BioC 3.3: CHECK report for flipflop on windows2.bioconductor.org

Package: flipflop

Version: 1.9.0

Command: rm -rf flipflop.buildbin-libdir flipflop.Rcheck && mkdir flipflop.buildbin-libdir flipflop.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flipflop.buildbin-libdir flipflop_1.9.0.tar.gz >flipflop.Rcheck\00install.out 2>&1 && cp flipflop.Rcheck\00install.out flipflop-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=flipflop.buildbin-libdir --install="check:flipflop-install.out" --force-multiarch --no-vignettes --timings flipflop_1.9.0.tar.gz

StartedAt: 2015-10-27 02:22:07 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:25:21 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 193.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flipflop.Rcheck

Warnings: 1

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###
### Running command:
###
###   rm -rf flipflop.buildbin-libdir flipflop.Rcheck && mkdir flipflop.buildbin-libdir flipflop.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flipflop.buildbin-libdir flipflop_1.9.0.tar.gz >flipflop.Rcheck\00install.out 2>&1 && cp flipflop.Rcheck\00install.out flipflop-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=flipflop.buildbin-libdir --install="check:flipflop-install.out" --force-multiarch --no-vignettes --timings flipflop_1.9.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/flipflop.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.9.0'
* 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: [enabled by default]
See 'c:/biocbld/bbs-3.3-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
** checking loading without being on the library search path ... 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 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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'c:/biocbld/bbs-3.3-bioc/meat/flipflop.buildbin-libdir/flipflop/libs/i386/flipflop.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'c:/biocbld/bbs-3.3-bioc/meat/flipflop.buildbin-libdir/flipflop/libs/x64/flipflop.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [3s] OK
** running examples for arch 'x64' ... [4s] 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: 1 WARNING, 2 NOTEs
See
  'c:/biocbld/bbs-3.3-bioc/meat/flipflop.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'flipflop' ...
** libs
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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: [enabled by default]
c:\rtools33\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../include/c++/4.6.3/bits/postypes.h:194:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int, std::fpos<_StateT> = std::fpos<int>, std::streamoff = long long int]
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
gcc -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_flipflop.c -o R_init_flipflop.o
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
align.cpp: In member function 'int Align::getReadLen() const':
align.cpp:19:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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: [enabled by default]
c:\rtools33\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../include/c++/4.6.3/bits/postypes.h:194:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int, std::fpos<_StateT> = std::fpos<int>, std::streamoff = long long int]
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
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]
auxiliaryio.cpp:53:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:63:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:158:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
auxiliaryio.cpp:218:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:223:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:225:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
auxiliaryio.cpp:244:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp: In function 'void writeannotation(ReadGroup&, int)':
auxiliaryio.cpp:318:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:339:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:342:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
auxiliaryio.cpp:434:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:436:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:441:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:443:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:450:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:453:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp: In function 'int write2rangeandinstance(ReadGroup&, range_t&)':
auxiliaryio.cpp:522:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:534:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
auxiliaryio.cpp:611:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:616:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:724:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:736:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:738:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:767:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:769:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:788:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:791:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:808:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:825:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:844:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:849:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:854:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp: In function 'int readgenerangefile(std::string, GeneRange&)':
auxiliaryio.cpp:904:9: warning: unused variable 'id' [-Wunused-variable]
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
bedio.cpp:76:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:78:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:82:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:84:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
cvganalysis.cpp:25:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:33:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:44:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
cvganalysis.cpp:79:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:85:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:86:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
cvganalysis.cpp:156:12: warning: unused variable 'prevjump' [-Wunused-variable]
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
instanceio.cpp:27:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:28:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:57:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
instanceio.cpp:90:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:95:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:125:9: warning: unused variable 'currenttypeorder' [-Wunused-variable]
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]
instanceio.cpp:158:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:165:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
parseopt.cpp:29:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:63:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:65:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:94:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:96:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:102:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:104:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
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]
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]
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]
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]
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]
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]
rangeset.cpp:292:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:293:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
