BioC 3.1: CHECK report for flipflop on petty

Package: flipflop

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flipflop_1.6.1.tar.gz

StartedAt: 2015-10-08 22:57:10 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:00:53 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 222.6 seconds

RetCode: 0

Status:  OK

CheckDir: flipflop.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flipflop_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/flipflop.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flipflop/DESCRIPTION’ ... OK
* this is package ‘flipflop’ version ‘1.6.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flipflop’ can be installed ... [63s/65s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/flipflop.Rcheck/00check.log’
for details.

* installing *source* package ‘flipflop’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c FileSplitter.cpp -o FileSplitter.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_flipflop.c -o R_init_flipflop.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c align.cpp -o align.o
align.cpp: In function ‘std::ostream& operator<<(std::ostream&, Align&)’:
align.cpp:11: warning: comparison between signed and unsigned integer expressions
align.cpp: In member function ‘int Align::getReadLen() const’:
align.cpp:19: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c auxiliaryio.cpp -o auxiliaryio.o
In file included from structdef.h:11,
                 from auxiliaryio.h:11,
                 from auxiliaryio.cpp:6:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108: warning: ‘ReadGroup::orientation’ will be initialized after
readgroup.h:24: warning:   ‘const Samples* ReadGroup::samples’
readgroup.h:119: warning:   when initialized here
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156: warning: comparison between signed and unsigned integer expressions
In file included from auxiliaryio.h:11,
                 from auxiliaryio.cpp:6:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘void prepareAuxFile(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::string, bool&)’:
auxiliaryio.cpp:52: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:53: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:63: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:158: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘void write2os(std::ostream&, std::string, int, std::vector<long int, std::allocator<long int> >&, std::vector<long int, std::allocator<long int> >&, bool)’:
auxiliaryio.cpp:216: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:218: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:223: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:225: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘void writeBound(std::ostream&, std::string, std::vector<long int, std::allocator<long int> >&, std::vector<long int, std::allocator<long int> >&)’:
auxiliaryio.cpp:240: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:244: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘void writeannotation(ReadGroup&, int)’:
auxiliaryio.cpp:318: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:339: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:342: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘void writeboundfs(range_t, int, std::string, std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&, int, int)’:
auxiliaryio.cpp:410: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:434: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:436: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:441: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:443: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:450: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:453: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘int write2rangeandinstance(ReadGroup&, range_t&)’:
auxiliaryio.cpp:522: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:534: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘void write2Instance(range_t&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, int, int, std::string, int, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, bool, bool)’:
auxiliaryio.cpp:609: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:611: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:616: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:724: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:736: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:738: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:767: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:769: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:788: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:791: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:808: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:825: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:844: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:849: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:854: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘int readgenerangefile(std::string, GeneRange&)’:
auxiliaryio.cpp:904: warning: unused variable ‘id’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c bedio.cpp -o bedio.o
bedio.cpp: In function ‘int writeBed(std::ostream&, bedrec)’:
bedio.cpp:61: warning: comparison between signed and unsigned integer expressions
bedio.cpp:76: warning: comparison between signed and unsigned integer expressions
bedio.cpp:78: warning: comparison between signed and unsigned integer expressions
