BioC 3.1: CHECK report for CoGAPS on petty

Package: CoGAPS

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CoGAPS_2.2.0.tar.gz

StartedAt: 2015-10-08 22:15:09 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:16:48 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 98.9 seconds

RetCode: 0

Status:  OK

CheckDir: CoGAPS.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CoGAPS_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/CoGAPS.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘2.2.0’
* 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 ‘CoGAPS’ can be installed ... [58s/62s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotP: no visible global function definition for ‘plotCI’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... NOTE
Found the following Makefile(s) without a final LF:
  src/Makevars
Some ‘make’ programs ignore lines not ending in LF.
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.

* installing *source* package ‘CoGAPS’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c AtomicSupport.cc -o AtomicSupport.o
AtomicSupport.cc: In member function ‘void gaps::AtomicSupport::updateAtomicBins(double*, unsigned int, bool)’:
AtomicSupport.cc:996: 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"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GAPSNorm.cpp -o GAPSNorm.o
GAPSNorm.cpp: In static member function ‘static double gaps::GAPSNorm::calChi2(const double* const*, const double* const*, const double* const*, const double* const*, unsigned int, unsigned int, unsigned int)’:
GAPSNorm.cpp:72: warning: comparison between signed and unsigned integer expressions
GAPSNorm.cpp:86: warning: comparison between signed and unsigned integer expressions
GAPSNorm.cpp: In static member function ‘static std::pair<double, double> gaps::GAPSNorm::calcAlphaParameters(char, unsigned int, unsigned int, unsigned int, const double* const*, const double* const*, double**, double**, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int)’:
GAPSNorm.cpp:623: warning: comparison between signed and unsigned integer expressions
GAPSNorm.cpp:626: warning: comparison between signed and unsigned integer expressions
GAPSNorm.cpp:639: warning: comparison between signed and unsigned integer expressions
GAPSNorm.cpp:643: warning: comparison between signed and unsigned integer expressions
GAPSNorm.cpp:665: warning: comparison between signed and unsigned integer expressions
GAPSNorm.cpp:668: warning: comparison between signed and unsigned integer expressions
GAPSNorm.cpp:680: warning: comparison between signed and unsigned integer expressions
GAPSNorm.cpp:684: 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"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GibbsSampler.cpp -o GibbsSampler.o
GibbsSampler.cpp: In member function ‘void GibbsSampler::compute_statistics_prepare_matrices(long unsigned int)’:
GibbsSampler.cpp:1768: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1770: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1783: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1785: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1786: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1792: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1794: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1795: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1801: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1803: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1804: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1810: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1812: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1813: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1823: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1824: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1829: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1830: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1835: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1836: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1841: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1842: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp: In member function ‘void GibbsSampler::compute_statistics(char*, char*, char*, char*, char*, char*, unsigned int)’:
GibbsSampler.cpp:1859: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1860: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1865: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1866: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1872: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1873: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1878: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1879: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1887: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp: In member function ‘void GibbsSampler::compute_statistics(unsigned int, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&)’:
GibbsSampler.cpp:1966: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1971: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1976: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1981: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1992: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1993: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:1999: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:2000: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:2008: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:2009: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:2016: warning: comparison between signed and unsigned integer expressions