rangeset.cpp:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:315:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'long int RangeSet::overlapLen(RangeSet&)':
rangeset.cpp:331:8: warning: unused variable 't' [-Wunused-variable]
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
readgroup.cpp:148:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp:209:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:218:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:222:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp: In member function 'range_t ReadGroup::getRange() const':
readgroup.cpp:273:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp:292:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:347:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:349:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:357:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:385:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:396:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:410:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:408:31: warning: variable 'vr_end' set but not used [-Wunused-but-set-variable]
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]
readgroup.cpp:443:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:474:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp: In member function 'void ReadGroup::calculateRangeSet()':
readgroup.cpp:586:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
readgroup.cpp:640:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:641:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:689:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp:728:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:736:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::calculateType()':
readgroup.cpp:796:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:809:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:830:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:832:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:841:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::validSize() const':
readgroup.cpp:848:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::removeWeakSegs(float)':
readgroup.cpp:860:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:867:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:874:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:886:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::calculateValidSegs()':
readgroup.cpp:912:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:914:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:922:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:926:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:928:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:931:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:936:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp:959:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:964:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp: In member function 'int ReadGroup::getReadLen(int) const':
readgroup.cpp:983:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:984:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::toStream(std::ostream&)':
readgroup.cpp:1003:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1005:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1013:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1030:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1031:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1033:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1042:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1053:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1064:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1073:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1079:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1083:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1098:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1118:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1147:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::peSize() const':
readgroup.cpp:1219:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp:1251:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1267:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::getDirSum()':
readgroup.cpp:1276:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1278:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1273:7: warning: unused variable 'r' [-Wunused-variable]
readgroup.cpp:1274:7: warning: unused variable 'npos' [-Wunused-variable]
readgroup.cpp:1274:14: warning: unused variable 'nneg' [-Wunused-variable]
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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: [enabled by default]
c:\rtools33\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../include/c++/4.6.3/bits/postypes.h:194:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int, std::fpos<_StateT> = std::fpos<int>, std::streamoff = long long int]
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
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]
samio.cpp:112:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
samio.cpp:145:11: warning: variable 'dp2' set but not used [-Wunused-but-set-variable]
samio.cpp:149:7: warning: unused variable 'rangecounter' [-Wunused-variable]
samio.cpp:153:7: warning: unused variable 'currentreadlen' [-Wunused-variable]
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -c samples.cpp -o samples.o
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
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]
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]
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]
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:1285:0:
./Rinterface.h: At global scope:
./Rinterface.h:53:12: warning: 'R_DirtyImage' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
In file included from spams.h:6:0,
                 from spams.cpp:1273:
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.h:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3693:16: warning: enumeration value 'SQUARE_MISSING' not handled in switch [-Wswitch]
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.h:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3720:19: warning: enumeration value 'MULTILOG' not handled in switch [-Wswitch]
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.h:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3752:19: warning: enumeration value 'SQUARE' not handled in switch [-Wswitch]
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.h:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3772:16: warning: enumeration value 'MULTILOG' not handled in switch [-Wswitch]
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.h:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3788:30: warning: unused variable 'duality' [-Wunused-variable]
spams/prox/fista.h: In function 'void FISTA::SepLossPathCoding(const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, loss_flow, const GraphPathStruct<T>*, SpMatrix<T>*) [with T = double]':
spams.h:1065:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3963:13: warning: enumeration value 'FLOW_LINEAR' not handled in switch [-Wswitch]
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 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:3692:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3396:10: warning: enumeration value 'L0' not handled in switch [-Wswitch]
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 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:3719:19:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3426:10: warning: enumeration value 'L1L2' not handled in switch [-Wswitch]
