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BioC 2.13: CHECK report for flipflop on moscato1

This page was generated on 2014-04-05 09:51:33 -0700 (Sat, 05 Apr 2014).

Package 246/750HostnameOS / ArchBUILDCHECKBUILD BIN
flipflop 1.0.1
Elsa Bernard
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flipflop
Last Changed Rev: 81983 / Revision: 88450
Last Changed Date: 2013-10-22 05:37:02 -0700 (Tue, 22 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: flipflop
Version: 1.0.1
Command: rm -rf flipflop.buildbin-libdir && mkdir flipflop.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flipflop.buildbin-libdir flipflop_1.0.1.tar.gz >flipflop-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=flipflop.buildbin-libdir --install="check:flipflop-install.out" --force-multiarch --no-vignettes --timings flipflop_1.0.1.tar.gz && mv flipflop.buildbin-libdir/* flipflop.Rcheck/ && rmdir flipflop.buildbin-libdir
StartedAt: 2014-04-05 03:48:36 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:53:28 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 291.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: flipflop.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/flipflop.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flipflop/DESCRIPTION' ... OK
* this is package 'flipflop' version '1.0.1'
* 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 whether package 'flipflop' can be installed ... 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 'D:/biocbld/bbs-2.13-bioc/meat/flipflop.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-2.13-bioc/meat/flipflop.buildbin-libdir/flipflop/libs/i386/flipflop.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbld/bbs-2.13-bioc/meat/flipflop.buildbin-libdir/flipflop/libs/x64/flipflop.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'flipflop.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [9s] OK
** running examples for arch 'x64' ... [13s] 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

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/flipflop.Rcheck/00check.log'
for details.

flipflop.Rcheck/00install.out:


install for i386

* installing *source* package 'flipflop' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_flipflop.c -o R_init_flipflop.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c align.cpp -o align.o
align.cpp: In function 'std::ostream& operator<<(std::ostream&, Align&)':
align.cpp:11:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
align.cpp: In member function 'int Align::getReadLen() const':
align.cpp:19:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c auxiliaryio.cpp -o auxiliaryio.o
In file included from structdef.h:11:0,
                 from auxiliaryio.h:11,
                 from auxiliaryio.cpp:6:
readgroup.h: In 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 'int 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]
auxiliaryio.cpp: In function 'int prepareAuxFile(std::vector<std::basic_string<char> >, std::string, bool&)':
auxiliaryio.cpp:157:1: warning: control reaches end of non-void function [-Wreturn-type]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -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++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c bedio.cpp -o bedio.o
bedio.cpp: In function 'int writeBed(std::ostream&, bedrec)':
bedio.cpp:61:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:76:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:78:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:82:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:84:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c common.cpp -o common.o
In file included from structdef.h:11:0,
                 from common.cpp:5:
readgroup.h: In 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++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c cvganalysis.cpp -o cvganalysis.o
In file included from structdef.h:11:0,
                 from cvganalysis.h:9,
                 from cvganalysis.cpp:2:
readgroup.h: In 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++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c ffProcesssam.cpp -o ffProcesssam.o
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from ffProcesssam.cpp:3:
readgroup.h: In 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++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c instanceio.cpp -o instanceio.o
In file included from structdef.h:11:0,
                 from instanceio.h:7,
                 from instanceio.cpp:2:
readgroup.h: In 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++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c parseopt.cpp -o parseopt.o
In file included from structdef.h:11:0,
                 from parseopt.h:9,
                 from parseopt.cpp:1:
readgroup.h: In 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++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c rangeset.cpp -o rangeset.o
rangeset.cpp: In function 'std::ostream& operator<<(std::ostream&, const RangeSet&)':
rangeset.cpp:15:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'int RangeSet::add(const std::vector<std::pair<long int, long int> >&)':
rangeset.cpp:49:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'int RangeSet::add(pos_t&, pos_t&)':
rangeset.cpp:56:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'bool RangeSet::isOverlap(pos_t&, pos_t&)':
rangeset.cpp:137:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'long int RangeSet::minDist(pos_t&, pos_t&)':
rangeset.cpp:144:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'pos_t RangeSet::getEnd() const':
rangeset.cpp:230:8: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
rangeset.cpp: In member function 'long int RangeSet::overlapLen(pos_t&, pos_t&)':
rangeset.cpp:291:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:292:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:293:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'long int RangeSet::overlapLen(const std::vector<std::pair<long int, long int> >&)':
rangeset.cpp:313:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:315:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'long int RangeSet::overlapLen(RangeSet&)':
rangeset.cpp:331:8: warning: unused variable 't' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c readgroup.cpp -o readgroup.o
In file included from readgroup.cpp:3:0:
readgroup.h: In 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:597:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:600:40: 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:625:33: 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:659:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:660:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:668:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::calculateType()':
readgroup.cpp:700:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:707:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:728:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::validSize() const':
readgroup.cpp:735:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::removeWeakSegs(float)':
readgroup.cpp:747:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:754:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:761:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:773:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::calculateValidSegs()':
readgroup.cpp:799:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:801:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:809:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:813:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:815:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:818:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:823:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'std::vector<int> ReadGroup::getReadsContainingSegs(int)':
readgroup.cpp:845:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:846:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:851:32: 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:863:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::getReadLen(int) const':
readgroup.cpp:870:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:871:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::toStream(std::ostream&) const':
readgroup.cpp:890:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:892:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:900:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:917:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:918:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:920:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:929:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:940:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:951:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:960:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:966:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:970:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:981:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:999:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1012:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1019:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::peSize() const':
readgroup.cpp:1042:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::removeTooLongReads(long int, int)':
readgroup.cpp:1072:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1074:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1090:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::getDirSum()':
readgroup.cpp:1099:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1101:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1096:7: warning: unused variable 'r' [-Wunused-variable]
readgroup.cpp:1097:7: warning: unused variable 'npos' [-Wunused-variable]
readgroup.cpp:1097:14: warning: unused variable 'nneg' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c samio.cpp -o samio.o
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from samio.cpp: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::vector<std::basic_string<char> >)':
samio.cpp:97:11: warning: variable 'dp2' set but not used [-Wunused-but-set-variable]
samio.cpp:101:7: warning: unused variable 'rangecounter' [-Wunused-variable]
samio.cpp:105:7: warning: unused variable 'currentreadlen' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c spams.cpp -o spams.o
In file included from spams.h:5:0,
                 from spams.cpp:1274:
spams/dags/dag.h:2:1: warning: "/*" within comment [-Wcomment]
In file included from spams/prox/fista.h:25:0,
                 from spams.h:6,
                 from spams.cpp:1274:
spams/decomp/decomp.h:2:1: warning: "/*" within comment [-Wcomment]
