002.47

flipflop.Rcheck/examples_x64/flipflop-Ex.timings

nameusersystemelapsed
flipflop0.820.021.06