bedio.cpp:82: warning: comparison between signed and unsigned integer expressions
bedio.cpp:84: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c common.cpp -o common.o
In file included from structdef.h:11,
                 from common.cpp:5:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108: warning: ‘ReadGroup::orientation’ will be initialized after
readgroup.h:24: warning:   ‘const Samples* ReadGroup::samples’
readgroup.h:119: warning:   when initialized here
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156: warning: comparison between signed and unsigned integer expressions
In file included from common.cpp:5:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c cvganalysis.cpp -o cvganalysis.o
In file included from structdef.h:11,
                 from cvganalysis.h:9,
                 from cvganalysis.cpp:2:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108: warning: ‘ReadGroup::orientation’ will be initialized after
readgroup.h:24: warning:   ‘const Samples* ReadGroup::samples’
readgroup.h:119: warning:   when initialized here
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156: warning: comparison between signed and unsigned integer expressions
In file included from cvganalysis.h:9,
                 from cvganalysis.cpp:2:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp: In function ‘void getconnectedcoverage(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, int)’:
cvganalysis.cpp:20: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:25: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:33: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:44: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp: In function ‘void getcoverage(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&)’:
cvganalysis.cpp:78: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:79: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:85: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:86: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp: In function ‘int cutcvg(const std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&, int, int)’:
cvganalysis.cpp:157: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:156: warning: unused variable ‘prevjump’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c ffProcesssam.cpp -o ffProcesssam.o
In file included from structdef.h:11,
                 from samio.h:10,
                 from ffProcesssam.cpp:3:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108: warning: ‘ReadGroup::orientation’ will be initialized after
readgroup.h:24: warning:   ‘const Samples* ReadGroup::samples’
readgroup.h:119: warning:   when initialized here
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156: warning: comparison between signed and unsigned integer expressions
In file included from samio.h:10,
                 from ffProcesssam.cpp:3:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c instanceio.cpp -o instanceio.o
In file included from structdef.h:11,
                 from instanceio.h:7,
                 from instanceio.cpp:2:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108: warning: ‘ReadGroup::orientation’ will be initialized after
readgroup.h:24: warning:   ‘const Samples* ReadGroup::samples’
readgroup.h:119: warning:   when initialized here
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156: warning: comparison between signed and unsigned integer expressions
In file included from instanceio.h:7,
                 from instanceio.cpp:2:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
instanceio.cpp: In function ‘void getallbound(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, range_t, vpos_t&, vpos_t&, std::map<long int, std::vector<double, std::allocator<double> >, std::less<long int>, std::allocator<std::pair<const long int, std::vector<double, std::allocator<double> > > > >&, bool)’:
instanceio.cpp:25: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:27: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:28: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:57: warning: comparison between signed and unsigned integer expressions
instanceio.cpp: In function ‘void getalltypeorders(std::map<std::vector<int, std::allocator<int> >, int, std::less<std::vector<int, std::allocator<int> > >, std::allocator<std::pair<const std::vector<int, std::allocator<int> >, int> > >&, std::map<std::vector<int, std::allocator<int> >, int, std::less<std::vector<int, std::allocator<int> > >, std::allocator<std::pair<const std::vector<int, std::allocator<int> >, int> > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<int, std::allocator<int> >&, std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&)’:
instanceio.cpp:87: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:90: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:95: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:125: warning: unused variable ‘currenttypeorder’
instanceio.cpp: In function ‘void removeoutofrangereads(range_t&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, int)’:
instanceio.cpp:151: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:158: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:165: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c parseopt.cpp -o parseopt.o
In file included from structdef.h:11,
                 from parseopt.h:9,
                 from parseopt.cpp:1:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108: warning: ‘ReadGroup::orientation’ will be initialized after
readgroup.h:24: warning:   ‘const Samples* ReadGroup::samples’
