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BioC 3.2: CHECK report for flipflop on zin1

This page was generated on 2015-08-24 10:49:40 -0700 (Mon, 24 Aug 2015).

Package 336/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flipflop 1.7.3
Elsa Bernard
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flipflop
Last Changed Rev: 105768 / Revision: 107696
Last Changed Date: 2015-07-02 02:21:27 -0700 (Thu, 02 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flipflop
Version: 1.7.3
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings flipflop_1.7.3.tar.gz
StartedAt: 2015-08-23 23:45:39 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 23:47:57 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 137.2 seconds
RetCode: 0
Status:  OK 
CheckDir: flipflop.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings flipflop_1.7.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/flipflop.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flipflop/DESCRIPTION’ ... OK
* this is package ‘flipflop’ version ‘1.7.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘flipflop’ can be installed ... [48s/49s] OK
* 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
* 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 loading without being on the library search path ... 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) ... OK
* checking compiled code ... NOTE
/usr/bin/nm: /home/biocbuild/bbs-3.2-bioc/meat/flipflop.Rcheck/flipflop/libs/flipflop.so: no symbols
/usr/bin/nm: /home/biocbuild/bbs-3.2-bioc/meat/flipflop.Rcheck/flipflop/libs/flipflop.so: no symbols


See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/flipflop.Rcheck/00check.log’
for details.


flipflop.Rcheck/00install.out:

* installing *source* package ‘flipflop’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c FileSplitter.cpp -o FileSplitter.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_flipflop.c -o R_init_flipflop.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c align.cpp -o align.o
align.cpp: In function ‘std::ostream& operator<<(std::ostream&, Align&)’:
align.cpp:11:30: 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:19:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<start.size();i++)
                            ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c auxiliaryio.cpp -o auxiliaryio.o
In file included from structdef.h:11:0,
                 from auxiliaryio.h:11,
                 from auxiliaryio.cpp:6:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
   int orientation;
       ^
In file included from structdef.h:11:0,
                 from auxiliaryio.h:11,
                 from auxiliaryio.cpp:6:
readgroup.h:24:18: warning:   ‘const Samples* ReadGroup::samples’ [-Wreorder]
   const Samples* samples; // 2015-01-15 ELSA
                  ^
In file included from structdef.h:11:0,
                 from auxiliaryio.h:11,
                 from auxiliaryio.cpp:6:
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
   ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
   ^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:46: 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:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   bool isEnd(){return index>=range.size();}
                                         ^
auxiliaryio.cpp: In function ‘void prepareAuxFile(std::vector<std::basic_string<char> >, std::string, bool&)’:
auxiliaryio.cpp:52:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<args.size();i++){
                           ^
auxiliaryio.cpp:53:22: 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:63:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<args.size();i++){
                           ^
auxiliaryio.cpp:158:30: 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:216:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<startpos.size();i++){
                                 ^
auxiliaryio.cpp:218:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(i!=startpos.size()-1)
                             ^
auxiliaryio.cpp:223:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<endpos.size();i++){
                               ^
auxiliaryio.cpp:225:27: 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:240:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=1;i<startpos.size();i++){
                                 ^
auxiliaryio.cpp:244:33: 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:318:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<rpoolstart.size();i++){
                                   ^
auxiliaryio.cpp:339:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<rpoolstart.size();i++){
                                   ^
auxiliaryio.cpp:342:44: 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:410:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<allrange.size();i++){
                                 ^
auxiliaryio.cpp:434:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<lencod.size();i++){
                               ^
auxiliaryio.cpp:436:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(i<lencod.size()-1)boundfs<<",";
                          ^
auxiliaryio.cpp:441:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<startcod.size();i++){
                                 ^
auxiliaryio.cpp:443:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(i<startcod.size()-1)boundfs<<",";
                            ^
auxiliaryio.cpp:450:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int n=0;n<startcod.size();n++){
                                   ^
auxiliaryio.cpp:453:30: 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:522:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<subg.size();i++){
                             ^
auxiliaryio.cpp:534:27: 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:609:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<annostart.size();i++){
                                ^
auxiliaryio.cpp:611:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j=0;j<annostart[i].size();j++) {
                                       ^
auxiliaryio.cpp:616:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j=0;j<annostart[i].size();j++) {
                                       ^
auxiliaryio.cpp:724:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int i=0;i<currentstat.size();i++)
                                        ^
auxiliaryio.cpp:736:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<refseriestype.size();i++){
                                    ^
auxiliaryio.cpp:738:41: 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:767:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<seriestype.size();i++){
                                 ^
auxiliaryio.cpp:769:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<seriestype[i].size();j++){
                                      ^
auxiliaryio.cpp:788:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<seriestype.size();i++){
                                 ^
auxiliaryio.cpp:791:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<seriestype[i].size();j++){
                                      ^
auxiliaryio.cpp:808:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<rpoolstart.size();i+=2){
