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CHECK report for CoGAPS on tokay1

This page was generated on 2018-04-12 13:20:18 -0400 (Thu, 12 Apr 2018).

Package 274/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 2.12.0
Elana J. Fertig
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CoGAPS
Branch: RELEASE_3_6
Last Commit: 9d7e1c2
Last Changed Date: 2017-10-30 12:39:30 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CoGAPS
Version: 2.12.0
Command: rm -rf CoGAPS.buildbin-libdir CoGAPS.Rcheck && mkdir CoGAPS.buildbin-libdir CoGAPS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CoGAPS.buildbin-libdir CoGAPS_2.12.0.tar.gz >CoGAPS.Rcheck\00install.out 2>&1 && cp CoGAPS.Rcheck\00install.out CoGAPS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CoGAPS.buildbin-libdir --install="check:CoGAPS-install.out" --force-multiarch --no-vignettes --timings CoGAPS_2.12.0.tar.gz
StartedAt: 2018-04-11 23:05:53 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:09:59 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 246.4 seconds
RetCode: 0
Status:  OK  
CheckDir: CoGAPS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CoGAPS.buildbin-libdir CoGAPS.Rcheck && mkdir CoGAPS.buildbin-libdir CoGAPS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CoGAPS.buildbin-libdir CoGAPS_2.12.0.tar.gz >CoGAPS.Rcheck\00install.out 2>&1 && cp CoGAPS.Rcheck\00install.out CoGAPS-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CoGAPS.buildbin-libdir --install="check:CoGAPS-install.out" --force-multiarch --no-vignettes --timings CoGAPS_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CoGAPS.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoGAPS/DESCRIPTION' ... OK
* this is package 'CoGAPS' version '2.12.0'
* 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 whether package 'CoGAPS' can be installed ... 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking 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
GWCoGAPS: no visible binding for global variable 'i'
patternMatcher : <anonymous>: no visible binding for global variable
  'Samples'
patternMatcher : <anonymous>: no visible binding for global variable
  'value'
patternMatcher : <anonymous>: no visible binding for global variable
  'BySet'
Undefined global functions or variables:
  BySet Samples i value
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/i386/CoGAPS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/CoGAPS.Rcheck/00check.log'
for details.