readgroup.h:119: warning:   when initialized here
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156: warning: comparison between signed and unsigned integer expressions
In file included from parseopt.h:9,
                 from parseopt.cpp:1:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
parseopt.cpp: In function ‘int parseopt(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >)’:
parseopt.cpp:13: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:29: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:63: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:65: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:94: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:96: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:102: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:104: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c rangeset.cpp -o rangeset.o
rangeset.cpp: In function ‘std::ostream& operator<<(std::ostream&, const RangeSet&)’:
rangeset.cpp:15: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘int RangeSet::add(const std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&)’:
rangeset.cpp:49: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘int RangeSet::add(pos_t&, pos_t&)’:
rangeset.cpp:56: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘bool RangeSet::isOverlap(pos_t&, pos_t&)’:
rangeset.cpp:137: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘long int RangeSet::minDist(pos_t&, pos_t&)’:
rangeset.cpp:144: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(pos_t&, pos_t&)’:
rangeset.cpp:291: warning: comparison between signed and unsigned integer expressions
rangeset.cpp:292: warning: comparison between signed and unsigned integer expressions
rangeset.cpp:293: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(const std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&)’:
rangeset.cpp:313: warning: comparison between signed and unsigned integer expressions
rangeset.cpp:314: warning: comparison between signed and unsigned integer expressions
rangeset.cpp:315: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(RangeSet&)’:
rangeset.cpp:331: warning: unused variable ‘t’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c readgroup.cpp -o readgroup.o
In file included from readgroup.cpp:3:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108: warning: ‘ReadGroup::orientation’ will be initialized after
readgroup.h:24: warning:   ‘const Samples* ReadGroup::samples’
readgroup.h:119: warning:   when initialized here
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156: warning: comparison between signed and unsigned integer expressions
In file included from cvganalysis.h:9,
                 from readgroup.cpp:5:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::getConnectedCoverage(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&)’:
readgroup.cpp:135: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:148: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::getCoverage(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, const range_t&)’:
readgroup.cpp:205: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:209: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:218: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:222: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::getPointCoverage(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&)’:
readgroup.cpp:258: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘range_t ReadGroup::getRange() const’:
readgroup.cpp:273: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::splitByRangeSet(std::vector<ReadGroup, std::allocator<ReadGroup> >&, long int)’:
readgroup.cpp:288: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:292: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:347: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:349: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:357: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:385: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:396: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:410: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::splitByRangeSet(std::vector<ReadGroup, std::allocator<ReadGroup> >&, std::vector<RangeSet, std::allocator<RangeSet> >&)’:
readgroup.cpp:437: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:443: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:474: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::splitByDirection(std::vector<ReadGroup, std::allocator<ReadGroup> >&, std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&)’:
readgroup.cpp:496: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::calculateRangeSet()’:
readgroup.cpp:586: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::setupBound(std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&)’:
readgroup.cpp:595: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::calculateBound(bool, int, int)’:
readgroup.cpp:637: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:640: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:641: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:689: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘type_t ReadGroup::getType(const pos_t&, const pos_t&) const’:
readgroup.cpp:727: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:728: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:736: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::calculateType()’:
readgroup.cpp:796: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:809: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:830: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:832: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:841: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘int ReadGroup::validSize() const’:
readgroup.cpp:848: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::removeWeakSegs(float)’:
readgroup.cpp:860: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:867: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:874: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:886: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::calculateValidSegs()’:
readgroup.cpp:912: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:914: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:922: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:926: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:928: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:931: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:936: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘std::vector<int, std::allocator<int> > ReadGroup::getReadsContainingSegs(int)’:
readgroup.cpp:958: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:959: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:964: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > > ReadGroup::getSegs() const’:
readgroup.cpp:976: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘int ReadGroup::getReadLen(int) const’:
readgroup.cpp:983: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:984: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::toStream(std::ostream&)’:
readgroup.cpp:1003: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1005: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1013: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1030: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1031: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1033: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1042: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1053: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1064: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1073: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1079: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1083: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1098: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1118: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1147: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘int ReadGroup::peSize() const’:
readgroup.cpp:1219: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::removeTooLongReads(long int, int)’:
readgroup.cpp:1249: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1251: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1267: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘int ReadGroup::getDirSum()’:
readgroup.cpp:1276: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1278: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1273: warning: unused variable ‘r’
readgroup.cpp:1274: warning: unused variable ‘npos’
readgroup.cpp:1274: warning: unused variable ‘nneg’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c samio.cpp -o samio.o
In file included from structdef.h:11,
                 from samio.h:10,
                 from samio.cpp:12:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108: warning: ‘ReadGroup::orientation’ will be initialized after
readgroup.h:24: warning:   ‘const Samples* ReadGroup::samples’
readgroup.h:119: warning:   when initialized here
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156: warning: comparison between signed and unsigned integer expressions
In file included from samio.h:10,
                 from samio.cpp:12:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
samio.cpp: In function ‘int readSamFile(std::string, std::string, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >)’:
samio.cpp:111: warning: comparison between signed and unsigned integer expressions
samio.cpp:112: warning: comparison between signed and unsigned integer expressions
samio.cpp:149: warning: unused variable ‘rangecounter’
samio.cpp:153: warning: unused variable ‘currentreadlen’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c samples.cpp -o samples.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c spams.cpp -o spams.o
In file included from spams/dags/dag.h:23,
                 from spams.h:4,
                 from spams.cpp:1273:
spams/linalg/linalg.h:1070: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:1234: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2366: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:2537: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:2580: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2589: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2621: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2630: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2709: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2722: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2890: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:4106: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:4249: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:4566: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4615: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4651: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4687: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4720: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4756: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4894: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:5013: warning: ignoring #pragma omp critical