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.cpp:1286:0:
./Rinterface.h: At global scope:
./Rinterface.h:53:12: warning: 'R_DirtyImage' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
spams.cpp: In function 'SEXPREC* R_swig_evalPathCoding(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
spams.cpp:1891:13: warning: unused variable 'nzmax' [-Wunused-variable]
spams.cpp: In function 'SEXPREC* R_swig_sepCostsPathCoding(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
spams.cpp:2111:13: warning: unused variable 'nzmax' [-Wunused-variable]
In file included from spams.cpp:1274:0:
spams.h: In function '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) [with T = double]':
spams.cpp:1676:273:   instantiated from here
spams.h:430:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
In file included from spams.h:6:0,
                 from spams.cpp:1274:
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:3664:19:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2766:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2829:12: 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:3668:19:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2849:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2919:12: warning: unused variable 'sec' [-Wunused-variable]
In file included from spams/dags/dag.h:23:0,
                 from spams.h:5,
                 from spams.cpp:1274:
spams/linalg/linalg.h: In member function 'T SpVector<T>::dot(const Vector<T>&) const [with T = double]':
spams/prox/fista.h:4046:22:   instantiated from 'void FISTA::poissonSolver(const Vector<T>&, U&, const Vector<T>&, Vector<T>&, const Vector<T>&, T, int, T) [with T = double, U = SpMatrix<double>]'
spams.h:983:3:   instantiated from 'void _solverPoisson(Vector<T>*, SpMatrix<T>*, Vector<T>*, Vector<T>*, Vector<T>*, T, int, T) [with T = double]'
spams.cpp:2270:69:   instantiated from here
spams/linalg/linalg.h:4992:7: warning: operation on 'countI' may be undefined [-Wsequence-point]
In file included from spams.h:6:0,
                 from spams.cpp:1274:
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:3488:16:   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:3604:16:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2766:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2829:12: 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:3492:16:   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:3604:16:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2849:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2919:12: 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:3530:16:   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:3626:16:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2766:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2829:12: 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:3534:16:   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:3626:16:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2849:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2919:12: warning: unused variable 'sec' [-Wunused-variable]
In file included from spams/prox/fista.h:24:0,
                 from spams.h:6,
                 from spams.cpp:1274:
spams/prox/project.h: In member function 'void DoubleMinCostFlow<T>::discharge(int, T) [with T = double]':
spams/prox/project.h:3891:7:   instantiated from 'void DoubleMinCostFlow<T>::refine(T) [with T = double]'
spams/prox/project.h:3815:7:   instantiated from 'void DoubleMinCostFlow<T>::solve_min_cost(T, bool) [with T = double]'
spams/prox/project.h:4656:4:   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:3859:13:   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:1067:3:   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:2099:170:   instantiated from here
spams/prox/project.h:3958:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
In file included from spams.h:6:0,
                 from spams.cpp:1274:
spams/prox/fista.h: In member function 'void FISTA::MixedL1LINF<T>::fenchel(const Matrix<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1930:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::MixedL1L2<T>::fenchel(const Matrix<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1885:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::GraphPathConv<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:2250:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In destructor 'FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normLINF<double>]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1718:29: 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:2722:1:   instantiated from here
spams/prox/fista.h:1725:32: 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:2722:1:   instantiated from here
spams/prox/fista.h:1754:32: 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:2722:1:   instantiated from here
spams/prox/fista.h:1781:32: 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:2722:1:   instantiated from here
spams/prox/fista.h:1718:29: 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:2722:1:   instantiated from here
spams/prox/fista.h:1725:32: 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:2722:1:   instantiated from here
spams/prox/fista.h:1754:32: 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:2722:1:   instantiated from here
spams/prox/fista.h:1781:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'void FISTA::TreeLasso<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1614:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::Ridge<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1255:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::normLINF<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1334:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::normL2<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1302:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::Lasso<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1171:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::GraphLasso<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1497:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In function 'void FISTA::LinADMM(const FISTA::SplittingFunction<T>&, const FISTA::SplittingFunction<T, SpMatrix<T> >&, const Vector<T>&, Vector<T>&, Vector<T>&, const FISTA::ParamFISTA<T>&) [with T = double]':
spams/prox/fista.h:3250:16: warning: 'los' may be used uninitialized in this function [-Wuninitialized]
spams/prox/fista.h:3250:16: warning: 'old_los' may be used uninitialized in this function [-Wuninitialized]
spams/prox/fista.h: In function 'void FISTA::ADMM(const FISTA::SplittingFunction<T>&, const FISTA::SplittingFunction<T, SpMatrix<T> >&, const Vector<T>&, Vector<T>&, Vector<T>&, const FISTA::ParamFISTA<T>&) [with T = double]':
spams/prox/fista.h:3133:16: warning: 'los' may be used uninitialized in this function [-Wuninitialized]
spams/prox/fista.h:3133:16: warning: 'old_los' may be used uninitialized in this function [-Wuninitialized]
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:3277:17: warning: 'reg' may be used uninitialized in this function [-Wuninitialized]
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:3326:17: 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:3659:16: warning: 'loss' may be used uninitialized in this function [-Wuninitialized]
In file included from spams/dags/dag.h:23:0,
                 from spams.h:5,
                 from spams.cpp:1274:
spams/linalg/cblas_alt_template.h: In member function 'void Matrix<T>::singularValues(Vector<T>&) const [with T = double]':
spams/linalg/cblas_alt_template.h:702:32: warning: 'vu' may be used uninitialized in this function [-Wuninitialized]
spams/linalg/linalg.h:1586:10: note: 'vu' was declared here
spams/linalg/cblas_alt_template.h:702:32: warning: 'vv' may be used uninitialized in this function [-Wuninitialized]
spams/linalg/linalg.h:1586:15: note: 'vv' was declared here
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c structdef.cpp -o structdef.o
In file included from structdef.h:11:0,
                 from structdef.cpp:6:
readgroup.h: In 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++ -m32 -shared -s -static-libgcc -o flipflop.dll tmp.def 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++ -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lRblas -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lRlapack -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/flipflop.buildbin-libdir/flipflop/libs/i386
** 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