Installation output

CoGAPS.Rcheck/00install.out


install for i386

* installing *source* package 'CoGAPS' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c AtomicSupport.cc -o AtomicSupport.o
AtomicSupport.cc: In member function 'void gaps::AtomicSupport::FixedBins_initializeAtomic(unsigned int, long long unsigned int, double, double, char, std::vector<std::vector<double> >)':
AtomicSupport.cc:109:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (length != nBin) {
                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -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:56:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < nRow; ++m) {
                       ^
GAPSNorm.cpp:71:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < nRow; ++m) {
                       ^
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:650:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int jSample = 0; jSample < nCol; jSample++) {
                                               ^
GAPSNorm.cpp:654:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                                     ^
GAPSNorm.cpp:668:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int jSample = 0; jSample < nCol; jSample++) {
                                               ^
GAPSNorm.cpp:672:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                                     ^
GAPSNorm.cpp:695:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int jGene = 0; jGene < nRow; jGene++) {
                                           ^
GAPSNorm.cpp:699:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                                     ^
GAPSNorm.cpp:712:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int jGene = 0; jGene < nRow; jGene++) {
                                           ^
GAPSNorm.cpp:716:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                                     ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GibbsSampler-atomic.cpp -o GibbsSampler-atomic.o
GibbsSampler-atomic.cpp: In member function 'std::vector<std::vector<std::vector<double> > > GibbsSampler::getNormedMatrices()':
GibbsSampler-atomic.cpp:60:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nFactor; ++m) {
                       ^
GibbsSampler-atomic.cpp:63:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nCol; ++n) {
                           ^
GibbsSampler-atomic.cpp:72:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nRow; ++m) {
                       ^
GibbsSampler-atomic.cpp:73:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nFactor; ++n) {
                           ^
GibbsSampler-atomic.cpp:78:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nFactor; ++m) {
                       ^
GibbsSampler-atomic.cpp:79:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nCol; ++n) {
                           ^
GibbsSampler-atomic.cpp: In member function 'std::vector<std::vector<double> > GibbsSampler::createSampleAMat(std::map<long long unsigned int, double>)':
GibbsSampler-atomic.cpp:112:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nRow; i++) {
                       ^
GibbsSampler-atomic.cpp: In member function 'std::vector<std::vector<double> > GibbsSampler::createSamplePMat(std::map<long long unsigned int, double>)':
GibbsSampler-atomic.cpp:136:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nFactor; i++) {
                       ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GibbsSampler-init.cpp -o GibbsSampler-init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GibbsSampler-update.cpp -o GibbsSampler-update.o
GibbsSampler-update.cpp: In member function 'bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler-update.cpp:691:12: warning: variable 'lambda' set but not used [-Wunused-but-set-variable]
     double lambda;
            ^
GibbsSampler-update.cpp:679:5: warning: 'bin1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (bin1 == bin2) {
     ^
GibbsSampler-update.cpp:679:5: warning: 'bin2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:721:80: warning: 'newMass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     _new_atomicProposal.insert(pair<unsigned long long, double>(loc1, newMass1 - mass1));
                                                                                ^
GibbsSampler-update.cpp:721:80: warning: 'mass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:722:80: warning: 'newMass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
     _new_atomicProposal.insert(pair<unsigned long long, double>(loc2, newMass2 - mass2));
                                                                                ^
GibbsSampler-update.cpp:722:80: warning: 'mass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:737:30: warning: 'delLLnew' may be used uninitialized in this function [-Wmaybe-uninitialized]
     tmp = priorLL + delLLnew * _annealingTemperature;
                              ^
GibbsSampler-update.cpp: In member function 'bool GibbsSampler::exchange(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler-update.cpp:851:5: warning: 'bin1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (bin1 == bin2) {
     ^
GibbsSampler-update.cpp:851:5: warning: 'bin2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:1124:34: warning: 'delLLnew' may be used uninitialized in this function [-Wmaybe-uninitialized]
         tmp = priorLL + delLLnew * _annealingTemperature;
                                  ^
GibbsSampler-update.cpp:1067:65: warning: 'lambda' may be used uninitialized in this function [-Wmaybe-uninitialized]
         pnew = sub_func::dgamma(newMass2, 2., 1. / lambda, false);
                                                                 ^
GibbsSampler-update.cpp:979:74: warning: 'sd' may be used uninitialized in this function [-Wmaybe-uninitialized]
         double pupper = sub_func::pnorm(mass2, mean, sd, DOUBLE_NEGINF, 0);
                                                                          ^
GibbsSampler-update.cpp:979:74: warning: 'mean' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:969:23: warning: 'su' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (s == 0. && su == 0.) {
                       ^
GibbsSampler-update.cpp:954:83: warning: 'iSample2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                                  iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                   ^
GibbsSampler-update.cpp:954:83: warning: 'iSample1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:954:83: warning: 'iPattern2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:954:83: warning: 'iGene2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:954:83: warning: 'iPattern1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:954:83: warning: 'iGene1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:1104:80: warning: 'newMass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
     _new_atomicProposal.insert(pair<unsigned long long, double>(loc2, newMass2 - mass2));
                                                                                ^
GibbsSampler-update.cpp:985:29: warning: 'newMass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 s < epsilon ||
                             ^
GibbsSampler-update.cpp:979:74: warning: 'mass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
         double pupper = sub_func::pnorm(mass2, mean, sd, DOUBLE_NEGINF, 0);
                                                                          ^
GibbsSampler-update.cpp:978:75: warning: 'mass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
         double plower = sub_func::pnorm(-mass1, mean, sd, DOUBLE_NEGINF, 0);
                                                                           ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GibbsSampler-util.cpp -o GibbsSampler-util.o
GibbsSampler-util.cpp: In member function 'void GibbsSampler::compute_statistics_prepare_matrices(long unsigned int)':