                                   ^
auxiliaryio.cpp:825:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i=0;i<(apitr->second).size();i++){
                                          ^
auxiliaryio.cpp:844:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=pst;i<rpoolstart.size();i+=step){
                                     ^
auxiliaryio.cpp:849:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<allstartrange.size();i++){
                                      ^
auxiliaryio.cpp:854:43: 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;
         ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c bedio.cpp -o bedio.o
bedio.cpp: In function ‘int writeBed(std::ostream&, bedrec)’:
bedio.cpp:61:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(rec.nsegs!=rec.segstart.size())rec.nsegs=rec.segstart.size();
                                   ^
bedio.cpp:76:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<rec.segend.size();i++){
                                 ^
bedio.cpp:78:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(i<rec.segend.size()-1) out<<",";
                            ^
bedio.cpp:82:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<rec.segstart.size();i++){
                                   ^
bedio.cpp:84:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(i<rec.segstart.size()-1) out<<",";
                              ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c common.cpp -o common.o
In file included from structdef.h:11:0,
                 from common.cpp:5:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
   int orientation;
       ^
In file included from structdef.h:11:0,
                 from common.cpp:5:
readgroup.h:24:18: warning:   ‘const Samples* ReadGroup::samples’ [-Wreorder]
   const Samples* samples; // 2015-01-15 ELSA
                  ^
In file included from structdef.h:11:0,
                 from common.cpp:5:
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
   ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
   ^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:46: 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:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   bool isEnd(){return index>=range.size();}
                                         ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c cvganalysis.cpp -o cvganalysis.o
In file included from structdef.h:11:0,
                 from cvganalysis.h:9,
                 from cvganalysis.cpp:2:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
   int orientation;
       ^
In file included from structdef.h:11:0,
                 from cvganalysis.h:9,
                 from cvganalysis.cpp:2:
readgroup.h:24:18: warning:   ‘const Samples* ReadGroup::samples’ [-Wreorder]
   const Samples* samples; // 2015-01-15 ELSA
                  ^
In file included from structdef.h:11:0,
                 from cvganalysis.h:9,
                 from cvganalysis.cpp:2:
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
   ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
   ^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:46: 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:37:41: 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:20:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<rpoolstart.size();i++){
                                   ^
cvganalysis.cpp:25:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<rpoolstart.size();i+=2){
                                   ^
cvganalysis.cpp:33:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<rpoolstart.size();i++){
                                   ^
cvganalysis.cpp:44:35: 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:78:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<rpoolstart.size();i++){
                                 ^
cvganalysis.cpp:79:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<rpoolstart[i].size();j++){
                                      ^
cvganalysis.cpp:85:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<rpoolstart.size();i++){
                                 ^
cvganalysis.cpp:86:38: 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:157:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i=0;i<cvgranges.size();i++){
                                    ^
cvganalysis.cpp:156:12: warning: unused variable ‘prevjump’ [-Wunused-variable]
       bool prevjump=false;
            ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c ffProcesssam.cpp -o ffProcesssam.o
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from ffProcesssam.cpp:3:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
   int orientation;
       ^
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from ffProcesssam.cpp:3:
readgroup.h:24:18: warning:   ‘const Samples* ReadGroup::samples’ [-Wreorder]
   const Samples* samples; // 2015-01-15 ELSA
                  ^
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from ffProcesssam.cpp:3:
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
   ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
   ^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:46: 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:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   bool isEnd(){return index>=range.size();}
                                         ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c instanceio.cpp -o instanceio.o
In file included from structdef.h:11:0,
                 from instanceio.h:7,
                 from instanceio.cpp:2:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
   int orientation;
       ^
In file included from structdef.h:11:0,
                 from instanceio.h:7,
                 from instanceio.cpp:2:
readgroup.h:24:18: warning:   ‘const Samples* ReadGroup::samples’ [-Wreorder]
   const Samples* samples; // 2015-01-15 ELSA
                  ^
In file included from structdef.h:11:0,
                 from instanceio.h:7,
                 from instanceio.cpp:2:
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
   ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
   ^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:46: 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:37:41: 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:25:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<rpoolstart.size();i++){
                                 ^
instanceio.cpp:27:40: 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:28:40: 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:57:35: 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:87:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<rpoolstart.size();i++){
                                 ^
instanceio.cpp:90:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<rpoolstart[i].size();j++){
                                      ^
instanceio.cpp:95:68: 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:151:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<rpoolstart.size();i++){
                                 ^
instanceio.cpp:158:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<rpoolstart.size();i++) 
                                   ^