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 function '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:3735:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3588:24: warning: unused variable 'duality' [-Wunused-variable]
spams/prox/fista.h: In function '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:3751:19:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3477:10: warning: enumeration value 'GROUPLASSO_L2' not handled in switch [-Wswitch]
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 function '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:3757:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3635:24: warning: unused variable 'duality' [-Wunused-variable]
spams/prox/fista.h: In function '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:3796:19:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
spams/prox/fista.h: In function '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:3800:19:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
spams/prox/fista.h: In function '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:3620:16:   instantiated 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:3735:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
spams/prox/fista.h: In function '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:3624:16:   instantiated 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:3735:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
spams/prox/fista.h: In function '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:3662:16:   instantiated 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:3757:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
spams/prox/fista.h: In function '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:3666:16:   instantiated 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:3757:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
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:3991:73:   instantiated from 'T DoubleMinCostFlow<T>::check_reduced_costs() const [with T = double]'
spams/prox/project.h:3804:4:   instantiated from 'void DoubleMinCostFlow<T>::solve_min_cost(T, bool) [with T = double]'
spams/prox/project.h:4664:4:   instantiated 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:   instantiated 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:1065:3:   instantiated 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:   instantiated from here
spams/prox/project.h:3738:4: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
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:4019:81:   instantiated from 'void DoubleMinCostFlow<T>::saturate_arc(int, int) [with T = double]'
spams/prox/project.h:3859:10:   instantiated from 'void DoubleMinCostFlow<T>::refine(T) [with T = double]'
spams/prox/project.h:3817:7:   instantiated from 'void DoubleMinCostFlow<T>::solve_min_cost(T, bool) [with T = double]'
spams/prox/project.h:4664:4:   instantiated 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:   instantiated 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:1065:3:   instantiated 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:   instantiated from here
spams/prox/project.h:3761:4: 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 destructor 'FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normLINF<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1807:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'void FISTA::GroupProx<T, Reg>::prox(const Vector<T>&, Vector<T>&, T) [with T = double, Reg = FISTA::normLINF<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1814:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'T FISTA::GroupProx<T, Reg>::eval(const Vector<T>&) const [with T = double, Reg = FISTA::normLINF<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1843:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'void FISTA::GroupProx<T, Reg>::fenchel(const Vector<T>&, T&, T&) const [with T = double, Reg = FISTA::normLINF<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1870:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In destructor 'FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normL2<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1807:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'void FISTA::GroupProx<T, Reg>::prox(const Vector<T>&, Vector<T>&, T) [with T = double, Reg = FISTA::normL2<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1814:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'T FISTA::GroupProx<T, Reg>::eval(const Vector<T>&) const [with T = double, Reg = FISTA::normL2<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1843:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'void FISTA::GroupProx<T, Reg>::fenchel(const Vector<T>&, T&, T&) const [with T = double, Reg = FISTA::normL2<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1870:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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_arc(int, int) const [with T = double]':
spams/prox/project.h:3696:10:   instantiated from 'T DoubleMinCostFlow<T>::compute_cost() const [with T = double]'
spams/prox/project.h:4545:42:   instantiated from 'T DoubleGraphPath<T>::eval_conv(const T*, List<Path<Int>*>*, bool) [with T = double]'
spams/prox/fista.h:2265:104:   instantiated from 'T FISTA::GraphPathConv<T>::eval(const Vector<T>&) const [with T = double]'
spams.cpp:2725:1:   instantiated from here
spams/prox/project.h:3709:4: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
spams/prox/project.h: In member function 'T DoubleMinCostFlow<T>::check_reduced_costs() const [with T = double]':
spams/prox/project.h:3991:73: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
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 [-Wuninitialized]
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 [-Wuninitialized]
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 [-Wuninitialized]
spams/prox/project.h:3737:6: note: 'tmp' was declared here
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 [-Wuninitialized]
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:3791:16: warning: 'loss' may be used uninitialized in this function [-Wuninitialized]
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 'void DoubleMinCostFlow<T>::refine(T) [with T = double]':
spams/prox/project.h:3773:4: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
spams/prox/project.h:3760:6: note: 'tmp' was declared here
spams/prox/project.h:3750:43: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
spams/prox/project.h:3737:6: note: 'tmp' was declared here
spams/prox/project.h:3773:4: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
spams/prox/project.h:3760:6: note: 'tmp' was declared here
spams/prox/project.h:3773:4: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
spams/prox/project.h:3760:6: note: 'tmp' was declared here
spams/prox/project.h:3750:43: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
spams/prox/project.h:3737:6: note: 'tmp' was declared here
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 [-Wuninitialized]
spams/prox/project.h:3708:6: note: 'tmp' was declared here
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
structdef.cpp: In member function 'int GeneRange::sort()':
structdef.cpp:47:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
structdef.cpp:52:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -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:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lRblas -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lRlapack -lgfortran -lm -lquadmath -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to c:/biocbld/bbs-3.3-bioc/meat/flipflop.buildbin-libdir/flipflop/libs/i386
** 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

install for x64

* installing *source* package 'flipflop' ...