GibbsSampler-util.cpp:61:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nFactor; ++m) {
                       ^
GibbsSampler-util.cpp:64:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nCol; ++n) {
                           ^
GibbsSampler-util.cpp:77:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow ; ++m) {
                           ^
GibbsSampler-util.cpp:81:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow; ++m) {
                           ^
GibbsSampler-util.cpp:82:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nFactor; ++n) {
                               ^
GibbsSampler-util.cpp:89:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow ; ++m) {
                           ^
GibbsSampler-util.cpp:93:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow; ++m) {
                           ^
GibbsSampler-util.cpp:94:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nFactor; ++n) {
                               ^
GibbsSampler-util.cpp:101:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor ; ++m) {
                           ^
GibbsSampler-util.cpp:105:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor; ++m) {
                           ^
GibbsSampler-util.cpp:106:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nCol; ++n) {
                               ^
GibbsSampler-util.cpp:113:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor ; ++m) {
                           ^
GibbsSampler-util.cpp:117:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor; ++m) {
                           ^
GibbsSampler-util.cpp:118:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nCol; ++n) {
                               ^
GibbsSampler-util.cpp:126:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow; ++m) {
                           ^
GibbsSampler-util.cpp:127:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nFactor; ++n) {
                               ^
GibbsSampler-util.cpp:132:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow; ++m) {
                           ^
GibbsSampler-util.cpp:133:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nFactor; ++n) {
                               ^
GibbsSampler-util.cpp:138:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor; ++m) {
                           ^
GibbsSampler-util.cpp:139:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nCol; ++n) {
                               ^
GibbsSampler-util.cpp:144:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor; ++m) {
                           ^
GibbsSampler-util.cpp:145:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nCol; ++n) {
                               ^
GibbsSampler-util.cpp: In member function 'void GibbsSampler::compute_statistics(unsigned int, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&)':
GibbsSampler-util.cpp:162:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nRow; i++) {
                       ^
GibbsSampler-util.cpp:168:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nRow; i++) {
                       ^
GibbsSampler-util.cpp:174:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nFactor; i++) {
                       ^
GibbsSampler-util.cpp:180:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nFactor; i++) {
                       ^
GibbsSampler-util.cpp:189:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nRow ; ++m) {
                       ^
GibbsSampler-util.cpp:190:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nFactor; ++n) {
                           ^
GibbsSampler-util.cpp:197:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nRow ; ++m) {
                       ^
GibbsSampler-util.cpp:198:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nFactor; ++n) {
                           ^
GibbsSampler-util.cpp:206:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nFactor ; ++m) {
                       ^
GibbsSampler-util.cpp:207:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nCol; ++n) {
                           ^
GibbsSampler-util.cpp:214:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nFactor ; ++m) {
                       ^
GibbsSampler-util.cpp:215:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nCol; ++n) {
                           ^
GibbsSampler-util.cpp: In member function 'double GibbsSampler::getMass(char, double, unsigned int, unsigned int, const double* const*, const double* const*, const double* const*, const double* const*, double)':
GibbsSampler-util.cpp:330:28: warning: 'lambda' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double mean  = (2 * su - lambda) / (2 * s);
                            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GibbsSamplerMap.cpp -o GibbsSamplerMap.o
GibbsSamplerMap.cpp: In constructor 'GibbsSamplerMap::GibbsSamplerMap(long unsigned int, long unsigned int, unsigned int, double, double, double, double, long unsigned int, long unsigned int, double, double, long long unsigned int, char, char, char, char, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, const string&, std::vector<std::vector<double> >&, char)':
GibbsSamplerMap.cpp:36:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < parameters.size(); i++) {
                       ^
GibbsSamplerMap.cpp:41:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int j = 0; j < parameters[0].size(); j++) {
                           ^
GibbsSamplerMap.cpp:45:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int j = 0; j < parameters[0].size(); j++) {
                           ^
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::init_Mapped_Matrix()':
GibbsSamplerMap.cpp:73:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iCol = 0; iCol < _nFixedMaps; iCol++) {
                                     ^
GibbsSamplerMap.cpp:82:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iRow = 0; iRow < _nFixedMaps; iRow++) {
                                     ^
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::initialize_atomic_domain_map()':
GibbsSamplerMap.cpp:106:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iCol = 0; iCol < _nFixedMaps; iCol++) {
                                     ^
GibbsSamplerMap.cpp:111:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int iAtom = 0; iAtom < _nRow; iAtom++) {
                                           ^
GibbsSamplerMap.cpp:130:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iRow = 0; iRow < _nFixedMaps; iRow++) {
                                     ^
GibbsSamplerMap.cpp:135:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int iAtom = 0; iAtom < _nCol; iAtom++) {
                                           ^
GibbsSamplerMap.cpp: In member function 'std::vector<std::vector<double> > GibbsSamplerMap::createSampleAMatMap(std::map<long long unsigned int, double>)':
GibbsSamplerMap.cpp:458:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nRow; i++) {
                       ^
GibbsSamplerMap.cpp:475:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iRow = 0; iRow < _nRow; iRow++) {
                                     ^
GibbsSamplerMap.cpp: In member function 'std::vector<std::vector<double> > GibbsSamplerMap::createSamplePMatMap(std::map<long long unsigned int, double>)':
GibbsSamplerMap.cpp:493:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nFactor; i++) {
                       ^
GibbsSamplerMap.cpp:512:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iCol = 0; iCol < _nCol; iCol++) {
                                     ^
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLBDMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:178:12: warning: 'DelLL' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return DelLL;
            ^
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLMEMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:205:12: warning: 'DelLL' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return DelLL;
