BioC 2.14: CHECK report for flipflop on zin2

Package: flipflop

Version: 1.2.2

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings flipflop_1.2.2.tar.gz

StartedAt: 2014-10-07 23:30:39 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:33:14 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 154.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flipflop.Rcheck

Warnings: 2

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###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings flipflop_1.2.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flipflop/DESCRIPTION’ ... OK
* this is package ‘flipflop’ version ‘1.2.2’
* 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 ... [43s/44s] WARNING
Found the following significant warnings:
  auxiliaryio.cpp:157:1: warning: control reaches end of non-void function [-Wreturn-type]
  Warning: class "numLike" is defined (with package slot ‘Matrix’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘flipflop’
See ‘/home/biocbuild/bbs-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 ... NOTE
/usr/bin/nm: /home/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck/flipflop/libs/flipflop.so: no symbols
/usr/bin/nm: /home/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck/flipflop/libs/flipflop.so: no symbols


See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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 2 warnings.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/flipflop.Rcheck/00check.log’
for details.

* installing *source* package ‘flipflop’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_flipflop.c -o R_init_flipflop.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c align.cpp -o align.o
align.cpp: In function ‘std::ostream& operator<<(std::ostream&, Align&)’:
align.cpp:11:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
align.cpp: In member function ‘int Align::getReadLen() const’:
align.cpp:19:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
align.cpp: In member function ‘int Align::parse(std::string)’:
align.cpp:43:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
align.cpp:53:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
align.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c auxiliaryio.cpp -o auxiliaryio.o
In file included from structdef.h:11:0,
                 from auxiliaryio.h:11,
                 from auxiliaryio.cpp:6:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from auxiliaryio.h:11:0,
                 from auxiliaryio.cpp:6:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
auxiliaryio.cpp: In function ‘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++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c bed2sam.cpp -o bed2sam.o
bed2sam.cpp: In function ‘std::string getisonamefromname(std::string)’:
bed2sam.cpp:116:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bed2sam.cpp: In function ‘void writeonerecord2sam(std::ofstream&, bedrec&, std::string)’:
bed2sam.cpp:149:9: warning: unused variable ‘xs’ [-Wunused-variable]
bed2sam.cpp: In function ‘int main(int, char**)’:
bed2sam.cpp:481:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bed2sam.cpp:501:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c bedio.cpp -o bedio.o
bedio.cpp: In function ‘int writeBed(std::ostream&, bedrec)’:
bedio.cpp:61:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:76:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:78:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:82:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bedio.cpp:84:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c common.cpp -o common.o
In file included from structdef.h:11:0,
                 from common.cpp:5:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from common.cpp:5:0:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c cvganalysis.cpp -o cvganalysis.o
In file included from structdef.h:11:0,
                 from cvganalysis.h:9,
                 from cvganalysis.cpp:2:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from cvganalysis.h:9:0,
                 from cvganalysis.cpp:2:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp: In function ‘void getconnectedcoverage(std::map<long int, int>&, std::vector<std::vector<long int> >&, std::vector<std::vector<long int> >&, int)’:
cvganalysis.cpp:20:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:25:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:33:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:44:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp: In function ‘void getcoverage(std::map<long int, int>&, std::vector<std::vector<long int> >&, std::vector<std::vector<long int> >&)’:
cvganalysis.cpp:78:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:79:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:85:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:86:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp: In function ‘int cutcvg(const std::map<long int, int>&, std::vector<std::pair<long int, long int> >&, int, int)’:
cvganalysis.cpp:157:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
cvganalysis.cpp:156:12: warning: unused variable ‘prevjump’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c ffProcesssam.cpp -o ffProcesssam.o
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from ffProcesssam.cpp:3:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from samio.h:10:0,
                 from ffProcesssam.cpp:3:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c instanceio.cpp -o instanceio.o
In file included from structdef.h:11:0,
                 from instanceio.h:7,
                 from instanceio.cpp:2:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from instanceio.h:7:0,
                 from instanceio.cpp:2:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp: In function ‘void getallbound(std::map<long int, int>&, range_t, vpos_t&, vpos_t&, std::map<long int, std::vector<double> >&, bool)’:
instanceio.cpp:25:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:27:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:28:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:57:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp: In function ‘void getalltypeorders(std::map<std::vector<int>, int>&, std::map<std::vector<int>, int>&, std::vector<std::vector<int> >&, std::vector<int>&, std::map<long int, int>&, std::vector<std::vector<long int> >&, std::vector<std::vector<long int> >&, std::map<long int, int>&)’:
instanceio.cpp:87:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:90:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:95:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:125:9: warning: unused variable ‘currenttypeorder’ [-Wunused-variable]
instanceio.cpp: In function ‘void removeoutofrangereads(range_t&, std::vector<std::vector<long int> >&, std::vector<std::vector<long int> >&, int)’:
instanceio.cpp:151:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:158:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
instanceio.cpp:165:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c parseopt.cpp -o parseopt.o
In file included from structdef.h:11:0,
                 from parseopt.h:9,
                 from parseopt.cpp:1:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from parseopt.h:9:0,
                 from parseopt.cpp:1:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp: In function ‘int parseopt(std::vector<std::basic_string<char> >)’:
parseopt.cpp:13:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:29:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:63:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:65:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:94:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:96:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:102:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
parseopt.cpp:104:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c rangeset.cpp -o rangeset.o
rangeset.cpp: In function ‘std::ostream& operator<<(std::ostream&, const RangeSet&)’:
rangeset.cpp:15:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function ‘int RangeSet::add(const std::vector<std::pair<long int, long int> >&)’:
rangeset.cpp:49:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function ‘int RangeSet::add(pos_t&, pos_t&)’:
rangeset.cpp:56:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function ‘bool RangeSet::isOverlap(pos_t&, pos_t&)’:
rangeset.cpp:137:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function ‘long int RangeSet::minDist(pos_t&, pos_t&)’:
rangeset.cpp:144:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function ‘pos_t RangeSet::getEnd() const’:
rangeset.cpp:230:8: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable]
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(pos_t&, pos_t&)’:
rangeset.cpp:291:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:292:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:293:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(const std::vector<std::pair<long int, long int> >&)’:
rangeset.cpp:313:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp:315:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
rangeset.cpp: In member function ‘long int RangeSet::overlapLen(RangeSet&)’:
rangeset.cpp:331:8: warning: unused variable ‘t’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c readgroup.cpp -o readgroup.o
In file included from readgroup.cpp:3:0:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from cvganalysis.h:9:0,
                 from readgroup.cpp:5:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::getConnectedCoverage(std::map<long int, int>&)’:
readgroup.cpp:129:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:142:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::getCoverage(std::map<long int, int>&, const range_t&)’:
readgroup.cpp:199:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:203:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:212:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:216:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::getPointCoverage(std::map<long int, int>&)’:
readgroup.cpp:252:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘range_t ReadGroup::getRange() const’:
readgroup.cpp:267:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::splitByRangeSet(std::vector<ReadGroup>&, long int)’:
readgroup.cpp:282:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:286:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:341:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:343:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:351:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:379:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:390:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:400:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::splitByRangeSet(std::vector<ReadGroup>&, std::vector<RangeSet>&)’:
readgroup.cpp:413:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:419:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:450:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::splitByDirection(std::vector<ReadGroup>&, std::vector<std::pair<long int, long int> >&)’:
readgroup.cpp:472:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::calculateRangeSet()’:
readgroup.cpp:563:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::setupBound(std::vector<std::pair<long int, long int> >&)’:
readgroup.cpp:572:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::calculateBound(bool, int, int)’:
readgroup.cpp: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: In member function ‘int ReadGroup::peSize() const’:
readgroup.cpp:1043:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘void ReadGroup::removeTooLongReads(long int, int)’:
readgroup.cpp:1073:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1075:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1091:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp: In member function ‘int ReadGroup::getDirSum()’:
readgroup.cpp:1100:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1102:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readgroup.cpp:1097:7: warning: unused variable ‘r’ [-Wunused-variable]
readgroup.cpp:1098:7: warning: unused variable ‘npos’ [-Wunused-variable]
readgroup.cpp:1098:14: warning: unused variable ‘nneg’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c samio.cpp -o samio.o
In file included from structdef.h:11:0,
                 from samio.h:10,
                 from samio.cpp:10:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from samio.h:10:0,
                 from samio.cpp:10:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
samio.cpp: In function ‘int readSamFile(std::string, std::string, std::vector<std::basic_string<char> >)’:
samio.cpp:98:11: warning: variable ‘dp2’ set but not used [-Wunused-but-set-variable]
samio.cpp:102:7: warning: unused variable ‘rangecounter’ [-Wunused-variable]
samio.cpp:106:7: warning: unused variable ‘currentreadlen’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c spams.cpp -o spams.o
spams.cpp: In function ‘SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)’:
spams.cpp:943:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
In file included from spams.h:5:0,
                 from spams.cpp:1273:
spams/prox/fista.h: In destructor ‘FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normLINF<double>]’:
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1807:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function ‘void FISTA::GroupProx<T, Reg>::prox(const Vector<T>&, Vector<T>&, T) [with T = double, Reg = FISTA::normLINF<double>]’:
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1814:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function ‘T FISTA::GroupProx<T, Reg>::eval(const Vector<T>&) const [with T = double, Reg = FISTA::normLINF<double>]’:
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1843:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function ‘void FISTA::GroupProx<T, Reg>::fenchel(const Vector<T>&, T&, T&) const [with T = double, Reg = FISTA::normLINF<double>]’:
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1870:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In destructor ‘FISTA::GroupProx<T, Reg>::˜GroupProx() [with T = double, Reg = FISTA::normL2<double>]’:
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1807:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function ‘void FISTA::GroupProx<T, Reg>::prox(const Vector<T>&, Vector<T>&, T) [with T = double, Reg = FISTA::normL2<double>]’:
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1814:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function ‘T FISTA::GroupProx<T, Reg>::eval(const Vector<T>&) const [with T = double, Reg = FISTA::normL2<double>]’:
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1843:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spams/prox/fista.h: In member function ‘void FISTA::GroupProx<T, Reg>::fenchel(const Vector<T>&, T&, T&) const [with T = double, Reg = FISTA::normL2<double>]’:
spams.cpp:2725:1:   instantiated from here
spams/prox/fista.h:1870:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp   -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fpic  -g -O2  -Wall -c structdef.cpp -o structdef.o
In file included from structdef.h:11:0,
                 from structdef.cpp:6:
readgroup.h: In member function ‘bool ReadGroup::hasPairEnd()’:
readgroup.h:147:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from structdef.cpp:6:0:
structdef.h: In member function ‘bool GeneRange::isEnd()’:
structdef.h:37:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
structdef.cpp: In member function ‘int GeneRange::sort()’:
structdef.cpp:47:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
structdef.cpp:52:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -shared -L/usr/local/lib -o flipflop.so R_init_flipflop.o align.o auxiliaryio.o bed2sam.o bedio.o common.o cvganalysis.o ffProcesssam.o instanceio.o parseopt.o rangeset.o readgroup.o samio.o spams.o structdef.o -s -fopenmp -lstdc++ -L/home/biocbuild/bbs-2.14-bioc/R/lib -lRblas -L/home/biocbuild/bbs-2.14-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/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)

name	user	system	elapsed
flipflop	0.372	0.016	0.390