instanceio.cpp:165:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<rpoolstart.size();i+=2){
                                   ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c parseopt.cpp -o parseopt.o
In file included from structdef.h:11:0,
                 from parseopt.h:9,
                 from parseopt.cpp:1:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
   int orientation;
       ^
In file included from structdef.h:11:0,
                 from parseopt.h:9,
                 from parseopt.cpp:1:
readgroup.h:24:18: warning:   ‘const Samples* ReadGroup::samples’ [-Wreorder]
   const Samples* samples; // 2015-01-15 ELSA
                  ^
In file included from structdef.h:11:0,
                 from parseopt.h:9,
                 from parseopt.cpp:1:
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
   ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
   ^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:46: 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:37:41: 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:13:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<args.size();i++){
                           ^
parseopt.cpp:29:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(i<args.size()-1){
                      ^
parseopt.cpp:63:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           for(int ai=0;ai<allchr.size();ai++){
                                       ^
parseopt.cpp:65:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for(int ri=0;ri<allr.size();ri++){
                                       ^
parseopt.cpp:94:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for(int ai=0;ai<allchr.size();ai++){
                                         ^
parseopt.cpp:96:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
               for(int ri=0;ri<allr.size();ri++){
                                         ^
parseopt.cpp:102:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for(int i=0;i<cs.size();i++){
                                       ^
parseopt.cpp:104:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                   for(int j=0;j<cs[i].size();j++){
                                            ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c rangeset.cpp -o rangeset.o
rangeset.cpp: In function ‘std::ostream& operator<<(std::ostream&, const RangeSet&)’:
rangeset.cpp:15:25: 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:49:26: 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:56:28: 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:137:28: 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:144:28: 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:291:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       while(bi<start.size()&& end[bi]<prev)bi++;
                           ^
rangeset.cpp:292:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(bi>=start.size())break;
                         ^
rangeset.cpp:293:27: 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:313:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       while(bi<vr.size()&& vr[bi].second<prev)bi++;
                        ^
rangeset.cpp:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(bi>=vr.size())break;
                      ^
rangeset.cpp:315:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       while(bi<vr.size() && vr[bi].first <= mit->first){
                        ^
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(RangeSet&)’:
rangeset.cpp:331:8: warning: unused variable ‘t’ [-Wunused-variable]
   long t=0;
        ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c readgroup.cpp -o readgroup.o
In file included from readgroup.cpp:3:0:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
   int orientation;
       ^
In file included from readgroup.cpp:3:0:
readgroup.h:24:18: warning:   ‘const Samples* ReadGroup::samples’ [-Wreorder]
   const Samples* samples; // 2015-01-15 ELSA
                  ^
In file included from readgroup.cpp:3:0:
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
   ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
   ^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:46: 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:37:41: 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:135:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<start.size();i++){
                            ^
readgroup.cpp:148:28: 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:205:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<start.size();i++){
                            ^
readgroup.cpp:209:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<start[i].size();j++){
                                 ^
readgroup.cpp:218:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<start.size();i++){
                            ^
readgroup.cpp:222:33: 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:258:28: 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:273:28: 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:288:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<start.size();i++){
                            ^
readgroup.cpp:292:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<vs.size();j++){
                           ^
readgroup.cpp:347:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i1=0;i1<vs.size();i1++){
                             ^
readgroup.cpp:349:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i2=i1+1;i2<vs.size();i2++){
                                  ^
readgroup.cpp:357:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           for(int i=0;i<vr[i2].start.size();i++){
                                           ^
readgroup.cpp:385:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j=0;j<subvr.size();j++) {
                                ^
readgroup.cpp:396:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<valid.size();i++){
                            ^
readgroup.cpp:410:22: 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:437:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<start.size();i++){
                            ^
readgroup.cpp:443:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<vs.size();j++){
                           ^
readgroup.cpp:474:25: 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:496:28: 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:586:28: 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:595:29: 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:637:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<rpoolstart.size();i++){
                                 ^
readgroup.cpp:640:40: 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:641:40: 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:689:30: 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:727:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<sn.size();i++){
                         ^
readgroup.cpp:728:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<segs.size();j++){
                             ^
readgroup.cpp:736:27: 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:796:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<start.size();i++){
                            ^