            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c Matrix.cpp -o Matrix.o
Matrix.cpp: In constructor 'Matrix::Matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:40:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp: In constructor 'Matrix::Matrix(std::vector<std::vector<double> >&, char)':
Matrix.cpp:55:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:60:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In constructor 'Matrix::Matrix(const char*, char)':
Matrix.cpp:88:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:92:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:93:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In destructor 'Matrix::˜Matrix()':
Matrix.cpp:100:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0 ; m < _n_row ; ++m) {
                        ^
Matrix.cpp: In member function 'void Matrix::born_matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:121:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp: In member function 'void Matrix::matrix_init()':
Matrix.cpp:132:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row; ++m) {
                       ^
Matrix.cpp:133:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In member function 'void Matrix::setRow(std::vector<double>, int)':
Matrix.cpp:142:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n = 0; n < _n_col; ++n) {
                       ^
Matrix.cpp: In member function 'void Matrix::setCol(std::vector<double>, int)':
Matrix.cpp:150:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n = 0; n < _n_row; ++n) {
                       ^
Matrix.cpp: In member function 'std::vector<double> Matrix::get_Row(int)':
Matrix.cpp:165:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iCol = 0; iCol < _n_col; iCol++) {
                             ^
Matrix.cpp: In member function 'std::vector<double> Matrix::get_Col(int)':
Matrix.cpp:175:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iRow = 0; iRow < _n_row; iRow++) {
                             ^
Matrix.cpp: In member function 'double Matrix::cal_mean() const':
Matrix.cpp:229:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row; ++m) {
                       ^
Matrix.cpp:230:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In member function 'double Matrix::cal_totalsum() const':
Matrix.cpp:242:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row; ++m) {
                       ^
Matrix.cpp:243:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In member function 'void Matrix::display_matrixF(std::ofstream&)':
Matrix.cpp:288:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row; ++m) {
                       ^
Matrix.cpp:289:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c cogapsR.cpp -o cogapsR.o
cogapsR.cpp: In function 'Rcpp::List cogaps(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector, int, bool)':
cogapsR.cpp:365:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned long ext_iter = 1; ext_iter <= nEquilCool; ++ext_iter) {
                                               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c cogapsmapR.cpp -o cogapsmapR.o
cogapsmapR.cpp: In function 'Rcpp::List cogapsMap(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector, int, bool)':
cogapsmapR.cpp:341:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned long ext_iter = 1; ext_iter <= nEquilCool; ++ext_iter) {
                                               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c cogapsmaptestR.cpp -o cogapsmaptestR.o
cogapsmaptestR.cpp: In function 'Rcpp::List cogapsMapTest(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector, int)':
cogapsmaptestR.cpp:357:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned long ext_iter = 1; ext_iter <= nEquilCool; ++ext_iter) {
                                               ^
cogapsmaptestR.cpp:451:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iEquil = 0; iEquil < nEquil; iEquil++) {
                                 ^
cogapsmaptestR.cpp:461:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iSample = 0; iSample < nSample; iSample++) {
                                   ^
cogapsmaptestR.cpp:530:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapsmaptestR.cpp:544:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapsmaptestR.cpp:558:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapsmaptestR.cpp:572:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapsmaptestR.cpp:598:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapsmaptestR.cpp:612:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapsmaptestR.cpp:626:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapsmaptestR.cpp:640:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c cogapstestR.cpp -o cogapstestR.o
cogapstestR.cpp: In function 'Rcpp::List cogapsTest(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector, int)':
cogapstestR.cpp:364:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned long ext_iter = 1; ext_iter <= nEquilCool; ++ext_iter) {
                                               ^
cogapstestR.cpp:456:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iEquil = 0; iEquil < nEquil; iEquil++) {
                                 ^
cogapstestR.cpp:466:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iSample = 0; iSample < nSample; iSample++) {
                                   ^
cogapstestR.cpp:534:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapstestR.cpp:548:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapstestR.cpp:562:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapstestR.cpp:576:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapstestR.cpp:602:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapstestR.cpp:616:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapstestR.cpp:630:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapstestR.cpp:644:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c randgen.cpp -o randgen.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c sub_func.cpp -o sub_func.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def AtomicSupport.o GAPSNorm.o GibbsSampler-atomic.o GibbsSampler-init.o GibbsSampler-update.o GibbsSampler-util.o GibbsSamplerMap.o Matrix.o RcppExports.o cogapsR.o cogapsmapR.o cogapsmaptestR.o cogapstestR.o randgen.o sub_func.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CoGAPS'
    finding HTML links ... done
    CoGAPS-package                          html  
    CoGAPS                                  html  
    GIST.D                                  html  
    GIST.S                                  html  
    GSets                                   html  
    GWCoGAPS                                html  
    PatternMatcher                          html  
    SimpSim.A                               html  
    SimpSim.D                               html  
    SimpSim.P                               html  
    SimpSim.S                               html  
    binaryA                                 html  
    calcCoGAPSStat                          html  
    calcGeneGSStat                          html  
    calcZ                                   html  
    computeGeneGSProb                       html  
    createGWCoGAPSSets                      html  
    gapsMapRun                              html  
    gapsMapTestRun                          html  
    gapsRun                                 html  
    gapsTestRun                             html  
    generateSeeds                           html  
    patternMarkers                          html  
    patternMatch4Parallel                   html  
    plotAtoms                               html  
    plotDiag                                html  
    plotGAPS                                html  
    plotP                                   html  
    plotPatternMarkers                      html  
    finding level-2 HTML links ... done