In file included from spams/prox/fista.h:25,
                 from spams.h:6,
                 from spams.cpp:1273:
spams/decomp/decomp.h:337: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:426: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:699: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:1155: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:1255: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:1327: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:1406: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:1509: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:2019: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:2228: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:2546: warning: ignoring #pragma omp parallel
In file included from spams.h:6,
                 from spams.cpp:1273:
spams/prox/fista.h:2373: warning: ignoring #pragma omp parallel
spams/prox/fista.h:2381: warning: ignoring #pragma omp parallel
spams/prox/fista.h:2416: warning: ignoring #pragma omp parallel
spams/prox/fista.h:2424: warning: ignoring #pragma omp critical
spams/prox/fista.h:3554: warning: ignoring #pragma omp parallel
spams/prox/fista.h:3602: warning: ignoring #pragma omp parallel
spams/prox/fista.h:3643: warning: ignoring #pragma omp parallel
spams/prox/fista.h:3840: warning: ignoring #pragma omp parallel
spams/prox/fista.h:3898: warning: ignoring #pragma omp parallel
spams/prox/fista.h:3972: warning: ignoring #pragma omp parallel
In file included from spams/prox/fista.h:24,
                 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: warning: enumeration value ‘FLOW_LINEAR’ not handled in switch
spams/prox/project.h:3450: warning: enumeration value ‘FLOW_SQUARE’ not handled in switch
spams/prox/project.h:3450: warning: enumeration value ‘FLOW_SQUARE_POS’ not handled in switch
spams/prox/project.h:3450: warning: enumeration value ‘FLOW_SQUARE_WEIGHTS’ not handled in switch
spams/prox/project.h:3450: warning: enumeration value ‘FLOW_SQUARE_POS_WEIGHTS’ not handled in switch
spams/prox/project.h:3450: warning: enumeration value ‘FLOW_POISSON’ not handled in switch
spams/prox/project.h:3450: warning: enumeration value ‘FLOW_POISSON_POS’ not handled in switch
spams/prox/project.h:3450: warning: enumeration value ‘FLOW_POISSON_WEIGHTS’ not handled in switch
spams/prox/project.h:3450: warning: enumeration value ‘FLOW_POISSON_WEIGHTS_POS’ not handled in switch
spams/prox/project.h:3450: warning: enumeration value ‘INCORRECT_LOSS_FLOW’ not handled in switch
In file included from spams.h:6,
                 from spams.cpp:1273:
spams/prox/fista.h: In function ‘void FISTA::print_loss(const FISTA::loss_t&)’:
spams/prox/fista.h:83: warning: enumeration value ‘SQUARE’ not handled in switch
spams/prox/fista.h:83: warning: enumeration value ‘SQUARE_MISSING’ not handled in switch
spams/prox/fista.h:83: warning: enumeration value ‘LOG’ not handled in switch
spams/prox/fista.h:83: warning: enumeration value ‘LOGWEIGHT’ not handled in switch
spams/prox/fista.h:83: warning: enumeration value ‘MULTILOG’ not handled in switch
spams/prox/fista.h:83: warning: enumeration value ‘CUR’ not handled in switch
spams/prox/fista.h:83: warning: enumeration value ‘HINGE’ not handled in switch
spams/prox/fista.h:83: warning: enumeration value ‘POISSON’ not handled in switch
spams/prox/fista.h:83: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch
spams/prox/fista.h: In function ‘void FISTA::print_regul(const FISTA::regul_t&)’:
spams/prox/fista.h:101: warning: enumeration value ‘L0’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘L1’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘RIDGE’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘L2’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘LINF’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘L1CONSTRAINT’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘ELASTICNET’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘FUSEDLASSO’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘GROUPLASSO_L2’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘GROUPLASSO_LINF’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘GROUPLASSO_L2_L1’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘GROUPLASSO_LINF_L1’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘L1L2’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘L1LINF’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘L1L2_L1’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘L1LINF_L1’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘TREE_L0’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘TREE_L2’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘TREE_LINF’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘GRAPH’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘GRAPH_RIDGE’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘GRAPH_L2’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘TREEMULT’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘GRAPHMULT’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘L1LINFCR’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘NONE’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘TRACE_NORM’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘TRACE_NORM_VEC’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘RANK’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘RANK_VEC’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘INCORRECT_REG’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘GRAPH_PATH_L0’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘GRAPH_PATH_CONV’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘GRAPH_PATH_CONV2’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘LOG_DC’ not handled in switch