readgroup.cpp:809:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<cty.size();j++){
                            ^
readgroup.cpp:830:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        if (vtc.size() <= tn) {
                          ^
readgroup.cpp:832:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (size_t nn = vtc.size(); nn <= tn; ++nn) {
                                       ^
readgroup.cpp:841:30: 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:848:32: 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:860:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<alltype.size();i++){
                              ^
readgroup.cpp:867:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int j=1;j<alltype[i].size()-1;j++){
                                         ^
readgroup.cpp:874:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int j=0;j<segs.size();j++){
                           ^
readgroup.cpp:886:22: 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:912:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<alltype.size();i++){
                                ^
readgroup.cpp:914:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j=0;j<alltype[i].size();j++){
                                     ^
readgroup.cpp:922:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<read2type.size();j++){
                                  ^
readgroup.cpp:926:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<segsCnt.size();i++) segsCnt[i]=0;
                                ^
readgroup.cpp:928:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<start.size();i++){
                              ^
readgroup.cpp:931:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j=0;j<alltype[ttype].size();j++)
                                         ^
readgroup.cpp:936:29: 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:958:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<alltype.size();i++){
                              ^
readgroup.cpp:959:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<alltype[i].size();j++)
                                   ^
readgroup.cpp:964:32: 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:976:27: 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:983:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   int l=0; if(n>=start.size())return l;
                             ^
readgroup.cpp:984:31: 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:1003:27: 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:1005:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<segs.size();i++){
                           ^
readgroup.cpp:1013:35: 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:1030:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<crt.size();j++) crtbin[crt[j]]=1;
                            ^
readgroup.cpp:1031:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<crtbin.size();j++){
                               ^
readgroup.cpp:1033:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(j!=crtbin.size()-1)out<<" ";
                           ^
readgroup.cpp:1042:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(i<rg.readid.size())out<<rg.readid[i];
                         ^
readgroup.cpp:1053:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<validSeg.size();i++){
                               ^
readgroup.cpp:1064:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<alltype.size();i++) {
                              ^
readgroup.cpp:1073:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<alltype.size();i++){
                              ^
readgroup.cpp:1079:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<alltype[i].size();j++) {
                                   ^
readgroup.cpp:1083:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<exonbin.size();j++) {
                                ^
readgroup.cpp:1098:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       out << (*begin).first << '=' << (v.size()>i?v[i]:0) << ' ';
                                                 ^
readgroup.cpp:1118:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<pairs.size();i++){
                            ^
readgroup.cpp:1147:42: 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:1219:28: 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:1249:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<start.size();i++){
                            ^
readgroup.cpp:1251:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=1;j<start[i].size();j++){
                                 ^
readgroup.cpp:1267:28: 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:1276:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<start.size();i++){
                            ^
readgroup.cpp:1278:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=1;j<start[i].size();j++){
                                 ^
readgroup.cpp:1273:7: warning: unused variable ‘r’ [-Wunused-variable]
   int r=0;
       ^
readgroup.cpp:1274:7: warning: unused variable ‘npos’ [-Wunused-variable]
   int npos=0,nneg=0;
       ^
readgroup.cpp:1274:14: warning: unused variable ‘nneg’ [-Wunused-variable]
   int npos=0,nneg=0;
              ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c samio.cpp -o samio.o
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from samio.cpp:12:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
   int orientation;
       ^
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from samio.cpp:12:
readgroup.h:24:18: warning:   ‘const Samples* ReadGroup::samples’ [-Wreorder]
   const Samples* samples; // 2015-01-15 ELSA
                  ^
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from samio.cpp:12:
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
   ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
   ^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:46: 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:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   bool isEnd(){return index>=range.size();}
                                         ^
samio.cpp: In function ‘int readSamFile(std::string, std::string, std::vector<std::basic_string<char> >)’:
samio.cpp:111:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<args.size();i++){
                           ^
samio.cpp:112:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(args[i]=="--samples" && i<args.size()-1){
                                              ^
samio.cpp:145:11: warning: variable ‘dp2’ set but not used [-Wunused-but-set-variable]
   range_t dp2=dp;
           ^
samio.cpp:149:7: warning: unused variable ‘rangecounter’ [-Wunused-variable]
   int rangecounter=1;
       ^
samio.cpp:153:7: warning: unused variable ‘currentreadlen’ [-Wunused-variable]
   int currentreadlen=0;
       ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c samples.cpp -o samples.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c spams.cpp -o spams.o
spams.cpp: In function ‘SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)’:
spams.cpp:943:15: 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:1273:
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:1273:
spams/prox/fista.h: In function ‘void FISTA::print_loss(const FISTA::loss_t&)’:
spams/prox/fista.h:83:14: warning: enumeration value ‘SQUARE’ not handled in switch [-Wswitch]
       switch (loss) {
              ^
spams/prox/fista.h:83:14: warning: enumeration value ‘SQUARE_MISSING’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘LOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘LOGWEIGHT’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘MULTILOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘CUR’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘HINGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘POISSON’ not handled in switch [-Wswitch]
spams/prox/fista.h:83:14: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch [-Wswitch]
spams/prox/fista.h: In function ‘void FISTA::print_regul(const FISTA::regul_t&)’:
spams/prox/fista.h:101:14: warning: enumeration value ‘L0’ not handled in switch [-Wswitch]
       switch (regul) {
              ^
spams/prox/fista.h:101:14: warning: enumeration value ‘L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘RIDGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1CONSTRAINT’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘ELASTICNET’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘FUSEDLASSO’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GROUPLASSO_L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GROUPLASSO_LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GROUPLASSO_L2_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GROUPLASSO_LINF_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1L2_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1LINF_L1’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TREE_L0’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TREE_L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TREE_LINF’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH_RIDGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH_L2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TREEMULT’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPHMULT’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘L1LINFCR’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘NONE’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TRACE_NORM’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘TRACE_NORM_VEC’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘RANK’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘RANK_VEC’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘INCORRECT_REG’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH_PATH_L0’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH_PATH_CONV’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘GRAPH_PATH_CONV2’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘LOG_DC’ not handled in switch [-Wswitch]
spams/prox/fista.h:101:14: warning: enumeration value ‘NA’ not handled in switch [-Wswitch]
spams/prox/fista.h: In instantiation of ‘void FISTA::solver(const Matrix<T>&, const AbstractMatrixB<T>&, const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, Matrix<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’:
spams.h:480:140:   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:1678:279:   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:2102:170:   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:1678:279:   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:1678:279:   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:1678:279:   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:1678:279:   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:1678:279:   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:1678:279:   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:1678:279:   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:1678:279:   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:1678:279:   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:1678:279:   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:1678:279:   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:1273:
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:4664:4:   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:2102:170:   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:4664:4:   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:2102:170:   required from here
spams/prox/project.h:3761:4: 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_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:2725:1:   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:1273:
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:1273:
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:1273:
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:1273:
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:3773:4: warning: ‘tmp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    tmp=_capacity[pointer] > 0 ? tmp : -tmp;
    ^
spams/prox/project.h: In member function ‘void DoubleMinCostFlow<T>::price_update(T) [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:3737:6: note: ‘tmp’ was declared here
    T tmp;
      ^
spams/prox/project.h: In member function ‘T DoubleGraphPath<T>::eval_conv(const T*, List<Path<Int>*>*, bool) [with T = double]’:
spams/prox/project.h:3696:10: warning: ‘tmp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
          cost+=this->eval_flow_arc(i,j);
          ^
spams/prox/project.h:3708:6: note: ‘tmp’ was declared here
    T tmp;
      ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c structdef.cpp -o structdef.o
In file included from structdef.h:11:0,
                 from structdef.cpp:6:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108:7: warning: ‘ReadGroup::orientation’ will be initialized after [-Wreorder]
   int orientation;
       ^
In file included from structdef.h:11:0,
                 from structdef.cpp:6:
readgroup.h:24:18: warning:   ‘const Samples* ReadGroup::samples’ [-Wreorder]
   const Samples* samples; // 2015-01-15 ELSA
                  ^
In file included from structdef.h:11:0,
                 from structdef.cpp:6:
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
   ReadGroup():forcesingle(false),isfixrange(false),orientation(0),samples(NULL){} // 2015-01-15 ELSA
   ^
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156:46: 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:37:41: 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:47:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<chr.size();i++)
                          ^
structdef.cpp:52:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<rangepos.size();i++)
                               ^
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o flipflop.so FileSplitter.o R_init_flipflop.o align.o auxiliaryio.o bedio.o common.o cvganalysis.o ffProcesssam.o instanceio.o parseopt.o rangeset.o readgroup.o samio.o samples.o spams.o structdef.o -s -fopenmp -lstdc++ -L/home/biocbuild/bbs-3.2-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.2-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/flipflop.Rcheck/flipflop/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘flipflop’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flipflop)

flipflop.Rcheck/flipflop-Ex.timings:

nameusersystemelapsed
flipflop0.3530.0040.358