    plotSmoothPatterns                      html  
    postFixed4Parallel                      html  
    reOrderBySet                            html  
    reconstructGene                         html  
    reorderByPatternMatch                   html  
    residuals                               html  
    tf2ugFC                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CoGAPS' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c AtomicSupport.cc -o AtomicSupport.o
AtomicSupport.cc: In member function 'void gaps::AtomicSupport::FixedBins_initializeAtomic(unsigned int, long long unsigned int, double, double, char, std::vector<std::vector<double> >)':
AtomicSupport.cc:109:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (length != nBin) {
                ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -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:56:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < nRow; ++m) {
                       ^
GAPSNorm.cpp:71:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < nRow; ++m) {
                       ^
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:650:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int jSample = 0; jSample < nCol; jSample++) {
                                               ^
GAPSNorm.cpp:654:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                                     ^
GAPSNorm.cpp:668:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int jSample = 0; jSample < nCol; jSample++) {
                                               ^
GAPSNorm.cpp:672:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                                     ^
GAPSNorm.cpp:695:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int jGene = 0; jGene < nRow; jGene++) {
                                           ^
GAPSNorm.cpp:699:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                                     ^
GAPSNorm.cpp:712:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int jGene = 0; jGene < nRow; jGene++) {
                                           ^
GAPSNorm.cpp:716:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (int jPattern = 0; jPattern < nFactor; jPattern++) {
                                                     ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GibbsSampler-atomic.cpp -o GibbsSampler-atomic.o
GibbsSampler-atomic.cpp: In member function 'std::vector<std::vector<std::vector<double> > > GibbsSampler::getNormedMatrices()':
GibbsSampler-atomic.cpp:60:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nFactor; ++m) {
                       ^
GibbsSampler-atomic.cpp:63:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nCol; ++n) {
                           ^
GibbsSampler-atomic.cpp:72:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nRow; ++m) {
                       ^
GibbsSampler-atomic.cpp:73:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nFactor; ++n) {
                           ^
GibbsSampler-atomic.cpp:78:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nFactor; ++m) {
                       ^
GibbsSampler-atomic.cpp:79:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nCol; ++n) {
                           ^
GibbsSampler-atomic.cpp: In member function 'std::vector<std::vector<double> > GibbsSampler::createSampleAMat(std::map<long long unsigned int, double>)':
GibbsSampler-atomic.cpp:112:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nRow; i++) {
                       ^
GibbsSampler-atomic.cpp: In member function 'std::vector<std::vector<double> > GibbsSampler::createSamplePMat(std::map<long long unsigned int, double>)':
GibbsSampler-atomic.cpp:136:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nFactor; i++) {
                       ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GibbsSampler-init.cpp -o GibbsSampler-init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GibbsSampler-update.cpp -o GibbsSampler-update.o
GibbsSampler-update.cpp: In member function 'bool GibbsSampler::move(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler-update.cpp:691:12: warning: variable 'lambda' set but not used [-Wunused-but-set-variable]
     double lambda;
            ^
GibbsSampler-update.cpp:679:5: warning: 'bin1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (bin1 == bin2) {
     ^
GibbsSampler-update.cpp:679:5: warning: 'bin2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:722:80: warning: 'newMass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
     _new_atomicProposal.insert(pair<unsigned long long, double>(loc2, newMass2 - mass2));
                                                                                ^
GibbsSampler-update.cpp:721:80: warning: 'newMass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     _new_atomicProposal.insert(pair<unsigned long long, double>(loc1, newMass1 - mass1));
                                                                                ^
GibbsSampler-update.cpp:722:80: warning: 'mass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
     _new_atomicProposal.insert(pair<unsigned long long, double>(loc2, newMass2 - mass2));
                                                                                ^
GibbsSampler-update.cpp:721:80: warning: 'mass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     _new_atomicProposal.insert(pair<unsigned long long, double>(loc1, newMass1 - mass1));
                                                                                ^
GibbsSampler-update.cpp:366:19: warning: 'delLLnew' may be used uninitialized in this function [-Wmaybe-uninitialized]
     _sysChi2 -= 2.*delsysChi2;
                   ^
GibbsSampler-update.cpp:705:12: note: 'delLLnew' was declared here
     double delLLnew;
            ^
GibbsSampler-update.cpp: In member function 'bool GibbsSampler::exchange(char, const double* const*, const double* const*, double**, double**)':
GibbsSampler-update.cpp:851:5: warning: 'bin1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (bin1 == bin2) {
     ^
GibbsSampler-update.cpp:851:5: warning: 'bin2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:1124:34: warning: 'delLLnew' may be used uninitialized in this function [-Wmaybe-uninitialized]
         tmp = priorLL + delLLnew * _annealingTemperature;