spams/prox/fista.h:101: warning: enumeration value ‘NA’ not handled in switch
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:   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:   instantiated from here
spams/prox/fista.h:3693: warning: enumeration value ‘SQUARE_MISSING’ not handled in switch
spams/prox/fista.h:3693: warning: enumeration value ‘LOG’ not handled in switch
spams/prox/fista.h:3693: warning: enumeration value ‘LOGWEIGHT’ not handled in switch
spams/prox/fista.h:3693: warning: enumeration value ‘MULTILOG’ not handled in switch
spams/prox/fista.h:3693: warning: enumeration value ‘CUR’ not handled in switch
spams/prox/fista.h:3693: warning: enumeration value ‘POISSON’ not handled in switch
spams/prox/fista.h:3693: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch
spams.h:480:   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:   instantiated from here
spams/prox/fista.h:3720: warning: enumeration value ‘MULTILOG’ not handled in switch
spams/prox/fista.h:3720: warning: enumeration value ‘CUR’ not handled in switch
spams/prox/fista.h:3720: warning: enumeration value ‘HINGE’ not handled in switch
spams/prox/fista.h:3720: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch
spams.h:480:   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:   instantiated from here
spams/prox/fista.h:3752: warning: enumeration value ‘SQUARE’ not handled in switch
spams/prox/fista.h:3752: warning: enumeration value ‘SQUARE_MISSING’ not handled in switch
spams/prox/fista.h:3752: warning: enumeration value ‘LOG’ not handled in switch
spams/prox/fista.h:3752: warning: enumeration value ‘LOGWEIGHT’ not handled in switch
spams/prox/fista.h:3752: warning: enumeration value ‘CUR’ not handled in switch
spams/prox/fista.h:3752: warning: enumeration value ‘HINGE’ not handled in switch
spams/prox/fista.h:3752: warning: enumeration value ‘POISSON’ not handled in switch
spams/prox/fista.h:3752: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch
spams.h:480:   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:   instantiated from here
spams/prox/fista.h:3772: warning: enumeration value ‘MULTILOG’ not handled in switch
spams/prox/fista.h:3772: warning: enumeration value ‘HINGE’ not handled in switch
spams/prox/fista.h:3772: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch
spams.h:480:   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:   instantiated from here
spams/prox/fista.h:3788: warning: unused variable ‘duality’
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:   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:   instantiated from here
spams/prox/fista.h:3963: warning: enumeration value ‘FLOW_LINEAR’ not handled in switch
spams/prox/fista.h:3963: warning: enumeration value ‘FLOW_SQUARE_POS’ not handled in switch
spams/prox/fista.h:3963: warning: enumeration value ‘FLOW_SQUARE_POS_WEIGHTS’ not handled in switch
spams/prox/fista.h:3963: warning: enumeration value ‘FLOW_POISSON_POS’ not handled in switch
spams/prox/fista.h:3963: warning: enumeration value ‘FLOW_POISSON_WEIGHTS_POS’ not handled in switch
spams/prox/fista.h:3963: warning: enumeration value ‘INCORRECT_LOSS_FLOW’ not handled in switch
spams/prox/fista.h: In function ‘FISTA::SplittingFunction<T, SpMatrix<T>, Vector<T>, Vector<T> >* FISTA::setRegularizerADMM(const FISTA::ParamFISTA<T>&, const GraphStruct<T>*, const TreeStruct<T>*) [with T = double]’:
spams/prox/fista.h:3692:   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:   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:   instantiated from here
spams/prox/fista.h:3396: warning: enumeration value ‘L0’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘L1’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘RIDGE’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘L2’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘LINF’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘L1CONSTRAINT’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘ELASTICNET’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘FUSEDLASSO’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘GROUPLASSO_L2’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘GROUPLASSO_LINF’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘GROUPLASSO_L2_L1’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘GROUPLASSO_LINF_L1’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘L1L2’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘L1LINF’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘L1L2_L1’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘L1LINF_L1’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘TREE_L0’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘TREE_L2’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘TREE_LINF’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘GRAPH_RIDGE’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘TREEMULT’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘GRAPHMULT’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘L1LINFCR’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘TRACE_NORM’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘TRACE_NORM_VEC’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘RANK’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘RANK_VEC’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘INCORRECT_REG’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘GRAPH_PATH_L0’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘GRAPH_PATH_CONV’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘GRAPH_PATH_CONV2’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘LOG_DC’ not handled in switch