** libs
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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: [enabled by default]
c:\rtools33\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../include/c++/4.6.3/bits/postypes.h:194:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int, std::fpos<_StateT> = std::fpos<int>, std::streamoff = long long int]
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
gcc -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_flipflop.c -o R_init_flipflop.o
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
align.cpp: In member function 'int Align::getReadLen() const':
align.cpp:19:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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: [enabled by default]
c:\rtools33\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../include/c++/4.6.3/bits/postypes.h:194:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int, std::fpos<_StateT> = std::fpos<int>, std::streamoff = long long int]
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
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]
auxiliaryio.cpp:53:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:63:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:158:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
auxiliaryio.cpp:218:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:223:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:225:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
auxiliaryio.cpp:244:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp: In function 'void writeannotation(ReadGroup&, int)':
auxiliaryio.cpp:318:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:339:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:342:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
auxiliaryio.cpp:434:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:436:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:441:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:443:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:450:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:453:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp: In function 'int write2rangeandinstance(ReadGroup&, range_t&)':
auxiliaryio.cpp:522:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:534:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
auxiliaryio.cpp:611:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:616:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:724:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:736:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:738:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:767:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:769:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:788:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:791:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:808:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:825:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:844:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:849:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:854:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp: In function 'int readgenerangefile(std::string, GeneRange&)':
auxiliaryio.cpp:904:9: warning: unused variable 'id' [-Wunused-variable]
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
bedio.cpp:76:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:78:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:82:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:84:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
cvganalysis.cpp:25:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:33:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:44:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
cvganalysis.cpp:79:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:85:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:86:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
cvganalysis.cpp:156:12: warning: unused variable 'prevjump' [-Wunused-variable]
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
instanceio.cpp:27:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:28:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:57:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
instanceio.cpp:90:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:95:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:125:9: warning: unused variable 'currenttypeorder' [-Wunused-variable]
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]
instanceio.cpp:158:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:165:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
parseopt.cpp:29:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:63:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:65:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:94:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:96:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:102:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:104:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
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]
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]
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]
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]
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]
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]
rangeset.cpp:292:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:293:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
rangeset.cpp:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:315:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'long int RangeSet::overlapLen(RangeSet&)':
rangeset.cpp:331:8: warning: unused variable 't' [-Wunused-variable]
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
readgroup.cpp:148:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp:209:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:218:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:222:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp: In member function 'range_t ReadGroup::getRange() const':
readgroup.cpp:273:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp:292:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:347:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:349:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:357:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:385:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:396:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:410:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:408:31: warning: variable 'vr_end' set but not used [-Wunused-but-set-variable]
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]
readgroup.cpp:443:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:474:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp: In member function 'void ReadGroup::calculateRangeSet()':
readgroup.cpp:586:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
readgroup.cpp:640:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:641:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:689:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp:728:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:736:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::calculateType()':