                                  ^
GibbsSampler-update.cpp:1067:65: warning: 'lambda' may be used uninitialized in this function [-Wmaybe-uninitialized]
         pnew = sub_func::dgamma(newMass2, 2., 1. / lambda, false);
                                                                 ^
GibbsSampler-update.cpp:979:74: warning: 'sd' may be used uninitialized in this function [-Wmaybe-uninitialized]
         double pupper = sub_func::pnorm(mass2, mean, sd, DOUBLE_NEGINF, 0);
                                                                          ^
GibbsSampler-update.cpp:979:74: warning: 'mean' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:969:23: warning: 'su' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (s == 0. && su == 0.) {
                       ^
GibbsSampler-update.cpp:954:83: warning: 'iSample2' may be used uninitialized in this function [-Wmaybe-uninitialized]
                                  iPattern1, iGene2, iPattern2, iSample1, iSample2);
                                                                                   ^
GibbsSampler-update.cpp:954:83: warning: 'iSample1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:954:83: warning: 'iPattern2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:954:83: warning: 'iGene2' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:954:83: warning: 'iPattern1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:954:83: warning: 'iGene1' may be used uninitialized in this function [-Wmaybe-uninitialized]
GibbsSampler-update.cpp:1104:80: warning: 'newMass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
     _new_atomicProposal.insert(pair<unsigned long long, double>(loc2, newMass2 - mass2));
                                                                                ^
GibbsSampler-update.cpp:985:29: warning: 'newMass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 s < epsilon ||
                             ^
GibbsSampler-update.cpp:979:74: warning: 'mass2' may be used uninitialized in this function [-Wmaybe-uninitialized]
         double pupper = sub_func::pnorm(mass2, mean, sd, DOUBLE_NEGINF, 0);
                                                                          ^
GibbsSampler-update.cpp:978:75: warning: 'mass1' may be used uninitialized in this function [-Wmaybe-uninitialized]
         double plower = sub_func::pnorm(-mass1, mean, sd, DOUBLE_NEGINF, 0);
                                                                           ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GibbsSampler-util.cpp -o GibbsSampler-util.o
GibbsSampler-util.cpp: In member function 'void GibbsSampler::compute_statistics_prepare_matrices(long unsigned int)':
GibbsSampler-util.cpp:61:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nFactor; ++m) {
                       ^
GibbsSampler-util.cpp:64:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nCol; ++n) {
                           ^
GibbsSampler-util.cpp:77:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow ; ++m) {
                           ^
GibbsSampler-util.cpp:81:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow; ++m) {
                           ^
GibbsSampler-util.cpp:82:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nFactor; ++n) {
                               ^
GibbsSampler-util.cpp:89:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow ; ++m) {
                           ^
GibbsSampler-util.cpp:93:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow; ++m) {
                           ^
GibbsSampler-util.cpp:94:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nFactor; ++n) {
                               ^
GibbsSampler-util.cpp:101:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor ; ++m) {
                           ^
GibbsSampler-util.cpp:105:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor; ++m) {
                           ^
GibbsSampler-util.cpp:106:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nCol; ++n) {
                               ^
GibbsSampler-util.cpp:113:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor ; ++m) {
                           ^
GibbsSampler-util.cpp:117:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor; ++m) {
                           ^
GibbsSampler-util.cpp:118:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nCol; ++n) {
                               ^
GibbsSampler-util.cpp:126:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow; ++m) {
                           ^
GibbsSampler-util.cpp:127:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nFactor; ++n) {
                               ^
GibbsSampler-util.cpp:132:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nRow; ++m) {
                           ^
GibbsSampler-util.cpp:133:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nFactor; ++n) {
                               ^
GibbsSampler-util.cpp:138:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor; ++m) {
                           ^
GibbsSampler-util.cpp:139:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nCol; ++n) {
                               ^
GibbsSampler-util.cpp:144:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int m = 0; m < _nFactor; ++m) {
                           ^
GibbsSampler-util.cpp:145:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int n = 0; n < _nCol; ++n) {
                               ^
GibbsSampler-util.cpp: In member function 'void GibbsSampler::compute_statistics(unsigned int, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&)':
GibbsSampler-util.cpp:162:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nRow; i++) {
                       ^
GibbsSampler-util.cpp:168:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nRow; i++) {
                       ^
GibbsSampler-util.cpp:174:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nFactor; i++) {
                       ^
GibbsSampler-util.cpp:180:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nFactor; i++) {
                       ^
GibbsSampler-util.cpp:189:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nRow ; ++m) {
                       ^
GibbsSampler-util.cpp:190:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nFactor; ++n) {
                           ^
GibbsSampler-util.cpp:197:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nRow ; ++m) {