spams/prox/fista.h:3396: warning: enumeration value ‘NA’ not handled in switch
spams/prox/fista.h: In function ‘FISTA::Regularizer<T, Vector<T> >* FISTA::setRegularizerVectors(const FISTA::ParamFISTA<T>&, const GraphStruct<T>*, const TreeStruct<T>*, const GraphPathStruct<T>*) [with T = double]’:
spams/prox/fista.h:3719:   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:   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:   instantiated from here
spams/prox/fista.h:3426: warning: enumeration value ‘L1L2’ not handled in switch
spams/prox/fista.h:3426: warning: enumeration value ‘L1LINF’ not handled in switch
spams/prox/fista.h:3426: warning: enumeration value ‘L1L2_L1’ not handled in switch
spams/prox/fista.h:3426: warning: enumeration value ‘L1LINF_L1’ not handled in switch
spams/prox/fista.h:3426: warning: enumeration value ‘TREEMULT’ not handled in switch
spams/prox/fista.h:3426: warning: enumeration value ‘GRAPHMULT’ not handled in switch
spams/prox/fista.h:3426: warning: enumeration value ‘L1LINFCR’ not handled in switch
spams/prox/fista.h:3426: warning: enumeration value ‘TRACE_NORM’ not handled in switch
spams/prox/fista.h:3426: warning: enumeration value ‘RANK’ not handled in switch
spams/prox/fista.h:3426: warning: enumeration value ‘INCORRECT_REG’ not handled in switch
spams/prox/fista.h:3426: warning: enumeration value ‘NA’ not handled in switch
spams/prox/fista.h: In function ‘void FISTA::solver_aux1(const Matrix<T>&, const Matrix<T>&, Matrix<T>&, Matrix<T>&, FISTA::Regularizer<T, Vector<T> >**, FISTA::Loss<T, Vector<T>, Vector<T> >**, const FISTA::ParamFISTA<T>&) [with T = double]’:
spams/prox/fista.h:3735:   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:   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:   instantiated from here
spams/prox/fista.h:3588: warning: unused variable ‘duality’
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:   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:   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:   instantiated from here
spams/prox/fista.h:3477: warning: enumeration value ‘GROUPLASSO_L2’ not handled in switch
spams/prox/fista.h:3477: warning: enumeration value ‘GROUPLASSO_LINF’ not handled in switch
spams/prox/fista.h:3477: warning: enumeration value ‘GROUPLASSO_L2_L1’ not handled in switch
spams/prox/fista.h:3477: warning: enumeration value ‘GROUPLASSO_LINF_L1’ not handled in switch
spams/prox/fista.h:3477: warning: enumeration value ‘GRAPH_RIDGE’ not handled in switch
spams/prox/fista.h:3477: warning: enumeration value ‘GRAPH_L2’ not handled in switch
spams/prox/fista.h:3477: warning: enumeration value ‘TRACE_NORM_VEC’ not handled in switch
spams/prox/fista.h:3477: warning: enumeration value ‘RANK_VEC’ not handled in switch
spams/prox/fista.h:3477: warning: enumeration value ‘INCORRECT_REG’ not handled in switch
spams/prox/fista.h:3477: warning: enumeration value ‘LOG_DC’ not handled in switch
spams/prox/fista.h:3477: warning: enumeration value ‘NA’ not handled in switch
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>, Vector<T> >**, const FISTA::ParamFISTA<T>&) [with T = double]’:
spams/prox/fista.h:3757:   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:   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:   instantiated from here
spams/prox/fista.h:3635: warning: unused variable ‘duality’
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:   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:   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:   instantiated from here
spams/prox/fista.h:2956: warning: unused variable ‘sec’
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:   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:   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:   instantiated from here
spams/prox/fista.h:3044: warning: unused variable ‘sec’
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:   instantiated from ‘void FISTA::solver_aux1(const Matrix<T>&, const Matrix<T>&, Matrix<T>&, Matrix<T>&, FISTA::Regularizer<T, Vector<T> >**, FISTA::Loss<T, Vector<T>, Vector<T> >**, const FISTA::ParamFISTA<T>&) [with T = double]’
spams/prox/fista.h:3735:   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:   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:   instantiated from here
spams/prox/fista.h:2956: warning: unused variable ‘sec’
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:   instantiated from ‘void FISTA::solver_aux1(const Matrix<T>&, const Matrix<T>&, Matrix<T>&, Matrix<T>&, FISTA::Regularizer<T, Vector<T> >**, FISTA::Loss<T, Vector<T>, Vector<T> >**, const FISTA::ParamFISTA<T>&) [with T = double]’
spams/prox/fista.h:3735:   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:   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:   instantiated from here
spams/prox/fista.h:3044: warning: unused variable ‘sec’
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:   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>, Vector<T> >**, const FISTA::ParamFISTA<T>&) [with T = double]’