readgroup.cpp:796:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:809:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:830:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:832:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:841:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::validSize() const':
readgroup.cpp:848:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::removeWeakSegs(float)':
readgroup.cpp:860:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:867:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:874:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:886:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::calculateValidSegs()':
readgroup.cpp:912:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:914:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:922:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:926:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:928:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:931:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:936:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp:959:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:964:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp: In member function 'int ReadGroup::getReadLen(int) const':
readgroup.cpp:983:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:984:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::toStream(std::ostream&)':
readgroup.cpp:1003:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1005:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1013:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1030:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1031:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1033:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1042:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1053:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1064:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1073:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1079:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1083:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1098:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1118:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1147:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::peSize() const':
readgroup.cpp:1219:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
readgroup.cpp:1251:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1267:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::getDirSum()':
readgroup.cpp:1276:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1278:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1273:7: warning: unused variable 'r' [-Wunused-variable]
readgroup.cpp:1274:7: warning: unused variable 'npos' [-Wunused-variable]
readgroup.cpp:1274:14: warning: unused variable 'nneg' [-Wunused-variable]
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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: [enabled by default]
c:\rtools33\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../include/c++/4.6.3/bits/postypes.h:194:7: note: candidate 1: std::fpos<_StateT> std::fpos<_StateT>::operator-(std::streamoff) const [with _StateT = int, std::fpos<_StateT> = std::fpos<int>, std::streamoff = long long int]
FileSplitter.h:52:64: note: candidate 2: operator-(std::streamoff {aka long long int}, off_t {aka long int}) <built-in>
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]
samio.cpp:112:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
samio.cpp:145:11: warning: variable 'dp2' set but not used [-Wunused-but-set-variable]
samio.cpp:149:7: warning: unused variable 'rangecounter' [-Wunused-variable]
samio.cpp:153:7: warning: unused variable 'currentreadlen' [-Wunused-variable]
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -c samples.cpp -o samples.o
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
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]
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]
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]
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:1285:0:
./Rinterface.h: At global scope:
./Rinterface.h:53:12: warning: 'R_DirtyImage' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
In file included from spams.h:6:0,
                 from spams.cpp:1273:
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.h:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3693:16: warning: enumeration value 'SQUARE_MISSING' not handled in switch [-Wswitch]
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.h:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3720:19: warning: enumeration value 'MULTILOG' not handled in switch [-Wswitch]
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.h:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3752:19: warning: enumeration value 'SQUARE' not handled in switch [-Wswitch]
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.h:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3772:16: warning: enumeration value 'MULTILOG' not handled in switch [-Wswitch]
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.h:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3788:30: warning: unused variable 'duality' [-Wunused-variable]
spams/prox/fista.h: In function 'void FISTA::SepLossPathCoding(const Matrix<T>&, Matrix<T>&, const FISTA::ParamFISTA<T>&, loss_flow, const GraphPathStruct<T>*, SpMatrix<T>*) [with T = double]':
spams.h:1065:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3963:13: warning: enumeration value 'FLOW_LINEAR' not handled in switch [-Wswitch]
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 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:3692:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3396:10: warning: enumeration value 'L0' not handled in switch [-Wswitch]
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 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:3719:19:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3426:10: warning: enumeration value 'L1L2' not handled in switch [-Wswitch]
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 function '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:3735:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3588:24: warning: unused variable 'duality' [-Wunused-variable]
spams/prox/fista.h: In function '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:3751:19:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3477:10: warning: enumeration value 'GROUPLASSO_L2' not handled in switch [-Wswitch]
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 function '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:3757:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3635:24: warning: unused variable 'duality' [-Wunused-variable]
spams/prox/fista.h: In function '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:3796:19:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
spams/prox/fista.h: In function '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:3800:19:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
spams/prox/fista.h: In function '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:3620:16:   instantiated 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:3735:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
spams/prox/fista.h: In function '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:3624:16:   instantiated 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:3735:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
