BioC 3.4: CHECK report for CoGAPS on zin1

Package: CoGAPS

Version: 2.7.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CoGAPS_2.7.0.tar.gz

StartedAt: 2016-09-20 04:52:23 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:54:13 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 110.0 seconds

RetCode: 0

Status:  OK

CheckDir: CoGAPS.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CoGAPS_2.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/CoGAPS.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘2.7.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.

* installing *source* package ‘CoGAPS’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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) {
                ^
AtomicSupport.cc: At global scope:
AtomicSupport.cc:31:14: warning: ‘DOUB_POSINF’ defined but not used [-Wunused-variable]
 const double DOUB_POSINF = std::numeric_limits<double>::max();
              ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -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: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++) {
                                                     ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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++) {
                       ^
In file included from GibbsSampler-atomic.cpp:1:0:
GibbsSampler.h: At global scope:
GibbsSampler.h:24:14: warning: ‘DOUBLE_POSINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_POSINF = std::numeric_limits<double>::max();
              ^
GibbsSampler.h:25:14: warning: ‘DOUBLE_NEGINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_NEGINF = -std::numeric_limits<double>::max();
              ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c GibbsSampler-init.cpp -o GibbsSampler-init.o
In file included from GibbsSampler-init.cpp:1:0:
GibbsSampler.h:24:14: warning: ‘DOUBLE_POSINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_POSINF = std::numeric_limits<double>::max();
              ^
GibbsSampler.h:25:14: warning: ‘DOUBLE_NEGINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_NEGINF = -std::numeric_limits<double>::max();
              ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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:1067:32: 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:1069:9: warning: ‘newMass2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         if (newMass1 > newMass2) {
         ^
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:978:40: warning: ‘mass1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         double plower = sub_func::pnorm(-mass1, mean, sd, DOUBLE_NEGINF, 0);
                                        ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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);
                            ^
In file included from GibbsSampler-util.cpp:1:0:
GibbsSampler.h: At global scope:
GibbsSampler.h:24:14: warning: ‘DOUBLE_POSINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_POSINF = std::numeric_limits<double>::max();
              ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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;
            ^
In file included from GibbsSamplerMap.h:9:0,
                 from GibbsSamplerMap.cpp:14:
GibbsSampler.h: At global scope:
GibbsSampler.h:24:14: warning: ‘DOUBLE_POSINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_POSINF = std::numeric_limits<double>::max();
              ^
GibbsSampler.h:25:14: warning: ‘DOUBLE_NEGINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_NEGINF = -std::numeric_limits<double>::max();
              ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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) {
                           ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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)’:
cogapsR.cpp:360:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned long ext_iter = 1; ext_iter <= nEquilCool; ++ext_iter) {
                                               ^
In file included from cogapsR.cpp:23:0:
GibbsSampler.h: At global scope:
GibbsSampler.h:24:14: warning: ‘DOUBLE_POSINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_POSINF = std::numeric_limits<double>::max();
              ^
GibbsSampler.h:25:14: warning: ‘DOUBLE_NEGINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_NEGINF = -std::numeric_limits<double>::max();
              ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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)’:
cogapsmapR.cpp:336:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned long ext_iter = 1; ext_iter <= nEquilCool; ++ext_iter) {
                                               ^
In file included from cogapsmapR.cpp:23:0:
GibbsSampler.h: At global scope:
GibbsSampler.h:24:14: warning: ‘DOUBLE_POSINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_POSINF = std::numeric_limits<double>::max();
              ^
GibbsSampler.h:25:14: warning: ‘DOUBLE_NEGINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_NEGINF = -std::numeric_limits<double>::max();
              ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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++) {
                       ^
In file included from cogapsmaptestR.cpp:28:0:
GibbsSampler.h: At global scope:
GibbsSampler.h:24:14: warning: ‘DOUBLE_POSINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_POSINF = std::numeric_limits<double>::max();
              ^
GibbsSampler.h:25:14: warning: ‘DOUBLE_NEGINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_NEGINF = -std::numeric_limits<double>::max();
              ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -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++) {
                       ^
In file included from cogapstestR.cpp:27:0:
GibbsSampler.h: At global scope:
GibbsSampler.h:24:14: warning: ‘DOUBLE_POSINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_POSINF = std::numeric_limits<double>::max();
              ^
GibbsSampler.h:25:14: warning: ‘DOUBLE_NEGINF’ defined but not used [-Wunused-variable]
 const double DOUBLE_NEGINF = -std::numeric_limits<double>::max();
              ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c randgen.cpp -o randgen.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c sub_func.cpp -o sub_func.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o CoGAPS.so 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 -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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
computeGeneGSProb	0.000	0.000	0.001