spams/prox/fista.h:3757:   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:   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:   instantiated from here
spams/prox/fista.h:2956: warning: unused variable ‘sec’
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:   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>, Vector<T> >**, const FISTA::ParamFISTA<T>&) [with T = double]’
spams/prox/fista.h:3757:   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:   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:   instantiated from here
spams/prox/fista.h:3044: warning: unused variable ‘sec’
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:   instantiated from ‘T DoubleMinCostFlow<T>::check_reduced_costs() const [with T = double]’
spams/prox/project.h:3804:   instantiated from ‘void DoubleMinCostFlow<T>::solve_min_cost(T, bool) [with T = double]’
spams/prox/project.h:4664:   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:   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:   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:   instantiated from here
spams/prox/project.h:3738: warning: enumeration value ‘INCORRECT_LOSS_FLOW’ not handled in switch
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:   instantiated from ‘void DoubleMinCostFlow<T>::saturate_arc(int, int) [with T = double]’
spams/prox/project.h:3859:   instantiated from ‘void DoubleMinCostFlow<T>::refine(T) [with T = double]’
spams/prox/project.h:3817:   instantiated from ‘void DoubleMinCostFlow<T>::solve_min_cost(T, bool) [with T = double]’
spams/prox/project.h:4664:   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:   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:   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:   instantiated from here
spams/prox/project.h:3761: warning: enumeration value ‘INCORRECT_LOSS_FLOW’ not handled in switch
spams/prox/fista.h: In destructor ‘FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normLINF<double>]’:
spams.cpp:2724:   instantiated from here
spams/prox/fista.h:1807: warning: comparison between signed and unsigned integer expressions
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:2724:   instantiated from here
spams/prox/fista.h:1814: warning: comparison between signed and unsigned integer expressions
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:2724:   instantiated from here
spams/prox/fista.h:1843: warning: comparison between signed and unsigned integer expressions
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:2724:   instantiated from here
spams/prox/fista.h:1870: warning: comparison between signed and unsigned integer expressions
spams/prox/fista.h: In destructor ‘FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normL2<double>]’:
spams.cpp:2724:   instantiated from here
spams/prox/fista.h:1807: warning: comparison between signed and unsigned integer expressions
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:2724:   instantiated from here
spams/prox/fista.h:1814: warning: comparison between signed and unsigned integer expressions
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:2724:   instantiated from here
spams/prox/fista.h:1843: warning: comparison between signed and unsigned integer expressions
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:2724:   instantiated from here
spams/prox/fista.h:1870: warning: comparison between signed and unsigned integer expressions
spams/prox/project.h: In member function ‘T DoubleMinCostFlow<T>::eval_flow_arc(int, int) const [with T = double]’:
spams/prox/project.h:3696:   instantiated from ‘T DoubleMinCostFlow<T>::compute_cost() const [with T = double]’
spams/prox/project.h:4545:   instantiated from ‘T DoubleGraphPath<T>::eval_conv(const T*, List<Path<Int>*>*, bool) [with T = double]’
spams/prox/fista.h:2265:   instantiated from ‘T FISTA::GraphPathConv<T>::eval(const Vector<T>&) const [with T = double]’
spams.cpp:2724:   instantiated from here
spams/prox/project.h:3709: warning: enumeration value ‘INCORRECT_LOSS_FLOW’ not handled in switch
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -fPIC  -mtune=core2 -g -O2 -Wall  -c structdef.cpp -o structdef.o
In file included from structdef.h:11,
                 from structdef.cpp:6:
readgroup.h: In constructor ‘ReadGroup::ReadGroup()’:
readgroup.h:108: warning: ‘ReadGroup::orientation’ will be initialized after
readgroup.h:24: warning:   ‘const Samples* ReadGroup::samples’
readgroup.h:119: warning:   when initialized here
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:156: warning: comparison between signed and unsigned integer expressions
In file included from structdef.cpp:6:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
structdef.cpp: In member function ‘int GeneRange::sort()’:
structdef.cpp:47: warning: comparison between signed and unsigned integer expressions
structdef.cpp:52: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o flipflop.so FileSplitter.o R_init_flipflop.o align.o auxiliaryio.o bedio.o common.o cvganalysis.o ffProcesssam.o instanceio.o parseopt.o rangeset.o readgroup.o samio.o samples.o spams.o structdef.o -s -lstdc++ -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -lcblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: option -s is obsolete and being ignored
installing to /Users/biocbuild/bbs-3.1-bioc/meat/flipflop.Rcheck/flipflop/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (flipflop)

name	user	system	elapsed
flipflop	0.553	0.022	0.582