                       ^
GibbsSampler-util.cpp:198:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nFactor; ++n) {
                           ^
GibbsSampler-util.cpp:206:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nFactor ; ++m) {
                       ^
GibbsSampler-util.cpp:207:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nCol; ++n) {
                           ^
GibbsSampler-util.cpp:214:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _nFactor ; ++m) {
                       ^
GibbsSampler-util.cpp:215:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _nCol; ++n) {
                           ^
GibbsSampler-util.cpp: In member function 'double GibbsSampler::getMass(char, double, unsigned int, unsigned int, const double* const*, const double* const*, const double* const*, const double* const*, double)':
GibbsSampler-util.cpp:330:28: warning: 'lambda' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double mean  = (2 * su - lambda) / (2 * s);
                            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c GibbsSamplerMap.cpp -o GibbsSamplerMap.o
GibbsSamplerMap.cpp: In constructor 'GibbsSamplerMap::GibbsSamplerMap(long unsigned int, long unsigned int, unsigned int, double, double, double, double, long unsigned int, long unsigned int, double, double, long long unsigned int, char, char, char, char, std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, const string&, std::vector<std::vector<double> >&, char)':
GibbsSamplerMap.cpp:36:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < parameters.size(); i++) {
                       ^
GibbsSamplerMap.cpp:41:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int j = 0; j < parameters[0].size(); j++) {
                           ^
GibbsSamplerMap.cpp:45:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int j = 0; j < parameters[0].size(); j++) {
                           ^
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::init_Mapped_Matrix()':
GibbsSamplerMap.cpp:73:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iCol = 0; iCol < _nFixedMaps; iCol++) {
                                     ^
GibbsSamplerMap.cpp:82:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iRow = 0; iRow < _nFixedMaps; iRow++) {
                                     ^
GibbsSamplerMap.cpp: In member function 'void GibbsSamplerMap::initialize_atomic_domain_map()':
GibbsSamplerMap.cpp:106:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iCol = 0; iCol < _nFixedMaps; iCol++) {
                                     ^
GibbsSamplerMap.cpp:111:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int iAtom = 0; iAtom < _nRow; iAtom++) {
                                           ^
GibbsSamplerMap.cpp:130:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iRow = 0; iRow < _nFixedMaps; iRow++) {
                                     ^
GibbsSamplerMap.cpp:135:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int iAtom = 0; iAtom < _nCol; iAtom++) {
                                           ^
GibbsSamplerMap.cpp: In member function 'std::vector<std::vector<double> > GibbsSamplerMap::createSampleAMatMap(std::map<long long unsigned int, double>)':
GibbsSamplerMap.cpp:458:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nRow; i++) {
                       ^
GibbsSamplerMap.cpp:475:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iRow = 0; iRow < _nRow; iRow++) {
                                     ^
GibbsSamplerMap.cpp: In member function 'std::vector<std::vector<double> > GibbsSamplerMap::createSamplePMatMap(std::map<long long unsigned int, double>)':
GibbsSamplerMap.cpp:493:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < _nFactor; i++) {
                       ^
GibbsSamplerMap.cpp:512:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int iCol = 0; iCol < _nCol; iCol++) {
                                     ^
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLBDMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:178:12: warning: 'DelLL' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return DelLL;
            ^
GibbsSamplerMap.cpp: In member function 'double GibbsSamplerMap::computeDeltaLLMEMap(char, const double* const*, const double* const*, const double* const*, const double* const*, std::vector<double>&, unsigned int, std::vector<double>&, unsigned int)':
GibbsSamplerMap.cpp:205:12: warning: 'DelLL' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return DelLL;
            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c Matrix.cpp -o Matrix.o
Matrix.cpp: In constructor 'Matrix::Matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:40:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp: In constructor 'Matrix::Matrix(std::vector<std::vector<double> >&, char)':
Matrix.cpp:55:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:59:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:60:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In constructor 'Matrix::Matrix(const char*, char)':
Matrix.cpp:88:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:92:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp:93:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In destructor 'Matrix::˜Matrix()':
Matrix.cpp:100:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0 ; m < _n_row ; ++m) {
                        ^
Matrix.cpp: In member function 'void Matrix::born_matrix(unsigned int, unsigned int, char, double)':
Matrix.cpp:121:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row ; ++m) {
                       ^
Matrix.cpp: In member function 'void Matrix::matrix_init()':
Matrix.cpp:132:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row; ++m) {
                       ^
Matrix.cpp:133:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In member function 'void Matrix::setRow(std::vector<double>, int)':
Matrix.cpp:142:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n = 0; n < _n_col; ++n) {
                       ^
Matrix.cpp: In member function 'void Matrix::setCol(std::vector<double>, int)':
Matrix.cpp:150:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n = 0; n < _n_row; ++n) {
                       ^
Matrix.cpp: In member function 'std::vector<double> Matrix::get_Row(int)':