spams/prox/fista.h: In function '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:3662:16:   instantiated 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:3757:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:2956:12: warning: unused variable 'sec' [-Wunused-variable]
spams/prox/fista.h: In function '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:3666:16:   instantiated 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:3757:16:   instantiated 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:480:3:   instantiated 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:   instantiated from here
spams/prox/fista.h:3044:12: warning: unused variable 'sec' [-Wunused-variable]
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:3991:73:   instantiated from 'T DoubleMinCostFlow<T>::check_reduced_costs() const [with T = double]'
spams/prox/project.h:3804:4:   instantiated from 'void DoubleMinCostFlow<T>::solve_min_cost(T, bool) [with T = double]'
spams/prox/project.h:4664:4:   instantiated 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:   instantiated 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:1065:3:   instantiated 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:   instantiated from here
spams/prox/project.h:3738:4: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
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:4019:81:   instantiated from 'void DoubleMinCostFlow<T>::saturate_arc(int, int) [with T = double]'
spams/prox/project.h:3859:10:   instantiated from 'void DoubleMinCostFlow<T>::refine(T) [with T = double]'
spams/prox/project.h:3817:7:   instantiated from 'void DoubleMinCostFlow<T>::solve_min_cost(T, bool) [with T = double]'
spams/prox/project.h:4664:4:   instantiated 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:   instantiated 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:1065:3:   instantiated 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:   instantiated from here
spams/prox/project.h:3761:4: 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 destructor 'FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normLINF<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1807:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'void FISTA::GroupProx<T, Reg>::prox(const Vector<T>&, Vector<T>&, T) [with T = double, Reg = FISTA::normLINF<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1814:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'T FISTA::GroupProx<T, Reg>::eval(const Vector<T>&) const [with T = double, Reg = FISTA::normLINF<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1843:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'void FISTA::GroupProx<T, Reg>::fenchel(const Vector<T>&, T&, T&) const [with T = double, Reg = FISTA::normLINF<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1870:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In destructor 'FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normL2<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1807:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'void FISTA::GroupProx<T, Reg>::prox(const Vector<T>&, Vector<T>&, T) [with T = double, Reg = FISTA::normL2<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1814:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'T FISTA::GroupProx<T, Reg>::eval(const Vector<T>&) const [with T = double, Reg = FISTA::normL2<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1843:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'void FISTA::GroupProx<T, Reg>::fenchel(const Vector<T>&, T&, T&) const [with T = double, Reg = FISTA::normL2<double>]':
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1870:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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_arc(int, int) const [with T = double]':
spams/prox/project.h:3696:10:   instantiated from 'T DoubleMinCostFlow<T>::compute_cost() const [with T = double]'
spams/prox/project.h:4545:42:   instantiated from 'T DoubleGraphPath<T>::eval_conv(const T*, List<Path<Int>*>*, bool) [with T = double]'
spams/prox/fista.h:2265:104:   instantiated from 'T FISTA::GraphPathConv<T>::eval(const Vector<T>&) const [with T = double]'
spams.cpp:2725:1:   instantiated from here
spams/prox/project.h:3709:4: warning: enumeration value 'INCORRECT_LOSS_FLOW' not handled in switch [-Wswitch]
spams/prox/project.h: In member function 'T DoubleMinCostFlow<T>::check_reduced_costs() const [with T = double]':
spams/prox/project.h:3991:73: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
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 [-Wuninitialized]
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 '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 [-Wuninitialized]
spams/prox/project.h:3737:6: note: 'tmp' was declared here
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 [-Wuninitialized]
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:3791:16: warning: 'loss' may be used uninitialized in this function [-Wuninitialized]
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 'void DoubleMinCostFlow<T>::price_update(T) [with T = double]':
spams/prox/project.h:3750:43: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
spams/prox/project.h:3737:6: note: 'tmp' was declared here
spams/prox/project.h: In member function 'void DoubleMinCostFlow<T>::refine(T) [with T = double]':
spams/prox/project.h:3773:4: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
spams/prox/project.h:3760:6: note: 'tmp' was declared here
spams/prox/project.h:3750:43: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
spams/prox/project.h:3737:6: note: 'tmp' was declared here
spams/prox/project.h:3773:4: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
spams/prox/project.h:3760:6: note: 'tmp' was declared here
spams/prox/project.h:3773:4: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
spams/prox/project.h:3760:6: note: 'tmp' was declared here
spams/prox/project.h:3750:43: warning: 'tmp' may be used uninitialized in this function [-Wuninitialized]
spams/prox/project.h:3737:6: note: 'tmp' was declared here
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 [-Wuninitialized]
spams/prox/project.h:3708:6: note: 'tmp' was declared here
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG   -O2 -Wall  -mtune=core2 -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]
readgroup.h:24:18: warning:   'const Samples* ReadGroup::samples' [-Wreorder]
readgroup.h:119:3: warning:   when initialized here [-Wreorder]
readgroup.h: In member function 'bool ReadGroup::hasPairEnd()':
readgroup.h:156:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
structdef.cpp: In member function 'int GeneRange::sort()':
structdef.cpp:47:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
structdef.cpp:52:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -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:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lRblas -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lRlapack -lgfortran -lm -lquadmath -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to c:/biocbld/bbs-3.3-bioc/meat/flipflop.buildbin-libdir/flipflop/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flipflop' as flipflop_1.9.0.zip
* DONE (flipflop)

name	user	system	elapsed
flipflop	0.27	0.04	0.30

name	user	system	elapsed
flipflop	0.34	0.00	0.35