install for x64

* installing *source* package 'flipflop' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_flipflop.c -o R_init_flipflop.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c align.cpp -o align.o
align.cpp: In function 'std::ostream& operator<<(std::ostream&, Align&)':
align.cpp:11:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
align.cpp: In member function 'int Align::getReadLen() const':
align.cpp:19:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c auxiliaryio.cpp -o auxiliaryio.o
In file included from structdef.h:11:0,
                 from auxiliaryio.h:11,
                 from auxiliaryio.cpp:6:
readgroup.h: In 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 'int 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]
auxiliaryio.cpp: In function 'int prepareAuxFile(std::vector<std::basic_string<char> >, std::string, bool&)':
auxiliaryio.cpp:157:1: warning: control reaches end of non-void function [-Wreturn-type]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -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++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c bedio.cpp -o bedio.o
bedio.cpp: In function 'int writeBed(std::ostream&, bedrec)':
bedio.cpp:61:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:76:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:78:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:82:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:84:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c common.cpp -o common.o
In file included from structdef.h:11:0,
                 from common.cpp:5:
readgroup.h: In 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++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c cvganalysis.cpp -o cvganalysis.o
In file included from structdef.h:11:0,
                 from cvganalysis.h:9,
                 from cvganalysis.cpp:2:
readgroup.h: In 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++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c ffProcesssam.cpp -o ffProcesssam.o
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from ffProcesssam.cpp:3:
readgroup.h: In 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++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c instanceio.cpp -o instanceio.o
In file included from structdef.h:11:0,
                 from instanceio.h:7,
                 from instanceio.cpp:2:
readgroup.h: In 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++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c parseopt.cpp -o parseopt.o
In file included from structdef.h:11:0,
                 from parseopt.h:9,
                 from parseopt.cpp:1:
readgroup.h: In 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++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c rangeset.cpp -o rangeset.o
rangeset.cpp: In function 'std::ostream& operator<<(std::ostream&, const RangeSet&)':
rangeset.cpp:15:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'int RangeSet::add(const std::vector<std::pair<long int, long int> >&)':
rangeset.cpp:49:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'int RangeSet::add(pos_t&, pos_t&)':
rangeset.cpp:56:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'bool RangeSet::isOverlap(pos_t&, pos_t&)':
rangeset.cpp:137:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'long int RangeSet::minDist(pos_t&, pos_t&)':
rangeset.cpp:144:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'pos_t RangeSet::getEnd() const':
rangeset.cpp:230:8: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
rangeset.cpp: In member function 'long int RangeSet::overlapLen(pos_t&, pos_t&)':
rangeset.cpp:291:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:292:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:293:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'long int RangeSet::overlapLen(const std::vector<std::pair<long int, long int> >&)':
rangeset.cpp:313:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:315:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function 'long int RangeSet::overlapLen(RangeSet&)':
rangeset.cpp:331:8: warning: unused variable 't' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c readgroup.cpp -o readgroup.o
In file included from readgroup.cpp:3:0:
readgroup.h: In 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:597:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:600:40: 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:625:33: 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:659:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:660:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:668:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::calculateType()':
readgroup.cpp:700:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:707:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:728:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::validSize() const':
readgroup.cpp:735:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::removeWeakSegs(float)':
readgroup.cpp:747:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:754:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:761:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:773:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::calculateValidSegs()':
readgroup.cpp:799:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:801:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:809:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:813:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:815:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:818:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:823:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'std::vector<int> ReadGroup::getReadsContainingSegs(int)':
readgroup.cpp:845:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:846:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:851:32: 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:863:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::getReadLen(int) const':
