BioC 3.0: CHECK report for flipflop on zin1

Package: flipflop

Version: 1.4.1

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings flipflop_1.4.1.tar.gz

StartedAt: 2015-04-09 23:47:59 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:51:05 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 186.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flipflop.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings flipflop_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/flipflop.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flipflop/DESCRIPTION’ ... OK
* this is package ‘flipflop’ version ‘1.4.1’
* 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 ... [49s/52s] WARNING
Found the following significant warnings:
  Warning: class "numLike" is defined (with package slot ‘Matrix’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘flipflop’
See ‘/home/biocbuild/bbs-3.0-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
* 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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
/usr/bin/nm: /home/biocbuild/bbs-3.0-bioc/meat/flipflop.Rcheck/flipflop/libs/flipflop.so: no symbols
/usr/bin/nm: /home/biocbuild/bbs-3.0-bioc/meat/flipflop.Rcheck/flipflop/libs/flipflop.so: no symbols


See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/8s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘GenomicFeatures’
* 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

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/flipflop.Rcheck/00check.log’
for details.

* installing *source* package ‘flipflop’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_flipflop.c -o R_init_flipflop.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c align.cpp -o align.o
align.cpp: In function ‘std::ostream& operator<<(std::ostream&, Align&)’:
align.cpp:11:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
align.cpp: In member function ‘int Align::getReadLen() const’:
align.cpp:19:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
align.cpp: In member function ‘int Align::parse(std::string)’:
align.cpp:43:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
align.cpp:53:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
align.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c auxiliaryio.cpp -o auxiliaryio.o
In file included from structdef.h:11:0,
                 from auxiliaryio.h:11,
                 from auxiliaryio.cpp:6:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: 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]
auxiliaryio.cpp: In function ‘void prepareAuxFile(std::vector<std::basic_string<char> >, std::string, bool&)’:
auxiliaryio.cpp:48:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:49:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:59:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:150:30: 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:206:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:208:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:213:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:215:27: 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:230:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:234:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp: In function ‘void writeannotation(ReadGroup&, int)’:
auxiliaryio.cpp:308:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:329:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:332:44: 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:400:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:424:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:426:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:431:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:433:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:440:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:443:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp: In function ‘int write2rangeandinstance(ReadGroup&, range_t&)’:
auxiliaryio.cpp:512:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:524:27: 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:597:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:599:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:604:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:712:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:724:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:726:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:755:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:757:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:776:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:779:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:796:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:813:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:832:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:837:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp:842:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp: In function ‘int readgenerangefile(std::string, GeneRange&)’:
auxiliaryio.cpp:892:9: warning: unused variable ‘id’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c bed2sam.cpp -o bed2sam.o
bed2sam.cpp: In function ‘std::string getisonamefromname(std::string)’:
bed2sam.cpp:116:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bed2sam.cpp: In function ‘void writeonerecord2sam(std::ofstream&, bedrec&, std::string)’:
bed2sam.cpp:149:9: warning: unused variable ‘xs’ [-Wunused-variable]
bed2sam.cpp: In function ‘int main(int, char**)’:
bed2sam.cpp:481:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bed2sam.cpp:501:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c bedio.cpp -o bedio.o
bedio.cpp: In function ‘int writeBed(std::ostream&, bedrec)’:
bedio.cpp:61:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c common.cpp -o common.o
In file included from structdef.h:11:0,
                 from common.cpp:5:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: 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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c cvganalysis.cpp -o cvganalysis.o
In file included from structdef.h:11:0,
                 from cvganalysis.h:9,
                 from cvganalysis.cpp:2:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: 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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c ffProcesssam.cpp -o ffProcesssam.o
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from ffProcesssam.cpp:3:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: 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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c instanceio.cpp -o instanceio.o
In file included from structdef.h:11:0,
                 from instanceio.h:7,
                 from instanceio.cpp:2:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: 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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c parseopt.cpp -o parseopt.o
In file included from structdef.h:11:0,
                 from parseopt.h:9,
                 from parseopt.cpp:1:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: 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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c rangeset.cpp -o rangeset.o
rangeset.cpp: In function ‘std::ostream& operator<<(std::ostream&, const RangeSet&)’:
rangeset.cpp:15:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c readgroup.cpp -o readgroup.o
In file included from readgroup.cpp:3:0:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: 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:129:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:142:28: 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:199:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:203:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:212:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:216:33: 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:252:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘range_t ReadGroup::getRange() const’:
readgroup.cpp:267:28: 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:282:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:286:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:341:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:343:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:351:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:379:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:390:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:400:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::splitByRangeSet(std::vector<ReadGroup>&, std::vector<RangeSet>&)’:
readgroup.cpp:413:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:419:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:450:25: 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:472:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::calculateRangeSet()’:
readgroup.cpp:563:28: 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:572:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::calculateBound(bool, int, int)’:
readgroup.cpp:598:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:601:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:602:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:646:33: 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:682:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:683:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:691:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::calculateType()’:
readgroup.cpp:729:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:736:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:757:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘int ReadGroup::validSize() const’:
readgroup.cpp:764:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::removeWeakSegs(float)’:
readgroup.cpp:776:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:783:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:790:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:802:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::calculateValidSegs()’:
readgroup.cpp:828:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:830:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:838:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:842:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:844:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:847:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:852:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘std::vector<int> ReadGroup::getReadsContainingSegs(int)’:
readgroup.cpp:874:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:875:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:880:32: 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:892:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘int ReadGroup::getReadLen(int) const’:
readgroup.cpp:899:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:900:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::toStream(std::ostream&) const’:
readgroup.cpp:919:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:921:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:929:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:946:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:947:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:949:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:958:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:969:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:980:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:989:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:995:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:999:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1010:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1028:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘int ReadGroup::peSize() const’:
readgroup.cpp:1072:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::removeTooLongReads(long int, int)’:
readgroup.cpp:1102:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1104:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1120:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘int ReadGroup::getDirSum()’:
readgroup.cpp:1129:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1131:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1126:7: warning: unused variable ‘r’ [-Wunused-variable]
readgroup.cpp:1127:7: warning: unused variable ‘npos’ [-Wunused-variable]
readgroup.cpp:1127:14: warning: unused variable ‘nneg’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c samio.cpp -o samio.o
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from samio.cpp:10:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from samio.h:10:0,
                 from samio.cpp:10:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
samio.cpp: In function ‘int readSamFile(std::string, std::string, std::vector<std::basic_string<char> >)’:
samio.cpp:98:11: warning: variable ‘dp2’ set but not used [-Wunused-but-set-variable]
samio.cpp:102:7: warning: unused variable ‘rangecounter’ [-Wunused-variable]
samio.cpp:106:7: warning: unused variable ‘currentreadlen’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c spams.cpp -o spams.o
spams.cpp: In function ‘SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)’:
spams.cpp:943:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
In file included from spams/prox/fista.h:24:0,
                 from spams.h:5,
                 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:5:0,
                 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]
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:479:3:   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:3691:16: warning: enumeration value ‘SQUARE_MISSING’ not handled in switch [-Wswitch]
spams/prox/fista.h:3691:16: warning: enumeration value ‘LOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:3691:16: warning: enumeration value ‘LOGWEIGHT’ not handled in switch [-Wswitch]
spams/prox/fista.h:3691:16: warning: enumeration value ‘MULTILOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:3691:16: warning: enumeration value ‘CUR’ not handled in switch [-Wswitch]
spams/prox/fista.h:3691:16: warning: enumeration value ‘POISSON’ not handled in switch [-Wswitch]
spams/prox/fista.h:3691:16: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch [-Wswitch]
spams.h:479:3:   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:3718:19: warning: enumeration value ‘MULTILOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:3718:19: warning: enumeration value ‘CUR’ not handled in switch [-Wswitch]
spams/prox/fista.h:3718:19: warning: enumeration value ‘HINGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:3718:19: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch [-Wswitch]
spams.h:479:3:   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:3750:19: warning: enumeration value ‘SQUARE’ not handled in switch [-Wswitch]
spams/prox/fista.h:3750:19: warning: enumeration value ‘SQUARE_MISSING’ not handled in switch [-Wswitch]
spams/prox/fista.h:3750:19: warning: enumeration value ‘LOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:3750:19: warning: enumeration value ‘LOGWEIGHT’ not handled in switch [-Wswitch]
spams/prox/fista.h:3750:19: warning: enumeration value ‘CUR’ not handled in switch [-Wswitch]
spams/prox/fista.h:3750:19: warning: enumeration value ‘HINGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:3750:19: warning: enumeration value ‘POISSON’ not handled in switch [-Wswitch]
spams/prox/fista.h:3750:19: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch [-Wswitch]
spams.h:479:3:   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:3770:16: warning: enumeration value ‘MULTILOG’ not handled in switch [-Wswitch]
spams/prox/fista.h:3770:16: warning: enumeration value ‘HINGE’ not handled in switch [-Wswitch]
spams/prox/fista.h:3770:16: warning: enumeration value ‘INCORRECT_LOSS’ not handled in switch [-Wswitch]
spams.h:479:3:   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:3786:30: 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:1064:3:   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:3961:13: warning: enumeration value ‘FLOW_LINEAR’ not handled in switch [-Wswitch]
spams/prox/fista.h:3961:13: warning: enumeration value ‘FLOW_SQUARE_POS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3961:13: warning: enumeration value ‘FLOW_SQUARE_POS_WEIGHTS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3961:13: warning: enumeration value ‘FLOW_POISSON_POS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3961:13: warning: enumeration value ‘FLOW_POISSON_WEIGHTS_POS’ not handled in switch [-Wswitch]
spams/prox/fista.h:3961:13: 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:3690:16:   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:479:3:   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:3717:19:   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:479:3:   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:3733:16:   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:479:3:   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:3749:19:   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:479:3:   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:3755:16:   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:479:3:   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:3633:24: 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:3794:19:   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:479:3:   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:3798:19:   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:479:3:   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:3618:16:   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:3733:16:   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:479:3:   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:3622:16:   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:3733:16:   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:479:3:   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:3660:16:   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:3755:16:   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:479:3:   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:3664:16:   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:3755:16:   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:479:3:   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:5,
                 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:4658:4:   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:3989:13:   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:1064:3:   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:4658:4:   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:3989:13:   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:1064:3:   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:5:0,
                 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:5,
                 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:4539:42:   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:5:0,
                 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:5,
                 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:5:0,
                 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:3789:16: warning: ‘loss’ may be used uninitialized in this function [-Wuninitialized]
In file included from spams/prox/fista.h:24:0,
                 from spams.h:5,
                 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++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -fpic  -g -O2  -Wall -c structdef.cpp -o structdef.o
In file included from structdef.h:11:0,
                 from structdef.cpp:6:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: 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++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o flipflop.so R_init_flipflop.o align.o auxiliaryio.o bed2sam.o bedio.o common.o cvganalysis.o ffProcesssam.o instanceio.o parseopt.o rangeset.o readgroup.o samio.o spams.o structdef.o -s -fopenmp -lstdc++ -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/flipflop.Rcheck/flipflop/libs
** R
** inst
** preparing package for lazy loading
Warning: class "numLike" is defined (with package slot ‘Matrix’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘flipflop’
Creating a generic function for ‘print’ from package ‘base’ in package ‘flipflop’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flipflop)

name	user	system	elapsed
flipflop	0.372	0.008	0.417