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BioC 2.14: CHECK report for flipflop on petty

This page was generated on 2014-10-08 09:01:27 -0700 (Wed, 08 Oct 2014).

Package 274/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flipflop 1.2.2
Elsa Bernard
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/flipflop
Last Changed Rev: 94109 / Revision: 95116
Last Changed Date: 2014-09-13 23:29:35 -0700 (Sat, 13 Sep 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: flipflop
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flipflop_1.2.2.tar.gz
StartedAt: 2014-10-07 21:55:10 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:00:21 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 311.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flipflop.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flipflop_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flipflop/DESCRIPTION’ ... OK
* this is package ‘flipflop’ version ‘1.2.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flipflop’ can be installed ... [74s/77s] WARNING
Found the following significant warnings:
  auxiliaryio.cpp:157: warning: control reaches end of non-void function
  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 ‘/Users/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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 ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
  -fopenmp -O3 -mtune=native -Wall
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘/Users/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck/flipflop/libs/flipflop.so’:
  Found ‘__ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘spams.o’
  Found ‘__ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘spams.o’
  Found ‘_exit’, possibly from ‘exit’ (C)
    Object: ‘spams.o’
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘spams.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/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 were 3 warnings.
NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck/00check.log’
for details.

flipflop.Rcheck/00install.out:

* installing *source* package ‘flipflop’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_flipflop.c -o R_init_flipflop.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c align.cpp -o align.o
align.cpp: In function ‘std::ostream& operator<<(std::ostream&, Align&)’:
align.cpp:11: warning: comparison between signed and unsigned integer expressions
align.cpp: In member function ‘int Align::getReadLen() const’:
align.cpp:19: warning: comparison between signed and unsigned integer expressions
align.cpp: In member function ‘int Align::parse(std::string)’:
align.cpp:43: warning: comparison between signed and unsigned integer expressions
align.cpp:53: warning: comparison between signed and unsigned integer expressions
align.cpp:59: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c auxiliaryio.cpp -o auxiliaryio.o
In file included from structdef.h:11,
                 from auxiliaryio.h:11,
                 from auxiliaryio.cpp:6:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147: warning: comparison between signed and unsigned integer expressions
In file included from auxiliaryio.h:11,
                 from auxiliaryio.cpp:6:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘int prepareAuxFile(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::string, bool&)’:
auxiliaryio.cpp:48: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:49: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:59: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:150: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘void write2os(std::ostream&, std::string, int, std::vector<long int, std::allocator<long int> >&, std::vector<long int, std::allocator<long int> >&, bool)’:
auxiliaryio.cpp:206: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:208: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:213: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:215: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘void writeBound(std::ostream&, std::string, std::vector<long int, std::allocator<long int> >&, std::vector<long int, std::allocator<long int> >&)’:
auxiliaryio.cpp:230: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:234: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘void writeannotation(ReadGroup&, int)’:
auxiliaryio.cpp:308: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:329: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:332: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘void writeboundfs(range_t, int, std::string, std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&, int, int)’:
auxiliaryio.cpp:400: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:424: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:426: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:431: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:433: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:440: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:443: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘int write2rangeandinstance(ReadGroup&, range_t&)’:
auxiliaryio.cpp:512: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:524: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘void write2Instance(range_t&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, int, int, std::string, int, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, bool, bool)’:
auxiliaryio.cpp:597: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:599: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:604: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:712: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:724: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:726: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:755: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:757: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:776: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:779: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:796: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:813: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:832: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:837: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp:842: warning: comparison between signed and unsigned integer expressions
auxiliaryio.cpp: In function ‘int readgenerangefile(std::string, GeneRange&)’:
auxiliaryio.cpp:892: warning: unused variable ‘id’
auxiliaryio.cpp: In function ‘int prepareAuxFile(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::string, bool&)’:
auxiliaryio.cpp:157: warning: control reaches end of non-void function
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c bed2sam.cpp -o bed2sam.o
bed2sam.cpp: In function ‘std::string getisonamefromname(std::string)’:
bed2sam.cpp:116: warning: comparison between signed and unsigned integer expressions
bed2sam.cpp: In function ‘void writeonerecord2sam(std::ofstream&, bedrec&, std::string)’:
bed2sam.cpp:149: warning: unused variable ‘xs’
bed2sam.cpp: In function ‘int main(int, char**)’:
bed2sam.cpp:481: warning: comparison between signed and unsigned integer expressions
bed2sam.cpp:501: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c bedio.cpp -o bedio.o
bedio.cpp: In function ‘int writeBed(std::ostream&, bedrec)’:
bedio.cpp:61: warning: comparison between signed and unsigned integer expressions
bedio.cpp:76: warning: comparison between signed and unsigned integer expressions
bedio.cpp:78: warning: comparison between signed and unsigned integer expressions
bedio.cpp:82: warning: comparison between signed and unsigned integer expressions
bedio.cpp:84: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c common.cpp -o common.o
In file included from structdef.h:11,
                 from common.cpp:5:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147: warning: comparison between signed and unsigned integer expressions
In file included from common.cpp:5:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c cvganalysis.cpp -o cvganalysis.o
In file included from structdef.h:11,
                 from cvganalysis.h:9,
                 from cvganalysis.cpp:2:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147: warning: comparison between signed and unsigned integer expressions
In file included from cvganalysis.h:9,
                 from cvganalysis.cpp:2:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp: In function ‘void getconnectedcoverage(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, int)’:
cvganalysis.cpp:20: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:25: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:33: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:44: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp: In function ‘void getcoverage(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&)’:
cvganalysis.cpp:78: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:79: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:85: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:86: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp: In function ‘int cutcvg(const std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&, int, int)’:
cvganalysis.cpp:157: warning: comparison between signed and unsigned integer expressions
cvganalysis.cpp:156: warning: unused variable ‘prevjump’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c ffProcesssam.cpp -o ffProcesssam.o
In file included from structdef.h:11,
                 from samio.h:10,
                 from ffProcesssam.cpp:3:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147: warning: comparison between signed and unsigned integer expressions
In file included from samio.h:10,
                 from ffProcesssam.cpp:3:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c instanceio.cpp -o instanceio.o
In file included from structdef.h:11,
                 from instanceio.h:7,
                 from instanceio.cpp:2:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147: warning: comparison between signed and unsigned integer expressions
In file included from instanceio.h:7,
                 from instanceio.cpp:2:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
instanceio.cpp: In function ‘void getallbound(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, range_t, vpos_t&, vpos_t&, std::map<long int, std::vector<double, std::allocator<double> >, std::less<long int>, std::allocator<std::pair<const long int, std::vector<double, std::allocator<double> > > > >&, bool)’:
instanceio.cpp:25: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:27: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:28: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:57: warning: comparison between signed and unsigned integer expressions
instanceio.cpp: In function ‘void getalltypeorders(std::map<std::vector<int, std::allocator<int> >, int, std::less<std::vector<int, std::allocator<int> > >, std::allocator<std::pair<const std::vector<int, std::allocator<int> >, int> > >&, std::map<std::vector<int, std::allocator<int> >, int, std::less<std::vector<int, std::allocator<int> > >, std::allocator<std::pair<const std::vector<int, std::allocator<int> >, int> > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<int, std::allocator<int> >&, std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&)’:
instanceio.cpp:87: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:90: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:95: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:125: warning: unused variable ‘currenttypeorder’
instanceio.cpp: In function ‘void removeoutofrangereads(range_t&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, std::vector<std::vector<long int, std::allocator<long int> >, std::allocator<std::vector<long int, std::allocator<long int> > > >&, int)’:
instanceio.cpp:151: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:158: warning: comparison between signed and unsigned integer expressions
instanceio.cpp:165: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c parseopt.cpp -o parseopt.o
In file included from structdef.h:11,
                 from parseopt.h:9,
                 from parseopt.cpp:1:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147: warning: comparison between signed and unsigned integer expressions
In file included from parseopt.h:9,
                 from parseopt.cpp:1:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
parseopt.cpp: In function ‘int parseopt(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >)’:
parseopt.cpp:13: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:29: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:63: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:65: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:94: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:96: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:102: warning: comparison between signed and unsigned integer expressions
parseopt.cpp:104: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c rangeset.cpp -o rangeset.o
rangeset.cpp: In function ‘std::ostream& operator<<(std::ostream&, const RangeSet&)’:
rangeset.cpp:15: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘int RangeSet::add(const std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&)’:
rangeset.cpp:49: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘int RangeSet::add(pos_t&, pos_t&)’:
rangeset.cpp:56: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘bool RangeSet::isOverlap(pos_t&, pos_t&)’:
rangeset.cpp:137: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘long int RangeSet::minDist(pos_t&, pos_t&)’:
rangeset.cpp:144: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(pos_t&, pos_t&)’:
rangeset.cpp:291: warning: comparison between signed and unsigned integer expressions
rangeset.cpp:292: warning: comparison between signed and unsigned integer expressions
rangeset.cpp:293: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(const std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&)’:
rangeset.cpp:313: warning: comparison between signed and unsigned integer expressions
rangeset.cpp:314: warning: comparison between signed and unsigned integer expressions
rangeset.cpp:315: warning: comparison between signed and unsigned integer expressions
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(RangeSet&)’:
rangeset.cpp:331: warning: unused variable ‘t’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c readgroup.cpp -o readgroup.o
In file included from readgroup.cpp:3:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147: warning: comparison between signed and unsigned integer expressions
In file included from cvganalysis.h:9,
                 from readgroup.cpp:5:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::getConnectedCoverage(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&)’:
readgroup.cpp:129: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:142: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::getCoverage(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&, const range_t&)’:
readgroup.cpp:199: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:203: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:212: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:216: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::getPointCoverage(std::map<long int, int, std::less<long int>, std::allocator<std::pair<const long int, int> > >&)’:
readgroup.cpp:252: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘range_t ReadGroup::getRange() const’:
readgroup.cpp:267: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::splitByRangeSet(std::vector<ReadGroup, std::allocator<ReadGroup> >&, long int)’:
readgroup.cpp:282: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:286: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:341: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:343: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:351: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:379: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:390: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:400: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::splitByRangeSet(std::vector<ReadGroup, std::allocator<ReadGroup> >&, std::vector<RangeSet, std::allocator<RangeSet> >&)’:
readgroup.cpp:413: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:419: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:450: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::splitByDirection(std::vector<ReadGroup, std::allocator<ReadGroup> >&, std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&)’:
readgroup.cpp:472: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::calculateRangeSet()’:
readgroup.cpp:563: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::setupBound(std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > >&)’:
readgroup.cpp:572: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::calculateBound(bool, int, int)’:
readgroup.cpp:597: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:600: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:601: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:625: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘type_t ReadGroup::getType(const pos_t&, const pos_t&) const’:
readgroup.cpp:659: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:660: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:668: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::calculateType()’:
readgroup.cpp:700: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:707: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:728: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘int ReadGroup::validSize() const’:
readgroup.cpp:735: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::removeWeakSegs(float)’:
readgroup.cpp:747: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:754: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:761: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:773: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::calculateValidSegs()’:
readgroup.cpp:799: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:801: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:809: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:813: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:815: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:818: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:823: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘std::vector<int, std::allocator<int> > ReadGroup::getReadsContainingSegs(int)’:
readgroup.cpp:845: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:846: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:851: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘std::vector<std::pair<long int, long int>, std::allocator<std::pair<long int, long int> > > ReadGroup::getSegs() const’:
readgroup.cpp:863: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘int ReadGroup::getReadLen(int) const’:
readgroup.cpp:870: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:871: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::toStream(std::ostream&) const’:
readgroup.cpp:890: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:892: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:900: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:917: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:918: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:920: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:929: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:940: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:951: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:960: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:966: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:970: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:981: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:999: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘int ReadGroup::peSize() const’:
readgroup.cpp:1043: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘void ReadGroup::removeTooLongReads(long int, int)’:
readgroup.cpp:1073: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1075: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1091: warning: comparison between signed and unsigned integer expressions
readgroup.cpp: In member function ‘int ReadGroup::getDirSum()’:
readgroup.cpp:1100: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1102: warning: comparison between signed and unsigned integer expressions
readgroup.cpp:1097: warning: unused variable ‘r’
readgroup.cpp:1098: warning: unused variable ‘npos’
readgroup.cpp:1098: warning: unused variable ‘nneg’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c samio.cpp -o samio.o
In file included from structdef.h:11,
                 from samio.h:10,
                 from samio.cpp:10:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147: warning: comparison between signed and unsigned integer expressions