readgroup.cpp:870:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:871:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::toStream(std::ostream&) const':
readgroup.cpp:890:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:892:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:900:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:917:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:918:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:920:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:929:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:940:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:951:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:960:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:966:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:970:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:981:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:999:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1012:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1019:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::peSize() const':
readgroup.cpp:1042:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'void ReadGroup::removeTooLongReads(long int, int)':
readgroup.cpp:1072:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1074:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1090:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function 'int ReadGroup::getDirSum()':
readgroup.cpp:1099:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1101:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1096:7: warning: unused variable 'r' [-Wunused-variable]
readgroup.cpp:1097:7: warning: unused variable 'npos' [-Wunused-variable]
readgroup.cpp:1097:14: warning: unused variable 'nneg' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c samio.cpp -o samio.o
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from samio.cpp: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::vector<std::basic_string<char> >)':
samio.cpp:97:11: warning: variable 'dp2' set but not used [-Wunused-but-set-variable]
samio.cpp:101:7: warning: unused variable 'rangecounter' [-Wunused-variable]
samio.cpp:105:7: warning: unused variable 'currentreadlen' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c spams.cpp -o spams.o
In file included from spams.h:5:0,
                 from spams.cpp:1274:
spams/dags/dag.h:2:1: warning: "/*" within comment [-Wcomment]
In file included from spams/prox/fista.h:25:0,
                 from spams.h:6,
                 from spams.cpp:1274:
spams/decomp/decomp.h:2:1: warning: "/*" within comment [-Wcomment]
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.cpp:1286:0:
./Rinterface.h: At global scope:
./Rinterface.h:53:12: warning: 'R_DirtyImage' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
spams.cpp: In function 'SEXPREC* R_swig_evalPathCoding(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
spams.cpp:1891:13: warning: unused variable 'nzmax' [-Wunused-variable]
spams.cpp: In function 'SEXPREC* R_swig_sepCostsPathCoding(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
spams.cpp:2111:13: warning: unused variable 'nzmax' [-Wunused-variable]
In file included from spams.cpp:1274:0:
spams.h: In function '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) [with T = double]':
spams.cpp:1676:273:   instantiated from here
spams.h:430:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
In file included from spams.h:6:0,
                 from spams.cpp:1274:
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:3664:19:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2766:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2829:12: 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:3668:19:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2849:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2919:12: warning: unused variable 'sec' [-Wunused-variable]
In file included from spams/dags/dag.h:23:0,
                 from spams.h:5,
                 from spams.cpp:1274:
spams/linalg/linalg.h: In member function 'T SpVector<T>::dot(const Vector<T>&) const [with T = double]':
spams/prox/fista.h:4046:22:   instantiated from 'void FISTA::poissonSolver(const Vector<T>&, U&, const Vector<T>&, Vector<T>&, const Vector<T>&, T, int, T) [with T = double, U = SpMatrix<double>]'
spams.h:983:3:   instantiated from 'void _solverPoisson(Vector<T>*, SpMatrix<T>*, Vector<T>*, Vector<T>*, Vector<T>*, T, int, T) [with T = double]'
spams.cpp:2270:69:   instantiated from here
spams/linalg/linalg.h:4992:7: warning: operation on 'countI' may be undefined [-Wsequence-point]
In file included from spams.h:6:0,
                 from spams.cpp:1274:
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:3488:16:   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:3604:16:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2766:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2829:12: 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:3492:16:   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:3604:16:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2849:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2919:12: 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:3530:16:   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:3626:16:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2766:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2829:12: 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:3534:16:   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:3626:16:   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:483:3:   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) [with T = double]'
spams.cpp:1676:273:   instantiated from here
spams/prox/fista.h:2849:12: warning: variable 'Lold' set but not used [-Wunused-but-set-variable]