GibbsSampler.cpp:2017: 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"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GibbsSamplerMap.cpp -o GibbsSamplerMap.o
GibbsSamplerMap.cpp: In member function ‘void GibbsSamplerMap::init_Mapped_Matrix()’:
GibbsSamplerMap.cpp:90: warning: comparison between signed and unsigned integer expressions
GibbsSamplerMap.cpp:96: warning: comparison between signed and unsigned integer expressions
GibbsSamplerMap.cpp: In member function ‘void GibbsSamplerMap::initialize_atomic_domain_map()’:
GibbsSamplerMap.cpp:118: warning: comparison between signed and unsigned integer expressions
GibbsSamplerMap.cpp:122: warning: comparison between signed and unsigned integer expressions
GibbsSamplerMap.cpp:139: warning: comparison between signed and unsigned integer expressions
GibbsSamplerMap.cpp:143: warning: comparison between signed and unsigned integer expressions
GibbsSamplerMap.cpp: In member function ‘bool GibbsSamplerMap::calc_new_matrix_Pattern(char, std::vector<double, std::allocator<double> >&, long long unsigned int, double)’:
GibbsSamplerMap.cpp:1370: warning: comparison between signed and unsigned integer expressions
GibbsSamplerMap.cpp:1392: 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"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Matrix.cpp -o Matrix.o
Matrix.cpp: In constructor ‘Matrix::Matrix(unsigned int, unsigned int, char, double)’:
Matrix.cpp:41: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In constructor ‘Matrix::Matrix(std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, char)’:
Matrix.cpp:56: warning: comparison between signed and unsigned integer expressions
Matrix.cpp:59: warning: comparison between signed and unsigned integer expressions
Matrix.cpp:60: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In constructor ‘Matrix::Matrix(const char*, char)’:
Matrix.cpp:87: warning: comparison between signed and unsigned integer expressions
Matrix.cpp:91: warning: comparison between signed and unsigned integer expressions
Matrix.cpp:92: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In destructor ‘Matrix::˜Matrix()’:
Matrix.cpp:100: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In member function ‘void Matrix::born_matrix(unsigned int, unsigned int, char, double)’:
Matrix.cpp:119: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In member function ‘void Matrix::matrix_init()’:
Matrix.cpp:131: warning: comparison between signed and unsigned integer expressions
Matrix.cpp:132: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In member function ‘void Matrix::setRow(std::vector<double, std::allocator<double> >&, int)’:
Matrix.cpp:141: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In member function ‘void Matrix::setCol(std::vector<double, std::allocator<double> >&, int)’:
Matrix.cpp:149: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In member function ‘void Matrix::setRow(const std::vector<double, std::allocator<double> >&, int)’:
Matrix.cpp:157: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In member function ‘void Matrix::setCol(const std::vector<double, std::allocator<double> >&, int)’:
Matrix.cpp:165: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In member function ‘void Matrix::get_Row(int, std::vector<double, std::allocator<double> >&) const’:
Matrix.cpp:178: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In member function ‘void Matrix::get_Col(int, std::vector<double, std::allocator<double> >&) const’:
Matrix.cpp:184: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In member function ‘double Matrix::cal_mean() const’:
Matrix.cpp:231: warning: comparison between signed and unsigned integer expressions
Matrix.cpp:232: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In member function ‘double Matrix::cal_totalsum() const’:
Matrix.cpp:242: warning: comparison between signed and unsigned integer expressions
Matrix.cpp:243: warning: comparison between signed and unsigned integer expressions
Matrix.cpp: In member function ‘void Matrix::display_matrixF(std::ofstream&)’:
Matrix.cpp:305: warning: comparison between signed and unsigned integer expressions
Matrix.cpp:306: 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"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RcppExports.cpp -o RcppExports.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c cogapsR.cpp -o cogapsR.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c cogapsmapR.cpp -o cogapsmapR.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c randgen.cpp -o randgen.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c sub_func.cpp -o sub_func.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o CoGAPS.so AtomicSupport.o GAPSNorm.o GibbsSampler.o GibbsSamplerMap.o Matrix.o RcppExports.o cogapsR.o cogapsmapR.o randgen.o sub_func.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/CoGAPS.Rcheck/CoGAPS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CoGAPS)

name	user	system	elapsed
CoGAPS	0.001	0.000	0.001
computeGeneGSProb	0.001	0.000	0.001
gapsMapRun	0.001	0.000	0.001
gapsRun	0.000	0.000	0.001
plotSmoothPatterns	0.002	0.000	0.001