In file included from samio.h:10,
                 from samio.cpp:10:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
samio.cpp: In function ‘int readSamFile(std::string, std::string, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >)’:
samio.cpp:102: warning: unused variable ‘rangecounter’
samio.cpp:106: warning: unused variable ‘currentreadlen’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c spams.cpp -o spams.o
In file included from spams/dags/dag.h:23,
                 from spams.h:4,
                 from spams.cpp:1273:
spams/linalg/linalg.h:1070: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:1234: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2366: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:2537: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:2580: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2589: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2621: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2630: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2709: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2722: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:2890: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:4106: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:4249: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:4566: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4615: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4651: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4687: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4720: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4756: warning: ignoring #pragma omp parallel
spams/linalg/linalg.h:4894: warning: ignoring #pragma omp critical
spams/linalg/linalg.h:5013: warning: ignoring #pragma omp critical
In file included from spams/prox/fista.h:25,
                 from spams.h:5,
                 from spams.cpp:1273:
spams/decomp/decomp.h:337: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:426: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:699: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:1155: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:1255: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:1327: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:1406: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:1509: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:2019: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:2228: warning: ignoring #pragma omp parallel
spams/decomp/decomp.h:2546: warning: ignoring #pragma omp parallel
In file included from spams.h:5,
                 from spams.cpp:1273:
spams/prox/fista.h:2373: warning: ignoring #pragma omp parallel
spams/prox/fista.h:2381: warning: ignoring #pragma omp parallel
spams/prox/fista.h:2416: warning: ignoring #pragma omp parallel
spams/prox/fista.h:2424: warning: ignoring #pragma omp critical
spams/prox/fista.h:3554: warning: ignoring #pragma omp parallel
spams/prox/fista.h:3600: warning: ignoring #pragma omp parallel
spams/prox/fista.h:3641: warning: ignoring #pragma omp parallel
spams/prox/fista.h:3838: warning: ignoring #pragma omp parallel
spams/prox/fista.h:3896: warning: ignoring #pragma omp parallel
spams/prox/fista.h:3970: warning: ignoring #pragma omp parallel
spams/prox/fista.h: In destructor ‘FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normLINF<double>]’:
spams.cpp:2724:   instantiated from here
spams/prox/fista.h:1807: warning: comparison between signed and unsigned integer expressions
spams/prox/fista.h: In member function ‘void FISTA::GroupProx<T, Reg>::prox(const Vector<T>&, Vector<T>&, T) [with T = double, Reg = FISTA::normLINF<double>]’:
spams.cpp:2724:   instantiated from here
spams/prox/fista.h:1814: warning: comparison between signed and unsigned integer expressions
spams/prox/fista.h: In member function ‘T FISTA::GroupProx<T, Reg>::eval(const Vector<T>&) const [with T = double, Reg = FISTA::normLINF<double>]’:
spams.cpp:2724:   instantiated from here
spams/prox/fista.h:1843: warning: comparison between signed and unsigned integer expressions
spams/prox/fista.h: In member function ‘void FISTA::GroupProx<T, Reg>::fenchel(const Vector<T>&, T&, T&) const [with T = double, Reg = FISTA::normLINF<double>]’:
spams.cpp:2724:   instantiated from here
spams/prox/fista.h:1870: warning: comparison between signed and unsigned integer expressions
spams/prox/fista.h: In destructor ‘FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normL2<double>]’:
spams.cpp:2724:   instantiated from here
spams/prox/fista.h:1807: warning: comparison between signed and unsigned integer expressions
spams/prox/fista.h: In member function ‘void FISTA::GroupProx<T, Reg>::prox(const Vector<T>&, Vector<T>&, T) [with T = double, Reg = FISTA::normL2<double>]’:
spams.cpp:2724:   instantiated from here
spams/prox/fista.h:1814: warning: comparison between signed and unsigned integer expressions
spams/prox/fista.h: In member function ‘T FISTA::GroupProx<T, Reg>::eval(const Vector<T>&) const [with T = double, Reg = FISTA::normL2<double>]’:
spams.cpp:2724:   instantiated from here
spams/prox/fista.h:1843: warning: comparison between signed and unsigned integer expressions
spams/prox/fista.h: In member function ‘void FISTA::GroupProx<T, Reg>::fenchel(const Vector<T>&, T&, T&) const [with T = double, Reg = FISTA::normL2<double>]’:
spams.cpp:2724:   instantiated from here
spams/prox/fista.h:1870: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags    -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c structdef.cpp -o structdef.o
In file included from structdef.h:11,
                 from structdef.cpp:6:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147: warning: comparison between signed and unsigned integer expressions
In file included from structdef.cpp:6:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37: warning: comparison between signed and unsigned integer expressions
structdef.cpp: In member function ‘int GeneRange::sort()’:
structdef.cpp:47: warning: comparison between signed and unsigned integer expressions
structdef.cpp:52: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o flipflop.so R_init_flipflop.o align.o auxiliaryio.o bed2sam.o bedio.o common.o cvganalysis.o ffProcesssam.o instanceio.o parseopt.o rangeset.o readgroup.o samio.o spams.o structdef.o -s -lstdc++ -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -lcblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: option -s is obsolete and being ignored
installing to /Users/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck/flipflop/libs
** R
** inst
** preparing package for lazy loading
Warning: class "numLike" is defined (with package slot ‘Matrix’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘flipflop’
Creating a generic function for ‘print’ from package ‘base’ in package ‘flipflop’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flipflop)

flipflop.Rcheck/flipflop-Ex.timings:

nameusersystemelapsed
flipflop0.7040.0270.732