spams/prox/fista.h:2919:12: warning: unused variable 'sec' [-Wunused-variable]
In file included from spams/prox/fista.h:24:0,
                 from spams.h:6,
                 from spams.cpp:1274:
spams/prox/project.h: In member function 'void DoubleMinCostFlow<T>::discharge(int, T) [with T = double]':
spams/prox/project.h:3891:7:   instantiated from 'void DoubleMinCostFlow<T>::refine(T) [with T = double]'
spams/prox/project.h:3815:7:   instantiated from 'void DoubleMinCostFlow<T>::solve_min_cost(T, bool) [with T = double]'
spams/prox/project.h:4656:4:   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:3859:13:   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:1067:3:   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:2099:170:   instantiated from here
spams/prox/project.h:3958:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
In file included from spams.h:6:0,
                 from spams.cpp:1274:
spams/prox/fista.h: In member function 'void FISTA::MixedL1LINF<T>::fenchel(const Matrix<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1930:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::MixedL1L2<T>::fenchel(const Matrix<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1885:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::GraphPathConv<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:2250:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In destructor 'FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normLINF<double>]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1718:29: 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:2722:1:   instantiated from here
spams/prox/fista.h:1725:32: 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:2722:1:   instantiated from here
spams/prox/fista.h:1754:32: 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:2722:1:   instantiated from here
spams/prox/fista.h:1781:32: 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:2722:1:   instantiated from here
spams/prox/fista.h:1718:29: 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:2722:1:   instantiated from here
spams/prox/fista.h:1725:32: 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:2722:1:   instantiated from here
spams/prox/fista.h:1754:32: 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:2722:1:   instantiated from here
spams/prox/fista.h:1781:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function 'void FISTA::TreeLasso<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1614:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::Ridge<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1255:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::normLINF<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1334:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::normL2<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1302:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::Lasso<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1171:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In member function 'void FISTA::GraphLasso<T>::fenchel(const Vector<T>&, T&, T&) const [with T = double]':
spams.cpp:2722:1:   instantiated from here
spams/prox/fista.h:1497:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
spams/prox/fista.h: In function 'void FISTA::LinADMM(const FISTA::SplittingFunction<T>&, const FISTA::SplittingFunction<T, SpMatrix<T> >&, const Vector<T>&, Vector<T>&, Vector<T>&, const FISTA::ParamFISTA<T>&) [with T = double]':
spams/prox/fista.h:3250:16: warning: 'los' may be used uninitialized in this function [-Wuninitialized]
spams/prox/fista.h:3250:16: warning: 'old_los' may be used uninitialized in this function [-Wuninitialized]
spams/prox/fista.h: In function 'void FISTA::ADMM(const FISTA::SplittingFunction<T>&, const FISTA::SplittingFunction<T, SpMatrix<T> >&, const Vector<T>&, Vector<T>&, Vector<T>&, const FISTA::ParamFISTA<T>&) [with T = double]':
spams/prox/fista.h:3133:16: warning: 'los' may be used uninitialized in this function [-Wuninitialized]
spams/prox/fista.h:3133:16: warning: 'old_los' may be used uninitialized in this function [-Wuninitialized]
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:3277:17: warning: 'reg' may be used uninitialized in this function [-Wuninitialized]
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:3326:17: 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:3659:16: warning: 'loss' may be used uninitialized in this function [-Wuninitialized]
In file included from spams/dags/dag.h:23:0,
                 from spams.h:5,
                 from spams.cpp:1274:
spams/linalg/cblas_alt_template.h: In member function 'void Matrix<T>::singularValues(Vector<T>&) const [with T = double]':
spams/linalg/cblas_alt_template.h:702:32: warning: 'vu' may be used uninitialized in this function [-Wuninitialized]
spams/linalg/linalg.h:1586:10: note: 'vu' was declared here
spams/linalg/cblas_alt_template.h:702:32: warning: 'vv' may be used uninitialized in this function [-Wuninitialized]
spams/linalg/linalg.h:1586:15: note: 'vv' was declared here
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp  -DUSE_BLAS_LIB -DNDEBUG    -O2 -Wall  -mtune=core2 -c structdef.cpp -o structdef.o
In file included from structdef.h:11:0,
                 from structdef.cpp:6:
readgroup.h: In 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++ -m64 -shared -s -static-libgcc -o flipflop.dll tmp.def 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++ -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lRblas -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lRlapack -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/flipflop.buildbin-libdir/flipflop/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flipflop' as flipflop_1.0.1.zip
* DONE (flipflop)

flipflop.Rcheck/examples_i386/flipflop-Ex.timings:

nameusersystemelapsed
flipflop0.740.010.75

flipflop.Rcheck/examples_x64/flipflop-Ex.timings:

nameusersystemelapsed
flipflop1.070.011.14