Matrix.cpp:165:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iCol = 0; iCol < _n_col; iCol++) {
                             ^
Matrix.cpp: In member function 'std::vector<double> Matrix::get_Col(int)':
Matrix.cpp:175:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iRow = 0; iRow < _n_row; iRow++) {
                             ^
Matrix.cpp: In member function 'double Matrix::cal_mean() const':
Matrix.cpp:229:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row; ++m) {
                       ^
Matrix.cpp:230:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In member function 'double Matrix::cal_totalsum() const':
Matrix.cpp:242:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row; ++m) {
                       ^
Matrix.cpp:243:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
Matrix.cpp: In member function 'void Matrix::display_matrixF(std::ofstream&)':
Matrix.cpp:288:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int m = 0; m < _n_row; ++m) {
                       ^
Matrix.cpp:289:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int n = 0; n < _n_col; ++n) {
                           ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c cogapsR.cpp -o cogapsR.o
cogapsR.cpp: In function 'Rcpp::List cogaps(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector, int, bool)':
cogapsR.cpp:365:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned long ext_iter = 1; ext_iter <= nEquilCool; ++ext_iter) {
                                               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c cogapsmapR.cpp -o cogapsmapR.o
cogapsmapR.cpp: In function 'Rcpp::List cogapsMap(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector, int, bool)':
cogapsmapR.cpp:341:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned long ext_iter = 1; ext_iter <= nEquilCool; ++ext_iter) {
                                               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c cogapsmaptestR.cpp -o cogapsmaptestR.o
cogapsmaptestR.cpp: In function 'Rcpp::List cogapsMapTest(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector, int)':
cogapsmaptestR.cpp:357:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned long ext_iter = 1; ext_iter <= nEquilCool; ++ext_iter) {
                                               ^
cogapsmaptestR.cpp:451:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iEquil = 0; iEquil < nEquil; iEquil++) {
                                 ^
cogapsmaptestR.cpp:461:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iSample = 0; iSample < nSample; iSample++) {
                                   ^
cogapsmaptestR.cpp:530:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapsmaptestR.cpp:544:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapsmaptestR.cpp:558:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapsmaptestR.cpp:572:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapsmaptestR.cpp:598:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapsmaptestR.cpp:612:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapsmaptestR.cpp:626:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapsmaptestR.cpp:640:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c cogapstestR.cpp -o cogapstestR.o
cogapstestR.cpp: In function 'Rcpp::List cogapsTest(Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::CharacterVector, Rcpp::NumericVector, int)':
cogapstestR.cpp:364:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned long ext_iter = 1; ext_iter <= nEquilCool; ++ext_iter) {
                                               ^
cogapstestR.cpp:456:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iEquil = 0; iEquil < nEquil; iEquil++) {
                                 ^
cogapstestR.cpp:466:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int iSample = 0; iSample < nSample; iSample++) {
                                   ^
cogapstestR.cpp:534:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapstestR.cpp:548:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapstestR.cpp:562:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapstestR.cpp:576:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapstestR.cpp:602:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapstestR.cpp:616:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
cogapstestR.cpp:630:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nEquil; k++) {
                       ^
cogapstestR.cpp:644:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int k = 0; k < nSample; k++) {
                       ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c randgen.cpp -o randgen.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c sub_func.cpp -o sub_func.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def AtomicSupport.o GAPSNorm.o GibbsSampler-atomic.o GibbsSampler-init.o GibbsSampler-update.o GibbsSampler-util.o GibbsSamplerMap.o Matrix.o RcppExports.o cogapsR.o cogapsmapR.o cogapsmaptestR.o cogapstestR.o randgen.o sub_func.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoGAPS' as CoGAPS_2.12.0.zip
* DONE (CoGAPS)
In R CMD INSTALL
In R CMD INSTALL

Tests output

CoGAPS.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CoGAPS)
Loading required package: Rcpp

Attaching package: 'CoGAPS'

The following object is masked from 'package:stats':

    residuals

> 
> test_check("CoGAPS")
== testthat results  ===========================================================
OK: 8 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   8.07    0.10    8.17

CoGAPS.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CoGAPS)
Loading required package: Rcpp

Attaching package: 'CoGAPS'

The following object is masked from 'package:stats':

    residuals

> 
> test_check("CoGAPS")
== testthat results  ===========================================================
OK: 8 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.23    0.10    7.32

Example timings

CoGAPS.Rcheck/examples_i386/CoGAPS-Ex.timings

nameusersystemelapsed
GWCoGAPS000
PatternMatcher000
computeGeneGSProb000
createGWCoGAPSSets000
generateSeeds000
patternMarkers000
plotPatternMarkers000
reOrderBySet000

CoGAPS.Rcheck/examples_x64/CoGAPS-Ex.timings

nameusersystemelapsed
GWCoGAPS000
PatternMatcher000
computeGeneGSProb000
createGWCoGAPSSets000
generateSeeds000
patternMarkers000
plotPatternMarkers000
reOrderBySet000